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Repository: rtyley/bfg-repo-cleaner
Branch: main
Commit: 1bd9715198dd
Files: 100
Total size: 203.9 KB

Directory structure:
gitextract_c1a_g3a9/

├── .github/
│   ├── PULL_REQUEST_TEMPLATE.md
│   └── workflows/
│       ├── ci.yml
│       └── release.yml
├── .gitignore
├── .tool-versions
├── BUILD.md
├── CONTRIBUTING.md
├── LICENSE
├── README.md
├── backers.md
├── bfg/
│   ├── build.sbt
│   └── src/
│       ├── main/
│       │   └── scala/
│       │       └── com/
│       │           └── madgag/
│       │               └── git/
│       │                   └── bfg/
│       │                       └── cli/
│       │                           ├── CLIConfig.scala
│       │                           └── Main.scala
│       └── test/
│           └── scala/
│               └── com/
│                   └── madgag/
│                       └── git/
│                           └── bfg/
│                               └── cli/
│                                   ├── CLIConfigSpecs.scala
│                                   ├── MainSpec.scala
│                                   ├── MassiveNonFileObjectsRequiresOwnJvmSpec.scala
│                                   └── test/
│                                       └── unpackedRepo.scala
├── bfg-benchmark/
│   ├── build.sbt
│   ├── resources/
│   │   ├── jars/
│   │   │   └── grabJars.sh
│   │   └── repos/
│   │       ├── chromium-src/
│   │       │   └── commands/
│   │       │       └── issue-23/
│   │       │           └── bfg.txt
│   │       ├── gcc/
│   │       │   └── commands/
│   │       │       └── delete-file/
│   │       │           ├── bfg.txt
│   │       │           └── gfb.txt
│   │       ├── git/
│   │       │   └── commands/
│   │       │       └── delete-file/
│   │       │           ├── bfg.txt
│   │       │           └── gfb.txt
│   │       ├── github-gem/
│   │       │   └── commands/
│   │       │       └── delete-file/
│   │       │           ├── bfg.txt
│   │       │           └── gfb.txt
│   │       ├── intellij/
│   │       │   └── commands/
│   │       │       ├── delete-binary-resources/
│   │       │       │   └── bfg.txt
│   │       │       ├── delete-file/
│   │       │       │   ├── bfg.txt
│   │       │       │   └── gfb.txt
│   │       │       └── git-lfs-binary-resources/
│   │       │           └── bfg.txt
│   │       ├── jgit/
│   │       │   └── commands/
│   │       │       ├── delete-file/
│   │       │       │   ├── bfg.txt
│   │       │       │   └── gfb.txt
│   │       │       ├── replace-1-existing-string/
│   │       │       │   ├── bfg.txt
│   │       │       │   └── passwords.1-existing-string.txt
│   │       │       ├── replace-20-existing-strings/
│   │       │       │   ├── bfg.txt
│   │       │       │   └── passwords.20-existing-strings.txt
│   │       │       └── replace-500-existing-strings/
│   │       │           ├── bfg.txt
│   │       │           └── passwords.500-existing-strings.txt
│   │       ├── linux/
│   │       │   └── commands/
│   │       │       └── delete-file/
│   │       │           ├── bfg.txt
│   │       │           └── gfb.txt
│   │       ├── rails/
│   │       │   └── commands/
│   │       │       └── delete-file/
│   │       │           ├── bfg.txt
│   │       │           └── gfb.txt
│   │       └── wine/
│   │           └── commands/
│   │               └── delete-file/
│   │                   ├── bfg.txt
│   │                   └── gfb.txt
│   └── src/
│       ├── main/
│       │   └── scala/
│       │       ├── Benchmark.scala
│       │       ├── BenchmarkConfig.scala
│       │       ├── JavaVersion.scala
│       │       ├── lib/
│       │       │   ├── Repo.scala
│       │       │   └── Timing.scala
│       │       └── model/
│       │           ├── BFGJar.scala
│       │           ├── InvocableEngine.scala
│       │           ├── InvocableEngineSet.scala
│       │           └── Java.scala
│       └── test/
│           └── scala/
│               └── JavaVersionSpec.scala
├── bfg-library/
│   ├── build.sbt
│   └── src/
│       ├── main/
│       │   └── scala/
│       │       └── com/
│       │           └── madgag/
│       │               ├── collection/
│       │               │   └── concurrent/
│       │               │       ├── ConcurrentMultiMap.scala
│       │               │       └── ConcurrentSet.scala
│       │               ├── git/
│       │               │   ├── LFS.scala
│       │               │   └── bfg/
│       │               │       ├── GitUtil.scala
│       │               │       ├── cleaner/
│       │               │       │   ├── BlobCharsetDetector.scala
│       │               │       │   ├── BlobTextModifier.scala
│       │               │       │   ├── LfsBlobConverter.scala
│       │               │       │   ├── ObjectIdCleaner.scala
│       │               │       │   ├── ObjectIdSubstitutor.scala
│       │               │       │   ├── RepoRewriter.scala
│       │               │       │   ├── Reporter.scala
│       │               │       │   ├── TreeBlobModifier.scala
│       │               │       │   ├── commits.scala
│       │               │       │   ├── kit/
│       │               │       │   │   └── BlobInserter.scala
│       │               │       │   ├── package.scala
│       │               │       │   ├── protection/
│       │               │       │   │   ├── ProtectedObjectCensus.scala
│       │               │       │   │   └── ProtectedObjectDirtReport.scala
│       │               │       │   └── treeblobs.scala
│       │               │       ├── memo.scala
│       │               │       ├── model/
│       │               │       │   ├── Commit.scala
│       │               │       │   ├── Footer.scala
│       │               │       │   └── package.scala
│       │               │       └── timing.scala
│       │               ├── inclusion/
│       │               │   └── inclusion.scala
│       │               └── text/
│       │                   ├── ByteSize.scala
│       │                   ├── Tables.scala
│       │                   └── text.scala
│       └── test/
│           └── scala/
│               └── com/
│                   └── madgag/
│                       ├── git/
│                       │   ├── LFSSpec.scala
│                       │   └── bfg/
│                       │       ├── GitUtilSpec.scala
│                       │       ├── MessageFooterSpec.scala
│                       │       ├── TreeEntrySpec.scala
│                       │       ├── cleaner/
│                       │       │   ├── LfsBlobConverterSpec.scala
│                       │       │   ├── ObjectIdCleanerSpec.scala
│                       │       │   ├── ObjectIdSubstitutorSpec.scala
│                       │       │   ├── RepoRewriteSpec.scala
│                       │       │   └── TreeBlobModifierSpec.scala
│                       │       └── model/
│                       │           └── CommitSpec.scala
│                       └── text/
│                           └── ByteSizeSpecs.scala
├── bfg-test/
│   ├── build.sbt
│   └── src/
│       └── main/
│           └── scala/
│               └── com/
│                   └── madgag/
│                       └── git/
│                           └── bfg/
│                               └── test/
│                                   └── unpackedRepo.scala
├── build.sbt
├── project/
│   ├── build.properties
│   ├── dependencies.scala
│   └── plugins.sbt
└── version.sbt

================================================
FILE CONTENTS
================================================

================================================
FILE: .github/PULL_REQUEST_TEMPLATE.md
================================================
I assert that this patch is my own work, and to [simplify the licensing of the BFG Repo-Cleaner](https://github.com/rtyley/bfg-repo-cleaner/blob/master/CONTRIBUTING.md#pull-requests):

_(choose 1 of these 2 options)_

- [ ] I assign the copyright on this contribution to Roberto Tyley
- [ ] I disclaim copyright and thus place this contribution in the public domain



================================================
FILE: .github/workflows/ci.yml
================================================
name: CI
on:
  workflow_dispatch:
  pull_request:

  # triggering CI default branch improves caching
  # see https://docs.github.com/en/free-pro-team@latest/actions/guides/caching-dependencies-to-speed-up-workflows#restrictions-for-accessing-a-cache
  push:
    branches:
      - main

jobs:
  test:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - uses: guardian/setup-scala@v1
      - name: Build and Test
        run: sbt -v test
      - name: Test Summary
        uses: test-summary/action@v2
        with:
          paths: "test-results/**/TEST-*.xml"
        if: always()

================================================
FILE: .github/workflows/release.yml
================================================
name: Release

on:
  workflow_dispatch:

jobs:
  release:
    uses: guardian/gha-scala-library-release-workflow/.github/workflows/reusable-release.yml@v1
    permissions: { contents: write, pull-requests: write }
    with:
      GITHUB_APP_ID: 930725
      SONATYPE_PROFILE_NAME: 'com.madgag'
      SONATYPE_CREDENTIAL_HOST: 's01.oss.sonatype.org'
    secrets:
      SONATYPE_TOKEN: ${{ secrets.AUTOMATED_MAVEN_RELEASE_SONATYPE_TOKEN }}
      PGP_PRIVATE_KEY: ${{ secrets.AUTOMATED_MAVEN_RELEASE_PGP_SECRET }}
      GITHUB_APP_PRIVATE_KEY: ${{ secrets.AUTOMATED_MAVEN_RELEASE_GITHUB_APP_PRIVATE_KEY }}


================================================
FILE: .gitignore
================================================
target
*~
.idea
.idea_modules
*.iml
*.jar
repo.git.zip
**/.project
**/.classpath
**/.settings
.bsp

.DS_Store
test-results/


================================================
FILE: .tool-versions
================================================
java corretto-11.0.25.9.1


================================================
FILE: BUILD.md
================================================
The BFG is written in Scala, a modern functional language that runs on the JVM - so it
can run anywhere Java can.

Here's a rough set of instructions for building the BFG, if you don't want to use the
pre-built [downloads](http://rtyley.github.io/bfg-repo-cleaner/#download):

* Install Java JDK 11 or above
* Install [sbt](https://www.scala-sbt.org/1.x/docs/Setup.html)
* `git clone git@github.com:rtyley/bfg-repo-cleaner.git`
* `cd bfg-repo-cleaner`
* `sbt`<- start the sbt console
* `bfg/assembly` <- download dependencies, run the tests, build the jar

To find the jar once it's built, just look at the last few lines of output from the
`assembly` task - it'll say something like this:

```
[info] Packaging /Users/roberto/development/bfg-repo-cleaner/bfg/target/bfg-1.11.9-SNAPSHOT-master-21d2115.jar ...
[info] Done packaging.
[success] Total time: 19 s, completed 26-Sep-2014 16:05:11
```

If you're going to make changes to the Scala code, you may want to use IntelliJ and it's Scala
plugin to help with the Scala syntax...!

If you use [Eclipse IDE](http://www.eclipse.org/), you can set-up your development environment by following these instructions:

* Install `sbt` and build as-above
* Install [Scala IDE for Eclipse](http://scala-ide.org/) into your Eclipse installation if not already installed
* Add the `sbteclipse-plugin` to your set of local sbt plugins:

```
mkdir -p ~/.sbt/1.0/plugins && tee ~/.sbt/1.0/plugins/plugins.sbt <<EOF
addSbtPlugin("com.typesafe.sbteclipse" % "sbteclipse-plugin" % "5.2.2")
EOF
```

* `sbt`<- start the sbt console
* `eclipse` <- first-time only setup of the Eclipse plugin
* `eclipse` <- again, generate Eclipse project files (note that these are `.gitignore`d)
* In Eclipse, `File -> Import -> Existing Projects into Workspace`, browse to your `bfg` working-copy, and ensure that you select `Search for nested projects`
* You should now have the 4 `sbt` projects imported into your Eclipse workspace.

I personally found Coursera's [online Scala course](https://www.coursera.org/course/progfun) very helpful in
learning Scala, YMMV.


================================================
FILE: CONTRIBUTING.md
================================================
Issues and Questions
--------------------

If you've found what looks like a bug, or have a feature request for the BFG, please check
[issues on GitHub](https://github.com/rtyley/bfg-repo-cleaner/issues), and create a new issue
if necessary.

If you just have a general question, or there's something you don't understand, ask on [stackoverflow.com](http://stackoverflow.com/questions/ask) (tag it with [`git-rewrite-history`](http://stackoverflow.com/questions/tagged/git-rewrite-history) and
[`bfg-repo-cleaner`](http://stackoverflow.com/questions/tagged/bfg-repo-cleaner) so I see it) - there are
many more people who can answer that sort of question on Stackoverflow, you stand a good chance
of getting your question answered quicker!

Pull Requests
-------------

BFG Repo-Cleaner is licensed under the [GPL v3](http://www.gnu.org/licenses/gpl.html), and to be in the best position to enforce the GPL the copyright status of BFG Repo Cleaner needs to be as simple as possible. To achieve this, contributors should only provide contributions which are **their own work**, and either:

a) Assign the copyright on the contribution to myself, Roberto Tyley

**or**

b) Disclaim copyright on it and thus put it in the public domain

**Please specify which option you want to use when creating your pull request.**

See the [GNU FAQ](http://www.gnu.org/licenses/gpl-faq.html#AssignCopyright) for a fuller explanation of the need for this. If you still want to retain copyright on your contribution, let me know and I'll see if we can work something out.


================================================
FILE: LICENSE
================================================
                    GNU GENERAL PUBLIC LICENSE
                       Version 3, 29 June 2007

 Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
 Everyone is permitted to copy and distribute verbatim copies
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Also add information on how to contact you by electronic and paper mail.

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The hypothetical commands `show w' and `show c' should show the appropriate
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Public License instead of this License.  But first, please read
<http://www.gnu.org/philosophy/why-not-lgpl.html>.


================================================
FILE: README.md
================================================
BFG Repo-Cleaner 
================

[![CI](https://github.com/rtyley/bfg-repo-cleaner/actions/workflows/ci.yml/badge.svg)](https://github.com/rtyley/bfg-repo-cleaner/actions/workflows/ci.yml)
[![Release](https://github.com/rtyley/bfg-repo-cleaner/actions/workflows/release.yml/badge.svg)](https://github.com/rtyley/bfg-repo-cleaner/actions/workflows/release.yml)

_Removes large or troublesome blobs like git-filter-branch does, but faster - and written in Scala_ - [Fund the BFG](https://j.mp/fund-bfg)

```
$ bfg --strip-blobs-bigger-than 1M --replace-text banned.txt repo.git
```

The BFG is a simpler, faster ([10 - 720x](https://docs.google.com/spreadsheet/ccc?key=0AsR1d5Zpes8HdER3VGU1a3dOcmVHMmtzT2dsS2xNenc) faster)
alternative to `git-filter-branch` for cleansing bad data out of your Git repository:

* Removing **Crazy Big Files**
* Removing **Passwords, Credentials** & other **Private data**

Main documentation for The BFG is here : **https://rtyley.github.io/bfg-repo-cleaner/**


================================================
FILE: backers.md
================================================
Many thanks to supporters of the BFG!
-----

Contribute towards the open-source development of the BFG on [**BountySource**](https://www.bountysource.com/teams/bfg-repo-cleaner)

* [Thomas Ferris Nicolaisen](http://www.tfnico.com/) - host of the excellent [GitMinutes](http://www.gitminutes.com) podcast
* [Alec Clews](https://alecthegeek.github.io/)
* [ramtej](https://github.com/ramtej)


================================================
FILE: bfg/build.sbt
================================================
import java.io.{File, FileOutputStream}

import Dependencies.*
import sbt.taskKey

import scala.sys.process.Process
import scala.util.Try

val gitDescription = taskKey[String]("Git description of working dir")

gitDescription := Try[String](Process("git describe --all --always --dirty --long").lineStream.head.replace("heads/","").replace("-0-g","-")).getOrElse("unknown")

libraryDependencies += useNewerJava

mainClass := Some("use.newer.java.Version8")
Compile / packageBin / packageOptions +=
  Package.ManifestAttributes( "Main-Class-After-UseNewerJava-Check" -> "com.madgag.git.bfg.cli.Main" )

// note you don't want the jar name to collide with the non-assembly jar, otherwise confusion abounds.
assembly / assemblyJarName := s"${name.value}-${version.value}-${gitDescription.value}${jgitVersionOverride.map("-jgit-" + _).mkString}.jar"

assembly / assemblyMergeStrategy := {
  case PathList("META-INF", "versions", "9", "module-info.class") => MergeStrategy.discard
  case x =>
    val oldStrategy = (assembly / assemblyMergeStrategy).value
    oldStrategy(x)
}

buildInfoKeys := Seq[BuildInfoKey](version, scalaVersion, gitDescription)

buildInfoPackage := "com.madgag.git.bfg"

crossPaths := false

Compile / packageBin / publishArtifact := false

// replace the conventional main artifact with an uber-jar
addArtifact(Compile / packageBin / artifact, assembly)

val cliUsageDump = taskKey[File]("Dump the CLI 'usage' output to a file")

cliUsageDump := {
  val usageDumpFile = File.createTempFile("bfg-usage", "dump.txt")
  val scalaRun = new ForkRun(ForkOptions().withOutputStrategy(CustomOutput(new FileOutputStream(usageDumpFile))))

  val mainClassName = (Compile / run / mainClass).value getOrElse sys.error("No main class detected.")
  val classpath = Attributed.data((Runtime / fullClasspath).value)
  val args = Seq.empty

  scalaRun.run(mainClassName, classpath, args, streams.value.log).failed foreach (sys error _.getMessage)
  usageDumpFile
}

addArtifact( Artifact("bfg", "usage", "txt"), cliUsageDump )

libraryDependencies ++= Seq(
  scopt,
  jgit,
  scalaGitTest % "test"
)

import Tests.*
{
  def isolateTestsWhichRequireTheirOwnJvm(tests: Seq[TestDefinition]) = {
    val (testsRequiringIsolation, testsNotNeedingIsolation) = tests.partition(_.name.contains("RequiresOwnJvm"))

    val groups: Seq[Seq[TestDefinition]] = testsRequiringIsolation.map(Seq(_)) :+ testsNotNeedingIsolation

    groups map { group =>
      Group(group.size.toString, group, SubProcess(ForkOptions()))
    }
  }

  Test / testGrouping := isolateTestsWhichRequireTheirOwnJvm( (Test / definedTests).value )
}

Test / fork := true // JGit uses static (ie JVM-wide) config

Test / logBuffered := false

Test / parallelExecution := false



================================================
FILE: bfg/src/main/scala/com/madgag/git/bfg/cli/CLIConfig.scala
================================================
/*
 * Copyright (c) 2012, 2013 Roberto Tyley
 *
 * This file is part of 'BFG Repo-Cleaner' - a tool for removing large
 * or troublesome blobs from Git repositories.
 *
 * BFG Repo-Cleaner is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * BFG Repo-Cleaner is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see http://www.gnu.org/licenses/ .
 */

package com.madgag.git.bfg.cli

import com.madgag.git.bfg.BuildInfo
import com.madgag.git.bfg.GitUtil._
import com.madgag.git.bfg.cleaner._
import com.madgag.git.bfg.cleaner.kit.BlobInserter
import com.madgag.git.bfg.cleaner.protection.ProtectedObjectCensus
import com.madgag.git.bfg.model.FileName.ImplicitConversions._
import com.madgag.git.bfg.model.{FileName, Tree, TreeBlobEntry, TreeBlobs, TreeSubtrees}
import com.madgag.git.{SizedObject, _}
import com.madgag.inclusion.{IncExcExpression, _}
import com.madgag.text.ByteSize
import com.madgag.textmatching.{Glob, TextMatcher, TextMatcherType, TextReplacementConfig}
import org.eclipse.jgit.internal.storage.file.FileRepository
import org.eclipse.jgit.lib._
import org.eclipse.jgit.storage.file.FileRepositoryBuilder
import scopt.{OptionParser, Read}

import java.io.File
import java.nio.file.Files
import scala.jdk.CollectionConverters._


object CLIConfig {
  val parser = new OptionParser[CLIConfig]("bfg") {

    def fileMatcher(name: String, defaultType: TextMatcherType = Glob) = {
      implicit val textMatcherRead: Read[TextMatcher] = Read.reads { TextMatcher(_, defaultType) }

      opt[TextMatcher](name).valueName(s"<${defaultType.expressionPrefix}>").validate { m =>
        if (m.expression.contains('/')) {
          failure("*** Can only match on filename, NOT path *** - remove '/' path segments")
        } else success
      }
    }

    def readLinesFrom(v: File): Seq[String] = Files.readAllLines(v.toPath).asScala.toSeq

    val exactVersion = BuildInfo.version + (if (BuildInfo.version.contains("-SNAPSHOT")) s" (${BuildInfo.gitDescription})" else "")

    head("bfg", exactVersion)
    version("version").hidden()

    opt[String]('b', "strip-blobs-bigger-than").valueName("<size>").text("strip blobs bigger than X (eg '128K', '1M', etc)").action {
      (v , c) => c.copy(stripBlobsBiggerThan = Some(ByteSize.parse(v)))
    }
    opt[Int]('B', "strip-biggest-blobs").valueName("NUM").text("strip the top NUM biggest blobs").action {
      (v, c) => c.copy(stripBiggestBlobs = Some(v))
    }
    opt[File]("strip-blobs-with-ids").abbr("bi").valueName("<blob-ids-file>").text("strip blobs with the specified Git object ids").action {
      (v, c) =>
        c.copy(stripBlobsWithIds = Some(readLinesFrom(v).map(_.trim).filterNot(_.isEmpty).map(_.asObjectId).toSet))
    }
    fileMatcher("delete-files").abbr("D").text("delete files with the specified names (eg '*.class', '*.{txt,log}' - matches on file name, not path within repo)").action {
      (v, c) => c.copy(deleteFiles = Some(v))
    }
    fileMatcher("delete-folders").text("delete folders with the specified names (eg '.svn', '*-tmp' - matches on folder name, not path within repo)").action {
      (v, c) => c.copy(deleteFolders = Some(v))
    }
    opt[String]("convert-to-git-lfs").text("extract files with the specified names (eg '*.zip' or '*.mp4') into Git LFS").action {
      (v, c) => c.copy(lfsConversion = Some(v))
    }
    opt[File]("replace-text").abbr("rt").valueName("<expressions-file>").text("filter content of files, replacing matched text. Match expressions should be listed in the file, one expression per line - " +
      "by default, each expression is treated as a literal, but 'regex:' & 'glob:' prefixes are supported, with '==>' to specify a replacement " +
      "string other than the default of '***REMOVED***'.").action {
      (v, c) => c.copy(textReplacementExpressions = readLinesFrom(v).filterNot(_.trim.isEmpty))
    }
    fileMatcher("filter-content-including").abbr("fi").text("do file-content filtering on files that match the specified expression (eg '*.{txt,properties}')").action {
      (v, c) => c.copy(filenameFilters = c.filenameFilters :+ Include(v))
    }
    fileMatcher("filter-content-excluding").abbr("fe").text("don't do file-content filtering on files that match the specified expression (eg '*.{xml,pdf}')").action {
      (v, c) => c.copy(filenameFilters = c.filenameFilters :+ Exclude(v))
    }
    opt[String]("filter-content-size-threshold").abbr("fs").valueName("<size>").text("only do file-content filtering on files smaller than <size> (default is %1$d bytes)".format(CLIConfig().filterSizeThreshold)).action {
      (v, c) => c.copy(filterSizeThreshold = ByteSize.parse(v))
    }
    opt[String]('p', "protect-blobs-from").valueName("<refs>").text("protect blobs that appear in the most recent versions of the specified refs (default is 'HEAD')").action {
      (v, c) => c.copy(protectBlobsFromRevisions = v.split(',').toSet)
    }
    opt[Unit]("no-blob-protection").text("allow the BFG to modify even your *latest* commit. Not recommended: you should have already ensured your latest commit is clean.").action {
      (_, c) => c.copy(protectBlobsFromRevisions = Set.empty)
    }
    opt[Unit]("strict-object-checking").text("perform additional checks on integrity of consumed & created objects").hidden().action {
      (_, c) => c.copy(strictObjectChecking = true)
    }
    opt[Unit]("private").text("treat this repo-rewrite as removing private data (for example: omit old commit ids from commit messages)").action {
      (_, c) => c.copy(sensitiveData = Some(true))
    }
    opt[String]("massive-non-file-objects-sized-up-to").valueName("<size>").text("increase memory usage to handle over-size Commits, Tags, and Trees that are up to X in size (eg '10M')").action {
      (v, c) => c.copy(massiveNonFileObjects = Some(ByteSize.parse(v)))
    }
    opt[String]("fix-filename-duplicates-preferring").valueName("<filemode>").text("Fix corrupt trees which contain multiple entries with the same filename, favouring the 'tree' or 'blob'").hidden().action {
      (v, c) =>
        val preferredFileMode = v.toLowerCase match {
          case "tree" | "folder" => FileMode.TREE
          case "blob" | "file" => FileMode.REGULAR_FILE
          case other => throw new IllegalArgumentException(s"'$other' should be 'tree' or 'blob'")
        }
        val ord: Option[Ordering[FileMode]] = Some(Ordering.by[FileMode, Int](filemode => if (filemode==preferredFileMode) 0 else 1))

        c.copy(fixFilenameDuplicatesPreferring = ord)
    }
    arg[File]("<repo>").optional().action { (x, c) =>
      c.copy(repoLocation = x) } text("file path for Git repository to clean")
  }
}

case class CLIConfig(stripBiggestBlobs: Option[Int] = None,
                     stripBlobsBiggerThan: Option[Long] = None,
                     protectBlobsFromRevisions: Set[String] = Set("HEAD"),
                     deleteFiles: Option[TextMatcher] = None,
                     deleteFolders: Option[TextMatcher] = None,
                     fixFilenameDuplicatesPreferring: Option[Ordering[FileMode]] = None,
                     filenameFilters: Seq[Filter[String]] = Nil,
                     filterSizeThreshold: Long = BlobTextModifier.DefaultSizeThreshold,
                     textReplacementExpressions: Iterable[String] = List.empty,
                     stripBlobsWithIds: Option[Set[ObjectId]] = None,
                     lfsConversion: Option[String] = None,
                     strictObjectChecking: Boolean = false,
                     sensitiveData: Option[Boolean] = None,
                     massiveNonFileObjects: Option[Long] = None,
                     repoLocation: File = new File(System.getProperty("user.dir"))) {

  lazy val gitdir = resolveGitDirFor(repoLocation)

  implicit lazy val repo: FileRepository = FileRepositoryBuilder.create(gitdir.get).asInstanceOf[FileRepository]

  lazy val objectProtection = ProtectedObjectCensus(protectBlobsFromRevisions)

  lazy val objectChecker = if (strictObjectChecking) Some(new ObjectChecker()) else None

  lazy val fileDeletion: Option[Cleaner[TreeBlobs]] = deleteFiles.map {
    textMatcher => new FileDeleter(textMatcher)
  }

  lazy val folderDeletion: Option[Cleaner[TreeSubtrees]] = deleteFolders.map {
    textMatcher => { subtrees: TreeSubtrees =>
      TreeSubtrees(subtrees.entryMap.view.filterKeys(filename => !textMatcher(filename)).toMap)
    }
  }

  lazy val fixFileNameDuplication: Option[Cleaner[Seq[Tree.Entry]]] = fixFilenameDuplicatesPreferring.map {
    implicit preferredFileModes =>
    { treeEntries: Seq[Tree.Entry] => treeEntries.groupBy(_.name).values.map(_.minBy(_.fileMode)).toSeq }
  }

  lazy val lineModifier: Option[String => String] =
    TextReplacementConfig(textReplacementExpressions, "***REMOVED***")

  lazy val filterContentPredicate: (FileName => Boolean) = f => IncExcExpression(filenameFilters) includes (f.string)

  lazy val blobTextModifier: Option[BlobTextModifier] = lineModifier.map {
    replacer =>
      new BlobTextModifier {
        override val sizeThreshold = filterSizeThreshold

        def lineCleanerFor(entry: TreeBlobEntry) = if (filterContentPredicate(entry.filename)) Some(replacer) else None

        val threadLocalObjectDBResources = repo.getObjectDatabase.threadLocalResources
      }
  }

  lazy val lfsBlobConverter: Option[LfsBlobConverter] = lfsConversion.map { lfsGlobExpr =>
    new LfsBlobConverter(lfsGlobExpr, repo)
  }

  lazy val privateDataRemoval = sensitiveData.getOrElse(Seq(fileDeletion, folderDeletion, blobTextModifier).flatten.nonEmpty)

  lazy val objectIdSubstitutor = if (privateDataRemoval) ObjectIdSubstitutor.OldIdsPrivate else ObjectIdSubstitutor.OldIdsPublic

  lazy val treeEntryListCleaners = fixFileNameDuplication.toSeq

  lazy val commitNodeCleaners = {
    lazy val formerCommitFooter = if (privateDataRemoval) None else Some(FormerCommitFooter)

    Seq(new CommitMessageObjectIdsUpdater(objectIdSubstitutor)) ++ formerCommitFooter
  }

  lazy val treeBlobCleaners: Seq[Cleaner[TreeBlobs]] = {

    lazy val blobsByIdRemover: Option[BlobRemover] = stripBlobsWithIds.map(new BlobRemover(_))

    lazy val blobRemover: Option[Cleaner[TreeBlobs]] = {
      implicit val progressMonitor: ProgressMonitor = new TextProgressMonitor()

      val sizeBasedBlobTargetSources = Seq(
        stripBlobsBiggerThan.map(threshold => (s: LazyList[SizedObject]) => s.takeWhile(_.size > threshold)),
        stripBiggestBlobs.map(num => (s: LazyList[SizedObject]) => s.take(num))
      ).flatten

      if (sizeBasedBlobTargetSources.isEmpty) None else {
        val sizedBadIds = sizeBasedBlobTargetSources.flatMap(_(biggestBlobs(repo.getObjectDatabase, progressMonitor))).toSet
        if (sizedBadIds.isEmpty) {
          println("Warning : no large blobs matching criteria found in packfiles - does the repo need to be packed?")
          None
        } else {
          println("Found " + sizedBadIds.size + " blob ids for large blobs - biggest=" + sizedBadIds.max.size + " smallest=" + sizedBadIds.min.size)
          println("Total size (unpacked)=" + sizedBadIds.map(_.size).sum)
          Some(new BlobReplacer(sizedBadIds.map(_.objectId), new BlobInserter(repo.getObjectDatabase.threadLocalResources.inserter())))
        }
      }
    }

    Seq(blobsByIdRemover, blobRemover, fileDeletion, blobTextModifier, lfsBlobConverter).flatten
  }

  lazy val definesNoWork = treeBlobCleaners.isEmpty && folderDeletion.isEmpty && treeEntryListCleaners.isEmpty

  def objectIdCleanerConfig: ObjectIdCleaner.Config =
    ObjectIdCleaner.Config(
      objectProtection,
      objectIdSubstitutor,
      commitNodeCleaners,
      treeEntryListCleaners,
      treeBlobCleaners,
      folderDeletion.toSeq,
      objectChecker
    )

  def describe = {
    if (privateDataRemoval) {
      "is removing private data, so the '" + FormerCommitFooter.Key + "' footer will not be added to commit messages."
    } else {
      "is only removing non-private data (eg, blobs that are just big, not private) : '" + FormerCommitFooter.Key + "' footer will be added to commit messages."
    }
  }
}


================================================
FILE: bfg/src/main/scala/com/madgag/git/bfg/cli/Main.scala
================================================
/*
 * Copyright (c) 2012 Roberto Tyley
 *
 * This file is part of 'BFG Repo-Cleaner' - a tool for removing large
 * or troublesome blobs from Git repositories.
 *
 * BFG Repo-Cleaner is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * BFG Repo-Cleaner is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see http://www.gnu.org/licenses/ .
 */

package com.madgag.git.bfg.cli

import com.madgag.git._
import com.madgag.git.bfg.GitUtil._
import com.madgag.git.bfg.cleaner._

object Main extends App {

  if (args.isEmpty) {
    CLIConfig.parser.showUsage()
  } else {

    CLIConfig.parser.parse(args, CLIConfig()) map {
      config =>

        tweakStaticJGitConfig(config.massiveNonFileObjects)

        if (config.gitdir.isEmpty) {
          CLIConfig.parser.showUsage()
          Console.err.println("Aborting : " + config.repoLocation + " is not a valid Git repository.\n")
        } else {
          implicit val repo = config.repo

          println("\nUsing repo : " + repo.getDirectory.getAbsolutePath + "\n")

          // do this before implicitly initiating big-blob search
          if (hasBeenProcessedByBFGBefore(repo)) {
            println("\nThis repo has been processed by The BFG before! Will prune repo before proceeding - to avoid unnecessary cleaning work on unused objects...")
            repo.git.gc.call()
            println("Completed prune of old objects - will now proceed with the main job!\n")
          }

          if (config.definesNoWork) {
            Console.err.println("Please specify tasks for The BFG :")
            CLIConfig.parser.showUsage()
          } else {
            println("Found " + config.objectProtection.fixedObjectIds.size + " objects to protect")

            RepoRewriter.rewrite(repo, config.objectIdCleanerConfig)
            repo.close()
          }
        }
    }
  }

}

================================================
FILE: bfg/src/test/scala/com/madgag/git/bfg/cli/CLIConfigSpecs.scala
================================================
package com.madgag.git.bfg.cli

import com.madgag.git.bfg.model.FileName
import org.scalatest.flatspec.AnyFlatSpec
import org.scalatest.matchers.should.Matchers

class CLIConfigSpecs extends AnyFlatSpec with Matchers {


  def parse(args: String) = CLIConfig.parser.parse(args.split(' ') :+ "my-repo.git", CLIConfig()).get.filterContentPredicate

  "CLI config" should "understand lone include" in {
    val predicate = parse("-fi *.txt")
    predicate(FileName("panda")) shouldBe false
    predicate(FileName("foo.txt")) shouldBe true
    predicate(FileName("foo.java")) shouldBe false
  }

  it should "understand lone exclude" in {
    val predicate = parse("-fe *.txt")
    predicate(FileName("panda")) shouldBe true
    predicate(FileName("foo.txt")) shouldBe false
    predicate(FileName("foo.java")) shouldBe true
  }

  it should "understand include followed by exclude" in {
    val predicate = parse("-fi *.txt -fe Poison.*")
    predicate(FileName("panda")) shouldBe false
    predicate(FileName("foo.txt")) shouldBe true
    predicate(FileName("foo.java")) shouldBe false
    predicate(FileName("Poison.txt")) shouldBe false
  }

  it should "understand exclude followed by include" in {
    val predicate = parse("-fe *.xml -fi hbm.xml")
    predicate(FileName("panda")) shouldBe true
    predicate(FileName("foo.xml")) shouldBe false
    predicate(FileName("hbm.xml")) shouldBe true
  }

}


================================================
FILE: bfg/src/test/scala/com/madgag/git/bfg/cli/MainSpec.scala
================================================
/*
 * Copyright (c) 2012, 2013 Roberto Tyley
 *
 * This file is part of 'BFG Repo-Cleaner' - a tool for removing large
 * or troublesome blobs from Git repositories.
 *
 * BFG Repo-Cleaner is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * BFG Repo-Cleaner is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see http://www.gnu.org/licenses/ .
 */

package com.madgag.git.bfg.cli

import com.madgag.git._
import com.madgag.git.bfg.cli.test.unpackedRepo
import com.madgag.git.bfg.model._
import org.eclipse.jgit.lib.{ObjectId, ObjectReader}
import org.scalatest.flatspec.AnyFlatSpec
import org.scalatest.matchers.should.Matchers
import org.scalatest.{Inspectors, OptionValues}

import java.nio.file.Files
import scala.jdk.CollectionConverters._

class MainSpec extends AnyFlatSpec with Matchers with OptionValues with Inspectors {

  // concurrent testing against scala.App is not safe https://twitter.com/rtyley/status/340376844916387840

  "CLI" should "not change commits unnecessarily" in new unpackedRepo("/sample-repos/exampleWithInitialCleanHistory.git.zip") {
    implicit val r: ObjectReader = reader

    ensureInvariantValue(commitHist() take 2) {
      ensureRemovalFrom(commitHist()).ofCommitsThat(haveCommitWhereObjectIds(contain(abbrId("294f")))) {
        run("--strip-blobs-bigger-than 1K")
      }
    }
  }


  "removing empty trees" should "work" in new unpackedRepo("/sample-repos/folder-example.git.zip") {
    ensureRemovalFrom(commitHist()).ofCommitsThat(haveFolder("secret-files")) {
      run("--delete-files {credentials,passwords}.txt")
    }
  }

  "removing big blobs" should "definitely still remove blobs even if they have identical size" in new unpackedRepo("/sample-repos/moreThanOneBigBlobWithTheSameSize.git.zip") {
    ensureRemovalOfBadEggs(packedBlobsOfSize(1024), (contain allElementsOf Set(abbrId("06d7"), abbrId("cb2c"))).matcher[Iterable[ObjectId]]) {
      run("--strip-blobs-bigger-than 512B")
    }
  }

  "converting to Git LFS" should "create a file in lfs/objects" in new unpackedRepo("/sample-repos/repoWithBigBlobs.git.zip") {
    ensureRemovalOfBadEggs(packedBlobsOfSize(11238), (contain only abbrId("596c")).matcher[Iterable[ObjectId]]) {
      run("--convert-to-git-lfs *.png --no-blob-protection")
    }
    val lfsFile = repo.getDirectory.toPath.resolve(Seq("lfs", "objects", "e0", "eb", "e0ebd49837a1cced34b9e7d3ff2fa68a8100df8f158f165ce139e366a941ba6e"))

    Files.size(lfsFile) shouldBe 11238
  }

  "removing a folder named '.git'" should "work" in new unpackedRepo("/sample-repos/badRepoContainingDotGitFolder.git.zip") {
    ensureRemovalFrom(commitHist()).ofCommitsThat(haveFolder(".git")) {
      run("--delete-folders .git --no-blob-protection")
    }
  }

  "cleaning" should "not crash encountering a protected an annotated tag" in new unpackedRepo("/sample-repos/annotatedTagExample.git.zip") {
    ensureInvariantCondition(haveRef("chapter1", haveFile("chapter1.txt"))) {
      ensureRemovalFrom(commitHist("master")).ofCommitsThat(haveFile("chapter2.txt")) {
        run("--strip-blobs-bigger-than 10B --protect-blobs-from chapter1")
      }
    }
  }

  "cleaning" should "not crash encountering a protected branch containing a slash in it's name" in new unpackedRepo("/sample-repos/branchNameWithASlash.git.zip") {
    ensureInvariantCondition(haveRef("feature/slashes-are-ugly", haveFile("bar"))) {
      ensureRemovalFrom(commitHist("master")).ofCommitsThat(haveFile("bar")) {
        run("--delete-files bar --protect-blobs-from feature/slashes-are-ugly")
      }
    }
  }

  "strip blobs by id" should "work" in new unpackedRepo("/sample-repos/example.git.zip") {
    implicit val r: ObjectReader = reader

    val badBlobs = Set(abbrId("db59"), abbrId("86f9"))
    val blobIdsFile = Files.createTempFile("test-strip-blobs",".ids")
    Files.write(blobIdsFile, badBlobs.map(_.name()).asJava)

    ensureRemovalFrom(commitHist()).ofCommitsThat(haveCommitWhereObjectIds(contain(abbrId("db59")))) {
      run(s"--strip-blobs-with-ids $blobIdsFile")
    }
  }

  "deleting a folder" should "not crash encountering a submodule" in new unpackedRepo("/sample-repos/usedToHaveASubmodule.git.zip") {
    ensureInvariantCondition(haveRef("master", haveFile("alpha"))) {
      ensureRemovalFrom(commitHist()).ofCommitsThat(haveFolder("shared")) {
        run("--delete-folders shared")
      }
    }
  }

  "deleting" should "not crash encountering a protected submodule" in new unpackedRepo("/sample-repos/unwantedSubmodule.git.zip") {
    ensureRemovalFrom(commitHist()).ofCommitsThat(haveFile("foo.txt")) {
      run("--delete-folders bar --delete-files foo.txt")
    }
  }

  "deleting" should "not crash on encountering a commit with bad encoding header" in new unpackedRepo("/sample-repos/badEncoding.git.zip") {
    ensureRemovalFrom(commitHist()).ofCommitsThat(haveFile("test.txt")) {
      run("--no-blob-protection --delete-files test.txt")
    }
  }

  "Corrupt trees containing duplicate filenames" should "be cleaned by removing the file with the duplicate FileName, leaving the folder" in new unpackedRepo("/sample-repos/corruptTreeDupFileName.git.zip") {
    ensureRemovalFrom(commitHist()).ofCommitsThat(haveFile("2.0.0")) {
      run("--fix-filename-duplicates-preferring tree")
    }
  }
}



================================================
FILE: bfg/src/test/scala/com/madgag/git/bfg/cli/MassiveNonFileObjectsRequiresOwnJvmSpec.scala
================================================
/*
 * Copyright (c) 2012, 2013 Roberto Tyley
 *
 * This file is part of 'BFG Repo-Cleaner' - a tool for removing large
 * or troublesome blobs from Git repositories.
 *
 * BFG Repo-Cleaner is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * BFG Repo-Cleaner is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see http://www.gnu.org/licenses/ .
 */

package com.madgag.git.bfg.cli

import com.madgag.git.bfg.cli.test.unpackedRepo
import org.scalatest.flatspec.AnyFlatSpec
import org.scalatest.matchers.should.Matchers

// JGit has JVM-wide configuration for cache window size: https://git.eclipse.org/r/#/q/Ibf2ef604bac08885b2b3bd85f0dc31995132b682,n,z
class MassiveNonFileObjectsRequiresOwnJvmSpec extends AnyFlatSpec with Matchers {

  // concurrent testing against scala.App is not safe https://twitter.com/rtyley/status/340376844916387840

  "Massive commit messages" should "be handled without crash (ie LargeObjectException) if the user specifies that the repo contains massive non-file objects" in
    new unpackedRepo("/sample-repos/huge10MBCommitMessage.git.zip") {
      ensureRemovalFrom(commitHist("master")).ofCommitsThat(haveFile("16-kb-zeros")) {
        run("--strip-blobs-bigger-than 1K --massive-non-file-objects-sized-up-to 20M")
      }
    }

}


================================================
FILE: bfg/src/test/scala/com/madgag/git/bfg/cli/test/unpackedRepo.scala
================================================
/*
 * Copyright (c) 2012, 2013 Roberto Tyley
 *
 * This file is part of 'BFG Repo-Cleaner' - a tool for removing large
 * or troublesome blobs from Git repositories.
 *
 * BFG Repo-Cleaner is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * BFG Repo-Cleaner is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see http://www.gnu.org/licenses/ .
 */

package com.madgag.git.bfg.cli.test

import com.madgag.git.bfg
import com.madgag.git.bfg.cli.Main

class unpackedRepo(filePath: String) extends bfg.test.unpackedRepo(filePath) {
  def run(options: String): Unit = {
    Main.main(options.split(' ') :+ repo.getDirectory.getAbsolutePath)
  }
}

================================================
FILE: bfg-benchmark/build.sbt
================================================
import Dependencies.*

libraryDependencies ++= guava ++ Seq(
  madgagCompress,
  textmatching,
  scopt
)

================================================
FILE: bfg-benchmark/resources/jars/grabJars.sh
================================================
#!/bin/bash
for i in 4.0 5.0 6.0 7.0 12.0 13.0 13.1 13.2
do
	VERSION="1.$i"
	curl -O "https://repo1.maven.org/maven2/com/madgag/bfg/$VERSION/bfg-$VERSION.jar"
done


================================================
FILE: bfg-benchmark/resources/repos/chromium-src/commands/issue-23/bfg.txt
================================================
--delete-files *.{52,50,crx,xib,png,pdf,jpg,zip,jar,pdb,psd,jpeg,dylib,dll,DLL,exe,EXE,vcproj,so,sln,scons,nib,graffle,yuv,webm}


================================================
FILE: bfg-benchmark/resources/repos/gcc/commands/delete-file/bfg.txt
================================================
-D README-fixinc


================================================
FILE: bfg-benchmark/resources/repos/gcc/commands/delete-file/gfb.txt
================================================
--index-filter
git rm --cached --ignore-unmatch gcc/README-fixinc
--prune-empty
--tag-name-filter
cat
--
--all


================================================
FILE: bfg-benchmark/resources/repos/git/commands/delete-file/bfg.txt
================================================
-D object.c


================================================
FILE: bfg-benchmark/resources/repos/git/commands/delete-file/gfb.txt
================================================
--index-filter
git rm --cached --ignore-unmatch object.c
--prune-empty
--tag-name-filter
cat
--
--all


================================================
FILE: bfg-benchmark/resources/repos/github-gem/commands/delete-file/bfg.txt
================================================
-D Rakefile


================================================
FILE: bfg-benchmark/resources/repos/github-gem/commands/delete-file/gfb.txt
================================================
--index-filter
git rm --cached --ignore-unmatch Rakefile
--prune-empty
--tag-name-filter
cat
--
--all


================================================
FILE: bfg-benchmark/resources/repos/intellij/commands/delete-binary-resources/bfg.txt
================================================
--delete-files *.{zip,jar} --no-blob-protection


================================================
FILE: bfg-benchmark/resources/repos/intellij/commands/delete-file/bfg.txt
================================================
-D breakgen.dll


================================================
FILE: bfg-benchmark/resources/repos/intellij/commands/delete-file/gfb.txt
================================================
--index-filter
git rm --cached --ignore-unmatch bin/breakgen.dll
--prune-empty
--tag-name-filter
cat
--
--all


================================================
FILE: bfg-benchmark/resources/repos/intellij/commands/git-lfs-binary-resources/bfg.txt
================================================
--convert-to-git-lfs *.{zip,jar,exe,dll} --no-blob-protection


================================================
FILE: bfg-benchmark/resources/repos/jgit/commands/delete-file/bfg.txt
================================================
-D make_jgit.sh


================================================
FILE: bfg-benchmark/resources/repos/jgit/commands/delete-file/gfb.txt
================================================
--index-filter
git rm --cached --ignore-unmatch make_jgit.sh
--prune-empty
--tag-name-filter
cat
--
--all


================================================
FILE: bfg-benchmark/resources/repos/jgit/commands/replace-1-existing-string/bfg.txt
================================================
--replace-text passwords.1-existing-string.txt


================================================
FILE: bfg-benchmark/resources/repos/jgit/commands/replace-1-existing-string/passwords.1-existing-string.txt
================================================
invalidAdvertisementOf


================================================
FILE: bfg-benchmark/resources/repos/jgit/commands/replace-20-existing-strings/bfg.txt
================================================
--replace-text passwords.20-existing-strings.txt


================================================
FILE: bfg-benchmark/resources/repos/jgit/commands/replace-20-existing-strings/passwords.20-existing-strings.txt
================================================
invalidAdvertisementOf
abbreviationLengthMustBeNonNegative
abortingRebase
abortingRebaseFailed
abortingRebaseFailedNoOrigHead
advertisementCameBefore
advertisementOfCameBefore
amazonS3ActionFailed
amazonS3ActionFailedGivingUp
ambiguousObjectAbbreviation
aNewObjectIdIsRequired
anExceptionOccurredWhileTryingToAddTheIdOfHEAD
anSSHSessionHasBeenAlreadyCreated
applyingCommitnvalidType
corruptObjectInvalidType2
corruptObjectMalformedHeader
dirCacheIsNotLocked
DIRCChecksumMismatch
enumValueNotSupported3
errorDecodingFromFile


================================================
FILE: bfg-benchmark/resources/repos/jgit/commands/replace-500-existing-strings/bfg.txt
================================================
--replace-text passwords.500-existing-strings.txt


================================================
FILE: bfg-benchmark/resources/repos/jgit/commands/replace-500-existing-strings/passwords.500-existing-strings.txt
================================================
abbreviationLengthMustBeNonNegative
abortingRebase
abortingRebaseFailed
abortingRebaseFailedNoOrigHead
advertisementCameBefore
advertisementOfCameBefore
amazonS3ActionFailed
amazonS3ActionFailedGivingUp
ambiguousObjectAbbreviation
aNewObjectIdIsRequired
anExceptionOccurredWhileTryingToAddTheIdOfHEAD
anSSHSessionHasBeenAlreadyCreated
applyingCommit
archiveFormatAlreadyAbsent
archiveFormatAlreadyRegistered
atLeastOnePathIsRequired
atLeastOnePatternIsRequired
atLeastTwoFiltersNeeded
authenticationNotSupported
badBase64InputCharacterAt
badEntryDelimiter
badEntryName
badEscape
badGroupHeader
badObjectType
badSectionEntry
bareRepositoryNoWorkdirAndIndex
base64InputNotProperlyPadded
baseLengthIncorrect
bitmapMissingObject
bitmapsMustBePrepared
blameNotCommittedYet
blobNotFound
blobNotFoundForPath
branchNameInvalid
buildingBitmaps
cachedPacksPreventsIndexCreation
cachedPacksPreventsListingObjects
cannotBeCombined
cannotBeRecursiveWhenTreesAreIncluded
cannotCombineSquashWithNoff
cannotCombineTreeFilterWithRevFilter
cannotCommitOnARepoWithState
cannotCommitWriteTo
cannotConnectPipes
cannotConvertScriptToText
cannotCreateConfig
cannotCreateDirectory
cannotCreateHEAD
cannotCreateIndexfile
cannotDeleteCheckedOutBranch
cannotDeleteFile
cannotDeleteStaleTrackingRef
cannotDeleteStaleTrackingRef2
cannotDetermineProxyFor
cannotDownload
cannotExecute
cannotGet
cannotListRefs
cannotLock
cannotLockPackIn
cannotMatchOnEmptyString
cannotMoveIndexTo
cannotMovePackTo
cannotOpenService
cannotParseDate
cannotParseGitURIish
cannotPullOnARepoWithState
cannotRead
cannotReadBlob
cannotReadCommit
cannotReadFile
cannotReadHEAD
cannotReadObject
cannotReadTree
cannotRebaseWithoutCurrentHead
cannotResolveLocalTrackingRefForUpdating
cannotStoreObjects
cannotUnloadAModifiedTree
cannotWorkWithOtherStagesThanZeroRightNow
canOnlyCherryPickCommitsWithOneParent
canOnlyRevertCommitsWithOneParent
cantFindObjectInReversePackIndexForTheSpecifiedOffset
cantPassMeATree
channelMustBeInRange0_255
characterClassIsNotSupported
checkoutConflictWithFile
checkoutConflictWithFiles
checkoutUnexpectedResult
classCastNotA
cloneNonEmptyDirectory
collisionOn
commandWasCalledInTheWrongState
commitAlreadyExists
commitMessageNotSpecified
commitOnRepoWithoutHEADCurrentlyNotSupported
commitAmendOnInitialNotPossible
compressingObjects
connectionFailed
connectionTimeOut
contextMustBeNonNegative
corruptionDetectedReReadingAt
corruptObjectBadStream
corruptObjectBadStreamCorruptHeader
corruptObjectGarbageAfterSize
corruptObjectIncorrectLength
corruptObjectInvalidEntryMode
corruptObjectInvalidMode
corruptObjectInvalidMode2
corruptObjectInvalidMode3
corruptObjectInvalidType
corruptObjectInvalidType2
corruptObjectMalformedHeader
corruptObjectNegativeSize
corruptObjectNoAuthor
corruptObjectNoCommitter
corruptObjectNoHeader
corruptObjectNoObject
corruptObjectNoTaggerBadHeader
corruptObjectNoTaggerHeader
corruptObjectNoTagName
corruptObjectNotree
corruptObjectNoType
corruptObjectPackfileChecksumIncorrect
couldNotCheckOutBecauseOfConflicts
couldNotDeleteLockFileShouldNotHappen
couldNotDeleteTemporaryIndexFileShouldNotHappen
couldNotGetAdvertisedRef
couldNotGetRepoStatistics
couldNotLockHEAD
couldNotReadIndexInOneGo
couldNotReadObjectWhileParsingCommit
couldNotRenameDeleteOldIndex
couldNotRenameTemporaryFile
couldNotRenameTemporaryIndexFileToIndex
couldNotURLEncodeToUTF8
couldNotWriteFile
countingObjects
createBranchFailedUnknownReason
createBranchUnexpectedResult
createNewFileFailed
credentialPassword
credentialUsername
daemonAlreadyRunning
daysAgo
deleteBranchUnexpectedResult
deleteFileFailed
deleteTagUnexpectedResult
deletingNotSupported
destinationIsNotAWildcard
detachedHeadDetected
dirCacheDoesNotHaveABackingFile
dirCacheFileIsNotLocked
dirCacheIsNotLocked
DIRCChecksumMismatch
DIRCExtensionIsTooLargeAt
DIRCExtensionNotSupportedByThisVersion
DIRCHasTooManyEntries
DIRCUnrecognizedExtendedFlags
dirtyFilesExist
doesNotHandleMode
downloadCancelled
downloadCancelledDuringIndexing
duplicateAdvertisementsOf
duplicateRef
duplicateRemoteRefUpdateIsIllegal
duplicateStagesNotAllowed
eitherGitDirOrWorkTreeRequired
emptyCommit
emptyPathNotPermitted
encryptionError
endOfFileInEscape
entryNotFoundByPath
enumValueNotSupported2
enumValueNotSupported3
enumValuesNotAvailable
errorDecodingFromFile
errorEncodingFromFile
errorInBase64CodeReadingStream
errorInPackedRefs
errorInvalidProtocolWantedOldNewRef
errorListing
errorOccurredDuringUnpackingOnTheRemoteEnd
errorReadingInfoRefs
errorSymlinksNotSupported
exceptionCaughtDuringExecutionOfAddCommand
exceptionCaughtDuringExecutionOfArchiveCommand
exceptionCaughtDuringExecutionOfCherryPickCommand
exceptionCaughtDuringExecutionOfCommitCommand
exceptionCaughtDuringExecutionOfFetchCommand
exceptionCaughtDuringExecutionOfLsRemoteCommand
exceptionCaughtDuringExecutionOfMergeCommand
exceptionCaughtDuringExecutionOfPullCommand
exceptionCaughtDuringExecutionOfPushCommand
exceptionCaughtDuringExecutionOfResetCommand
exceptionCaughtDuringExecutionOfRevertCommand
exceptionCaughtDuringExecutionOfRmCommand
exceptionCaughtDuringExecutionOfTagCommand
exceptionOccurredDuringAddingOfOptionToALogCommand
exceptionOccurredDuringReadingOfGIT_DIR
expectedACKNAKFoundEOF
expectedACKNAKGot
expectedBooleanStringValue
expectedCharacterEncodingGuesses
expectedEOFReceived
expectedGot
expectedLessThanGot
expectedPktLineWithService
expectedReceivedContentType
expectedReportForRefNotReceived
failedUpdatingRefs
failureDueToOneOfTheFollowing
failureUpdatingFETCH_HEAD
failureUpdatingTrackingRef
fileCannotBeDeleted
fileIsTooBigForThisConvenienceMethod
fileIsTooLarge
fileModeNotSetForPath
flagIsDisposed
flagNotFromThis
flagsAlreadyCreated
funnyRefname
gcFailed
gitmodulesNotFound
headRequiredToStash
hoursAgo
hugeIndexesAreNotSupportedByJgitYet
hunkBelongsToAnotherFile
hunkDisconnectedFromFile
hunkHeaderDoesNotMatchBodyLineCountOf
illegalArgumentNotA
illegalCombinationOfArguments
illegalPackingPhase
illegalStateExists
improperlyPaddedBase64Input
incorrectHashFor
incorrectOBJECT_ID_LENGTH
indexFileIsInUse
indexFileIsTooLargeForJgit
indexSignatureIsInvalid
indexWriteException
inMemoryBufferLimitExceeded
inputStreamMustSupportMark
integerValueOutOfRange
internalRevisionError
internalServerError
interruptedWriting
inTheFuture
invalidAdvertisementOf
invalidAncestryLength
invalidBooleanValue
invalidChannel
invalidCharacterInBase64Data
invalidCommitParentNumber
invalidEncryption
invalidGitdirRef 
invalidGitType
invalidId
invalidIdLength
invalidIntegerValue
invalidKey
invalidLineInConfigFile
invalidModeFor
invalidModeForPath
invalidObject
invalidOldIdSent
invalidPacketLineHeader
invalidPath
invalidReflogRevision
invalidRefName
invalidRemote
invalidStageForPath
invalidTagOption
invalidTimeout
invalidURL
invalidWildcards
invalidRefSpec
invalidWindowSize
isAStaticFlagAndHasNorevWalkInstance
JRELacksMD5Implementation
kNotInRange
largeObjectExceedsByteArray
largeObjectExceedsLimit
largeObjectException
largeObjectOutOfMemory
lengthExceedsMaximumArraySize
listingAlternates
localObjectsIncomplete
localRefIsMissingObjects
lockCountMustBeGreaterOrEqual1
lockError
lockOnNotClosed
lockOnNotHeld
malformedpersonIdentString
maxCountMustBeNonNegative
mergeConflictOnNonNoteEntries
mergeConflictOnNotes
mergeStrategyAlreadyExistsAsDefault
mergeStrategyDoesNotSupportHeads
mergeUsingStrategyResultedInDescription
mergeRecursiveReturnedNoCommit
mergeRecursiveTooManyMergeBasesFor 
messageAndTaggerNotAllowedInUnannotatedTags 
minutesAgo
missingAccesskey
missingConfigurationForKey
missingDeltaBase
missingForwardImageInGITBinaryPatch
missingObject
missingPrerequisiteCommits
missingRequiredParameter
missingSecretkey
mixedStagesNotAllowed
mkDirFailed
mkDirsFailed
month
months
monthsAgo
multipleMergeBasesFor
need2Arguments
needPackOut
needsAtLeastOneEntry
needsWorkdir
newlineInQuotesNotAllowed
noApplyInDelete
noClosingBracket
noHEADExistsAndNoExplicitStartingRevisionWasSpecified
noHMACsupport
noMergeBase
noMergeHeadSpecified
noSuchRef
notABoolean
notABundle
notADIRCFile
notAGitDirectory
notAPACKFile
notARef
notASCIIString
notAuthorized
notAValidPack
notFound
nothingToFetch
nothingToPush
notMergedExceptionMessage
noXMLParserAvailable
objectAtHasBadZlibStream
objectAtPathDoesNotHaveId
objectIsCorrupt
objectIsNotA
objectNotFound
objectNotFoundIn
obtainingCommitsForCherryPick
offsetWrittenDeltaBaseForObjectNotFoundInAPack
onlyAlreadyUpToDateAndFastForwardMergesAreAvailable
onlyOneFetchSupported
onlyOneOperationCallPerConnectionIsSupported
openFilesMustBeAtLeast1
openingConnection
operationCanceled
outputHasAlreadyBeenStarted
packChecksumMismatch
packCorruptedWhileWritingToFilesystem
packDoesNotMatchIndex
packetSizeMustBeAtLeast
packetSizeMustBeAtMost
packfileCorruptionDetected
packFileInvalid
packfileIsTruncated
packHasUnresolvedDeltas
packingCancelledDuringObjectsWriting
packObjectCountMismatch
packRefs
packTooLargeForIndexVersion1
packWriterStatistics
panicCantRenameIndexFile
patchApplyException
patchFormatException
pathIsNotInWorkingDir
pathNotConfigured
peeledLineBeforeRef
peerDidNotSupplyACompleteObjectGraph
prefixRemote
problemWithResolvingPushRefSpecsLocally
progressMonUploading
propertyIsAlreadyNonNull
pruneLoosePackedObjects
pruneLooseUnreferencedObjects
pullOnRepoWithoutHEADCurrentlyNotSupported
pullTaskName
pushCancelled
pushIsNotSupportedForBundleTransport
pushNotPermitted
rawLogMessageDoesNotParseAsLogEntry
readingObjectsFromLocalRepositoryFailed
readTimedOut
receivePackObjectTooLarge1
receivePackObjectTooLarge2
receivingObjects
refAlreadyExists
refAlreadyExists1
reflogEntryNotFound
refNotResolved
refUpdateReturnCodeWas
remoteConfigHasNoURIAssociated
remoteDoesNotHaveSpec
remoteDoesNotSupportSmartHTTPPush
remoteHungUpUnexpectedly
remoteNameCantBeNull
renameBranchFailedBecauseTag
renameBranchFailedUnknownReason
renameBranchUnexpectedResult
renameFileFailed
renamesAlreadyFound
renamesBreakingModifies
renamesFindingByContent
renamesFindingExact
renamesRejoiningModifies
repositoryAlreadyExists
repositoryConfigFileInvalid
repositoryIsRequired
repositoryNotFound
repositoryState_applyMailbox
repositoryState_bisecting
repositoryState_conflicts
repositoryState_merged
repositoryState_normal
repositoryState_rebase
repositoryState_rebaseInteractive
repositoryState_rebaseOrApplyMailbox
repositoryState_rebaseWithMerge
requiredHashFunctionNotAvailable
resettingHead
resolvingDeltas
resultLengthIncorrect
rewinding
searchForReuse
searchForSizes
secondsAgo
selectingCommits
sequenceTooLargeForDiffAlgorithm
serviceNotEnabledNoName
serviceNotPermitted
serviceNotPermittedNoName
shallowCommitsAlreadyInitialized
shortCompressedStreamAt
shortReadOfBlock
shortReadOfOptionalDIRCExtensionExpectedAnotherBytes
shortSkipOfBlock
signingNotSupportedOnTag
similarityScoreMustBeWithinBounds
sizeExceeds2GB
skipMustBeNonNegative
smartHTTPPushDisabled
sourceDestinationMustMatch
sourceIsNotAWildcard
sourceRefDoesntResolveToAnyObject
sourceRefNotSpecifiedForRefspec
squashCommitNotUpdatingHEAD
staleRevFlagsOn
startingReadStageWithoutWrittenRequestDataPendingIsNotSupported
stashApplyConflict
stashApplyConflictInIndex
stashApplyFailed
stashApplyOnUnsafeRepository
stashApplyWithoutHead
stashCommitMissingTwoParents
stashDropDeleteRefFailed
stashDropFailed
stashDropMissingReflog
stashFailed
stashResolveFailed
statelessRPCRequiresOptionToBeEnabled
submoduleExists
submoduleParentRemoteUrlInvalid
submodulesNotSupported
symlinkCannotBeWrittenAsTheLinkTarget
systemConfigFileInvalid
tagAlreadyExists
tagNameInvalid
tagOnRepoWithoutHEADCurrentlyNotSupported
theFactoryMustNotBeNull
timerAlreadyTerminated
topologicalSortRequired
transportExceptionBadRef
transportExceptionEmptyRef
transportExceptionInvalid
transportExceptionMissingAssumed
transportExceptionReadRef
transportNeedsRepository
transportProtoAmazonS3
transportProtoBundleFile
transportProtoFTP
transportProtoGitAnon
transportProtoHTTP
transportProtoLocal
transportProtoSFTP
transportProtoSSH
treeEntryAlreadyExists
treeFilterMarkerTooManyFilters
treeIteratorDoesNotSupportRemove


================================================
FILE: bfg-benchmark/resources/repos/linux/commands/delete-file/bfg.txt
================================================
-D MAINTAINERS


================================================
FILE: bfg-benchmark/resources/repos/linux/commands/delete-file/gfb.txt
================================================
--index-filter
git rm --cached --ignore-unmatch MAINTAINERS
--prune-empty
--tag-name-filter
cat
--
--all


================================================
FILE: bfg-benchmark/resources/repos/rails/commands/delete-file/bfg.txt
================================================
-D pushgems.rb


================================================
FILE: bfg-benchmark/resources/repos/rails/commands/delete-file/gfb.txt
================================================
--index-filter
git rm --cached --ignore-unmatch pushgems.rb
--prune-empty
--tag-name-filter
cat
--
--all


================================================
FILE: bfg-benchmark/resources/repos/wine/commands/delete-file/bfg.txt
================================================
-D build-spec.txt


================================================
FILE: bfg-benchmark/resources/repos/wine/commands/delete-file/gfb.txt
================================================
--index-filter
git rm --cached --ignore-unmatch build-spec.txt
--prune-empty
--tag-name-filter
cat
--
--all


================================================
FILE: bfg-benchmark/src/main/scala/Benchmark.scala
================================================
import lib.Timing.measureTask
import lib._
import model._

import java.nio.file.Files
import java.nio.file.Files.isDirectory
import scala.concurrent.ExecutionContext.Implicits.global
import scala.concurrent._
import scala.concurrent.duration.Duration
import scala.jdk.StreamConverters._
import scala.sys.process._

/*
 * Vary BFG runs by:
 * Java version
 * BFG version (JGit version?)
 *
 */
object Benchmark extends App {

  BenchmarkConfig.parser.parse(args, BenchmarkConfig()) map {
    config =>
      println(s"Using resources dir : ${config.resourcesDir}")

      require(Files.exists(config.resourcesDir), s"Resources dir not found : ${config.resourcesDir}")
      require(Files.exists(config.jarsDir), s"Jars dir not found : ${config.jarsDir}")
      require(Files.exists(config.reposDir), s"Repos dir not found : ${config.reposDir}")

      val missingJars = config.bfgJars.filterNot(Files.exists(_))
      require(missingJars.isEmpty, s"Missing BFG jars : ${missingJars.mkString(",")}")

      val tasksFuture = for {
        bfgInvocableEngineSet <- bfgInvocableEngineSet(config)
      } yield {
        val gfbInvocableEngineSetOpt =
          Option.when(!config.onlyBfg)(InvocableEngineSet[GFBInvocation](GitFilterBranch, Seq(InvocableGitFilterBranch)))
        boogaloo(config, new RepoExtractor(config.scratchDir), Seq(bfgInvocableEngineSet) ++ gfbInvocableEngineSetOpt.toSeq)
      }

      Await.result(tasksFuture, Duration.Inf)
  }

  def bfgInvocableEngineSet(config: BenchmarkConfig): Future[InvocableEngineSet[BFGInvocation]] = for {
      javas <- Future.traverse(config.javaCmds)(jc => JavaVersion.version(jc).map(v => Java(jc, v)))
    } yield {
      val invocables = for {
        java <- javas
        bfgJar <- config.bfgJars
      } yield InvocableBFG(java, BFGJar.from(bfgJar))

      InvocableEngineSet[BFGInvocation](BFG, invocables)
    }

  /*
 * A Task says "here is something you can do to a given repo, and here is how to do
 * it with a BFG, and with git-filter-branch"
 */
  def boogaloo(config: BenchmarkConfig, repoExtractor: RepoExtractor, invocableEngineSets: Seq[InvocableEngineSet[_ <: EngineInvocation]]) = {

    for {
      repoSpecDir <- config.repoSpecDirs
      availableCommandDirs = Files.list(repoSpecDir.resolve("commands")).toScala(Seq).filter(isDirectory(_))
      // println(s"Available commands for $repoName : ${availableCommandDirs.map(_.name).mkString(", ")}")
      commandDir <- availableCommandDirs.filter(p => config.commands(p.getFileName.toString))
    } yield {
      val commandName: String = commandDir.getFileName.toString
      
      commandName -> (for {
        invocableEngineSet <- invocableEngineSets
      } yield for {
          (invocable, processMaker) <- invocableEngineSet.invocationsFor(commandDir)
        } yield {
        val cleanRepoDir = repoExtractor.extractRepoFrom(repoSpecDir.resolve("repo.git.zip"))
        Files.list(commandDir).toScala(Seq).foreach(p => Files.copy(p, cleanRepoDir.resolve(p.getFileName)))
        val process = processMaker(cleanRepoDir.toFile)

            val duration = measureTask(s"$commandName - $invocable") {
              process ! ProcessLogger(_ => ())
            }

            if (config.dieIfTaskTakesLongerThan.exists(_ < duration.toMillis)) {
              throw new Exception("This took too long: "+duration)
            }

            invocable -> duration
      })
    }
  }

  println(s"\n...benchmark finished.")
}


================================================
FILE: bfg-benchmark/src/main/scala/BenchmarkConfig.scala
================================================
import java.io.File
import com.madgag.textmatching.{Glob, TextMatcher}
import scopt.OptionParser

import java.nio.file.{Path, Paths}

object BenchmarkConfig {
  val parser = new OptionParser[BenchmarkConfig]("benchmark") {
    opt[File]("resources-dir").text("benchmark resources folder - contains jars and repos").action {
      (v, c) => c.copy(resourcesDirOption = v.toPath)
    }
    opt[String]("java").text("Java command paths").action {
      (v, c) => c.copy(javaCmds = v.split(',').toSeq)
    }
    opt[String]("versions").text("BFG versions to time - bfg-[version].jar - eg 1.4.0,1.5.0,1.6.0").action {
      (v, c) => c.copy(bfgVersions = v.split(",").toSeq)
    }
    opt[Int]("die-if-longer-than").text("Useful for git-bisect").action {
      (v, c) => c.copy(dieIfTaskTakesLongerThan = Some(v))
    }
    opt[String]("repos").text("Sample repos to test, eg github-gems,jgit,git").action {
      (v, c) => c.copy(repoNames = v.split(",").toSeq)
    }
    opt[String]("commands").valueName("<glob>").text("commands to exercise").action {
      (v, c) => c.copy(commands = TextMatcher(v, defaultType = Glob))
    }
    opt[File]("scratch-dir").text("Temp-dir for job runs - preferably ramdisk, eg tmpfs.").action {
      (v, c) => c.copy(scratchDir = v.toPath)
    }
    opt[Unit]("only-bfg") action { (_, c) => c.copy(onlyBfg = true) } text "Don't benchmark git-filter-branch"
  }
}
case class BenchmarkConfig(resourcesDirOption: Path = Paths.get(System.getProperty("user.dir"), "bfg-benchmark", "resources"),
                           scratchDir: Path = Paths.get("/dev/shm/"),
                           javaCmds: Seq[String] = Seq("java"),
                           bfgVersions: Seq[String] = Seq.empty,
                           commands: TextMatcher = Glob("*"),
                           onlyBfg: Boolean = false,
                           dieIfTaskTakesLongerThan: Option[Int] = None,
                           repoNames: Seq[String] = Seq.empty) {

  lazy val resourcesDir: Path = resourcesDirOption.toAbsolutePath

  lazy val jarsDir: Path = resourcesDir.resolve("jars")

  lazy val reposDir: Path = resourcesDir.resolve("repos")

  lazy val bfgJars: Seq[Path] = bfgVersions.map(version => jarsDir.resolve(s"bfg-$version.jar"))

  lazy val repoSpecDirs: Seq[Path] = repoNames.map(reposDir.resolve)
}


================================================
FILE: bfg-benchmark/src/main/scala/JavaVersion.scala
================================================
import scala.concurrent.ExecutionContext.Implicits.global
import scala.concurrent._
import scala.sys.process.{Process, ProcessLogger}

object JavaVersion {
  val VersionRegex = """(?:java|openjdk) version "(.*?)"""".r

  def version(javaCmd: String): Future[String] = {
    val resultPromise = Promise[String]()

    Future {
      val exitCode = Process(s"$javaCmd -version")!ProcessLogger(
        s => for (v <-versionFrom(s)) resultPromise.success(v)
      )
      resultPromise.tryFailure(new IllegalArgumentException(s"$javaCmd exited with code $exitCode, no Java version found"))
    }

    resultPromise.future
  }

  def versionFrom(javaVersionLine: String): Option[String] = {
    VersionRegex.findFirstMatchIn(javaVersionLine).map(_.group(1))
  }
}


================================================
FILE: bfg-benchmark/src/main/scala/lib/Repo.scala
================================================
package lib

import com.google.common.io.MoreFiles
import com.google.common.io.RecursiveDeleteOption.ALLOW_INSECURE
import com.madgag.compress.CompressUtil._

import java.nio.file.{Files, Path}
import scala.util.Using

class RepoExtractor(scratchDir: Path) {

  val repoDir = scratchDir.resolve( "repo.git")

  def extractRepoFrom(zipPath: Path) = {
    if (Files.exists(repoDir)) MoreFiles.deleteRecursively(repoDir, ALLOW_INSECURE)

    Files.createDirectories(repoDir)

    println(s"Extracting repo to ${repoDir.toAbsolutePath}")

    Using(Files.newInputStream(zipPath)) {
      stream => unzip(stream, repoDir.toFile)
    }

    repoDir
  }
}


================================================
FILE: bfg-benchmark/src/main/scala/lib/Timing.scala
================================================
package lib

import java.lang.System._
import java.util.concurrent.TimeUnit._

import scala.concurrent.duration.{Duration, FiniteDuration}

object Timing {

  def measureTask[T](description: String)(block: => T): Duration = {
    val start = nanoTime
    val result = block
    val duration = FiniteDuration(nanoTime - start, NANOSECONDS)
    println(s"$description completed in %,d ms.".format(duration.toMillis))
    duration
  }
}


================================================
FILE: bfg-benchmark/src/main/scala/model/BFGJar.scala
================================================
package model

import java.nio.file.Path

object BFGJar {
  def from(path: Path) = BFGJar(path, Map.empty)
}

case class BFGJar(path: Path, mavenDependencyVersions: Map[String, String])


================================================
FILE: bfg-benchmark/src/main/scala/model/InvocableEngine.scala
================================================
package model

import com.google.common.io.CharSource
import com.google.common.io.Files.asCharSource

import java.io.File
import java.nio.charset.StandardCharsets.UTF_8
import java.nio.file.{Files, Path}
import scala.jdk.StreamConverters._
import scala.sys.process.{Process, ProcessBuilder}

trait EngineInvocation

case class BFGInvocation(args: String) extends EngineInvocation

case class GFBInvocation(args: Seq[String]) extends EngineInvocation


trait InvocableEngine[InvocationArgs <: EngineInvocation] {

    def processFor(invocation: InvocationArgs)(repoPath: File): ProcessBuilder
}

case class InvocableBFG(java: Java, bfgJar: BFGJar) extends InvocableEngine[BFGInvocation] {

  def processFor(invocation: BFGInvocation)(repoPath: File) =
    Process(s"${java.javaCmd} -jar ${bfgJar.path} ${invocation.args}", repoPath)

}

object InvocableGitFilterBranch extends InvocableEngine[GFBInvocation] {

  def processFor(invocation: GFBInvocation)(repoPath: File) =
    Process(Seq("git", "filter-branch") ++ invocation.args, repoPath)
}

/*
We want to allow the user to vary:
 - BFGs (jars, javas)
 - Tasks (delete a file, replace text) in [selection of repos]

 Tasks will have a variety of different invocations for different engines
 */

trait EngineType[InvocationType <: EngineInvocation] {
  val configName: String

  def argsFor(config: CharSource): InvocationType

  def argsOptsFor(commandDir: Path): Option[InvocationType] = {
    val paramsPath = commandDir.resolve(s"$configName.txt")
    if (Files.exists(paramsPath)) Some(argsFor(asCharSource(paramsPath.toFile, UTF_8))) else None
  }
}

case object BFG extends EngineType[BFGInvocation] {

  val configName = "bfg"

  def argsFor(config: CharSource) = BFGInvocation(config.read())
}

case object GitFilterBranch extends EngineType[GFBInvocation] {

  val configName = "gfb"

  def argsFor(config: CharSource) = GFBInvocation(config.lines().toScala(Seq))
}


================================================
FILE: bfg-benchmark/src/main/scala/model/InvocableEngineSet.scala
================================================
package model

import java.io.File
import java.nio.file.Path

case class InvocableEngineSet[InvocationArgs <: EngineInvocation](
  engineType: EngineType[InvocationArgs],
  invocableEngines: Seq[InvocableEngine[InvocationArgs]]
) {

  def invocationsFor(commandDir: Path): Seq[(InvocableEngine[InvocationArgs], File => scala.sys.process.ProcessBuilder)] = {
    for {
      args <- engineType.argsOptsFor(commandDir).toSeq
      invocable <- invocableEngines
    } yield (invocable, invocable.processFor(args) _)
  }
}


================================================
FILE: bfg-benchmark/src/main/scala/model/Java.scala
================================================
package model

case class Java(javaCmd: String, version: String)


================================================
FILE: bfg-benchmark/src/test/scala/JavaVersionSpec.scala
================================================
import org.scalatest.OptionValues
import org.scalatest.flatspec.AnyFlatSpec
import org.scalatest.matchers.should.Matchers

object JavaVersionSpec extends AnyFlatSpec with OptionValues with Matchers {
  "version" should "parse an example line" in {
    JavaVersion.versionFrom("""java version "1.7.0_51"""").value shouldBe "1.7.0_51"
  }

  it should "parse openjdk weirdness" in {
    JavaVersion.versionFrom("""openjdk version "1.8.0_40-internal"""").value shouldBe "1.8.0_40-internal"
  }
}


================================================
FILE: bfg-library/build.sbt
================================================
import Dependencies.*

libraryDependencies ++= guava ++ Seq(
  parCollections,
  scalaCollectionPlus,
  textmatching,
  scalaGit,
  jgit,
  slf4jSimple,
  lineSplitting,
  scalaGitTest % Test,
  "org.apache.commons" % "commons-text" % "1.13.0" % Test
)



================================================
FILE: bfg-library/src/main/scala/com/madgag/collection/concurrent/ConcurrentMultiMap.scala
================================================
/*
 * Copyright (c) 2012, 2013 Roberto Tyley
 *
 * This file is part of 'BFG Repo-Cleaner' - a tool for removing large
 * or troublesome blobs from Git repositories.
 *
 * BFG Repo-Cleaner is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * BFG Repo-Cleaner is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see http://www.gnu.org/licenses/ .
 */

package com.madgag.collection.concurrent

import com.madgag.scala.collection.decorators._

class ConcurrentMultiMap[A, B] {

  val m: collection.concurrent.Map[A, ConcurrentSet[B]] = collection.concurrent.TrieMap.empty

  def addBinding(key: A, value: B): this.type = {
    val store = m.getOrElse(key, {
      val freshStore = new ConcurrentSet[B]
      m.putIfAbsent(key, freshStore).getOrElse(freshStore)
    })
    store += value
    this
  }

  def toMap: Map[A, Set[B]] = m.toMap.mapV(_.toSet)
}


================================================
FILE: bfg-library/src/main/scala/com/madgag/collection/concurrent/ConcurrentSet.scala
================================================
/*
 * Copyright (c) 2012, 2013 Roberto Tyley
 *
 * This file is part of 'BFG Repo-Cleaner' - a tool for removing large
 * or troublesome blobs from Git repositories.
 *
 * BFG Repo-Cleaner is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * BFG Repo-Cleaner is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see http://www.gnu.org/licenses/ .
 */

package com.madgag.collection.concurrent

import scala.collection.mutable.{AbstractSet, SetOps}
import scala.collection.{IterableFactory, IterableFactoryDefaults, mutable}

class ConcurrentSet[A]()
  extends AbstractSet[A]
    with SetOps[A, ConcurrentSet, ConcurrentSet[A]]
    with IterableFactoryDefaults[A, ConcurrentSet]
{

  val m: collection.concurrent.Map[A, Boolean] = collection.concurrent.TrieMap.empty

  override def iterableFactory: IterableFactory[ConcurrentSet] = ConcurrentSet

  override def clear(): Unit = m.clear()

  override def addOne(elem: A): ConcurrentSet.this.type = {
    m.put(elem, true)
    this
  }

  override def subtractOne(elem: A): ConcurrentSet.this.type = {
    m.remove(elem)
    this
  }

  override def contains(elem: A): Boolean = m.contains(elem)

  override def iterator: Iterator[A] = m.keysIterator

}

object ConcurrentSet extends IterableFactory[ConcurrentSet] {

  @transient
  private final val EmptySet = new ConcurrentSet()

  def empty[A]: ConcurrentSet[A] = EmptySet.asInstanceOf[ConcurrentSet[A]]

  def from[A](source: collection.IterableOnce[A]): ConcurrentSet[A] =
    source match {
      case hs: ConcurrentSet[A] => hs
      case _ if source.knownSize == 0 => empty[A]
      case _ => (newBuilder[A] ++= source).result()
    }

  /** Create a new Builder which can be reused after calling `result()` without an
   * intermediate call to `clear()` in order to build multiple related results.
   */
  def newBuilder[A]: mutable.Builder[A, ConcurrentSet[A]] = ???
}


================================================
FILE: bfg-library/src/main/scala/com/madgag/git/LFS.scala
================================================
/*
 * Copyright (c) 2015 Roberto Tyley
 *
 * This file is part of 'BFG Repo-Cleaner' - a tool for removing large
 * or troublesome blobs from Git repositories.
 *
 * BFG Repo-Cleaner is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * BFG Repo-Cleaner is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see http://www.gnu.org/licenses/ .
 */

package com.madgag.git

import com.google.common.base.Splitter
import com.madgag.git.bfg.model.FileName
import org.apache.commons.codec.binary.Hex._
import org.eclipse.jgit.lib.ObjectLoader

import java.nio.charset.Charset
import java.nio.charset.StandardCharsets.UTF_8
import java.nio.file.{Files, Path}
import java.security.{DigestOutputStream, MessageDigest}
import scala.jdk.CollectionConverters._
import scala.util.Using

object LFS {

  val ObjectsPath: Seq[String] = Seq("lfs" , "objects")

  val PointerCharset: Charset = UTF_8

  case class Pointer(shaHex: String, blobSize: Long) {

    lazy val text: String = s"""|version https://git-lfs.github.com/spec/v1
                                |oid sha256:$shaHex
                                |size $blobSize
                                |""".stripMargin

    lazy val bytes: Array[Byte] = text.getBytes(PointerCharset)

    lazy val path: Seq[String] = Seq(shaHex.substring(0, 2), shaHex.substring(2, 4), shaHex)
  }

  object Pointer {

    val splitter = Splitter.on('\n').omitEmptyStrings().trimResults().withKeyValueSeparator(' ')

    def parse(bytes: Array[Byte]) = {
      val text = new String(bytes, PointerCharset)
      val valuesByKey= splitter.split(text).asScala
      val size = valuesByKey("size").toLong
      val shaHex = valuesByKey("oid").stripPrefix("sha256:")
      Pointer(shaHex, size)
    }
  }

  val GitAttributesFileName = FileName(".gitattributes")

  def pointerFor(loader: ObjectLoader, tmpFile: Path) = {
    val digest = MessageDigest.getInstance("SHA-256")

    Using(Files.newOutputStream(tmpFile)) { outStream =>
      loader.copyTo(new DigestOutputStream(outStream, digest))
    }

    Pointer(encodeHexString(digest.digest()), loader.getSize)
  }
}


================================================
FILE: bfg-library/src/main/scala/com/madgag/git/bfg/GitUtil.scala
================================================
/*
 * Copyright (c) 2012 Roberto Tyley
 *
 * This file is part of 'BFG Repo-Cleaner' - a tool for removing large
 * or troublesome blobs from Git repositories.
 *
 * BFG Repo-Cleaner is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * BFG Repo-Cleaner is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see http://www.gnu.org/licenses/ .
 */

package com.madgag.git.bfg

import com.google.common.primitives.Ints
import com.madgag.git.bfg.cleaner._
import com.madgag.git.{SizedObject, _}
import org.eclipse.jgit.internal.storage.file.ObjectDirectory
import org.eclipse.jgit.lib.Constants.OBJ_BLOB
import org.eclipse.jgit.lib.ObjectReader._
import org.eclipse.jgit.lib._
import org.eclipse.jgit.revwalk.RevWalk
import org.eclipse.jgit.storage.file.WindowCacheConfig

import scala.jdk.CollectionConverters._
import scala.jdk.StreamConverters._
import scala.language.implicitConversions

trait CleaningMapper[V] extends Cleaner[V] {
  def isDirty(v: V) = apply(v) != v

  def substitution(oldId: V): Option[(V, V)] = {
    val newId = apply(oldId)
    if (newId == oldId) None else Some((oldId, newId))
  }

  def replacement(oldId: V): Option[V] = {
    val newId = apply(oldId)
    if (newId == oldId) None else Some(newId)
  }
}

object GitUtil {
  
  val ProbablyNoNonFileObjectsOverSizeThreshold: Long = 1024 * 1024
  
  def tweakStaticJGitConfig(massiveNonFileObjects: Option[Long]): Unit = {
    val wcConfig: WindowCacheConfig = new WindowCacheConfig()
    wcConfig.setStreamFileThreshold(Ints.saturatedCast(massiveNonFileObjects.getOrElse(ProbablyNoNonFileObjectsOverSizeThreshold)))
    wcConfig.install()
  }

  def hasBeenProcessedByBFGBefore(repo: Repository): Boolean = {
    // This method just checks the tips of all refs - a good-enough indicator for our purposes...
    implicit val revWalk = new RevWalk(repo)
    implicit val objectReader = revWalk.getObjectReader

    repo.getRefDatabase.getRefs().asScala.map(_.getObjectId).filter(_.open.getType == Constants.OBJ_COMMIT)
      .map(_.asRevCommit).exists(_.getFooterLines(FormerCommitFooter.Key).asScala.nonEmpty)
  }

  implicit def cleaner2CleaningMapper[V](f: Cleaner[V]): CleaningMapper[V] = new CleaningMapper[V] {
    def apply(v: V) = f(v)
  }

  def biggestBlobs(implicit objectDB: ObjectDirectory, progressMonitor: ProgressMonitor = NullProgressMonitor.INSTANCE): LazyList[SizedObject] = {
    Timing.measureTask("Scanning packfile for large blobs", ProgressMonitor.UNKNOWN) {
      val reader = objectDB.newReader
      objectDB.packedObjects.map {
            objectId =>
              progressMonitor update 1
              SizedObject(objectId, reader.getObjectSize(objectId, OBJ_ANY))
          }.toSeq.sorted.reverse.to(LazyList).filter { oid =>
        oid.size > ProbablyNoNonFileObjectsOverSizeThreshold || reader.open(oid.objectId).getType == OBJ_BLOB
      }
    }
  }
}


================================================
FILE: bfg-library/src/main/scala/com/madgag/git/bfg/cleaner/BlobCharsetDetector.scala
================================================
/*
 * Copyright (c) 2012 Roberto Tyley
 *
 * This file is part of 'BFG Repo-Cleaner' - a tool for removing large
 * or troublesome blobs from Git repositories.
 *
 * BFG Repo-Cleaner is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * BFG Repo-Cleaner is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see http://www.gnu.org/licenses/ .
 */

package com.madgag.git.bfg.cleaner

import com.google.common.io.ByteStreams
import com.google.common.io.ByteStreams.toByteArray
import com.madgag.git.bfg.model.TreeBlobEntry
import org.eclipse.jgit.diff.RawText
import org.eclipse.jgit.lib.ObjectLoader

import java.nio.ByteBuffer
import java.nio.charset.Charset
import java.nio.charset.CodingErrorAction._
import scala.util.{Try, Using}


trait BlobCharsetDetector {
  // should return None if this is a binary file that can not be converted to text
  def charsetFor(entry: TreeBlobEntry, objectLoader: ObjectLoader): Option[Charset]
}


object QuickBlobCharsetDetector extends BlobCharsetDetector {

  val CharSets: Seq[Charset] =
    Seq(Charset.forName("UTF-8"), Charset.defaultCharset(), Charset.forName("ISO-8859-1")).distinct

  def charsetFor(entry: TreeBlobEntry, objectLoader: ObjectLoader): Option[Charset] = {
    Using(ByteStreams.limit(objectLoader.openStream(), 8000))(toByteArray).toOption.filterNot(RawText.isBinary).flatMap {
      sampleBytes =>
        val b = ByteBuffer.wrap(sampleBytes)
        CharSets.find(cs => Try(decode(b, cs)).isSuccess)
    }
  }

  private def decode(b: ByteBuffer, charset: Charset): Unit = {
    charset.newDecoder.onMalformedInput(REPORT).onUnmappableCharacter(REPORT).decode(b)
  }
}





================================================
FILE: bfg-library/src/main/scala/com/madgag/git/bfg/cleaner/BlobTextModifier.scala
================================================
/*
 * Copyright (c) 2012 Roberto Tyley
 *
 * This file is part of 'BFG Repo-Cleaner' - a tool for removing large
 * or troublesome blobs from Git repositories.
 *
 * BFG Repo-Cleaner is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * BFG Repo-Cleaner is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see http://www.gnu.org/licenses/ .
 */

package com.madgag.git.bfg.cleaner

import com.madgag.git.ThreadLocalObjectDatabaseResources
import com.madgag.git.bfg.model.TreeBlobEntry
import com.madgag.linesplitting.LineBreakPreservingIterator
import org.eclipse.jgit.lib.Constants.OBJ_BLOB
import org.eclipse.jgit.lib.ObjectLoader

import java.io.{ByteArrayOutputStream, InputStreamReader}
import java.nio.charset.Charset


object BlobTextModifier {

  val DefaultSizeThreshold: Long = 1024 * 1024

}

trait BlobTextModifier extends TreeBlobModifier {

  val threadLocalObjectDBResources: ThreadLocalObjectDatabaseResources

  def lineCleanerFor(entry: TreeBlobEntry): Option[String => String]

  val charsetDetector: BlobCharsetDetector = QuickBlobCharsetDetector

  val sizeThreshold = BlobTextModifier.DefaultSizeThreshold

  override def fix(entry: TreeBlobEntry) = {

    def filterTextIn(e: TreeBlobEntry, lineCleaner: String => String): TreeBlobEntry = {
      def isDirty(line: String) = lineCleaner(line) != line

      val loader = threadLocalObjectDBResources.reader().open(e.objectId)
      val opt = for {
        charset <- charsetDetector.charsetFor(e, loader)
        if loader.getSize < sizeThreshold && linesFor(loader, charset).exists(isDirty)
      } yield {
        val b = new ByteArrayOutputStream(loader.getSize.toInt)
        linesFor(loader, charset).map(lineCleaner).foreach(line => b.write(line.getBytes(charset)))
        val oid = threadLocalObjectDBResources.inserter().insert(OBJ_BLOB, b.toByteArray)
        e.copy(objectId = oid)
      }

      opt.getOrElse(e)
    }

    lineCleanerFor(entry) match {
      case Some(lineCleaner) => filterTextIn(entry, lineCleaner).withoutName
      case None => entry.withoutName
    }
  }

  private def linesFor(loader: ObjectLoader, charset: Charset): Iterator[String] = {
    new LineBreakPreservingIterator(new InputStreamReader(loader.openStream(), charset))
  }
}


================================================
FILE: bfg-library/src/main/scala/com/madgag/git/bfg/cleaner/LfsBlobConverter.scala
================================================
/*
 * Copyright (c) 2015 Roberto Tyley
 *
 * This file is part of 'BFG Repo-Cleaner' - a tool for removing large
 * or troublesome blobs from Git repositories.
 *
 * BFG Repo-Cleaner is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * BFG Repo-Cleaner is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see http://www.gnu.org/licenses/ .
 */

package com.madgag.git.bfg.cleaner

import com.google.common.io.ByteSource
import com.google.common.io.Files.createParentDirs
import com.madgag.git.LFS._
import com.madgag.git._
import com.madgag.git.bfg.model._
import com.madgag.git.bfg.{MemoFunc, MemoUtil}
import com.madgag.textmatching.{Glob, TextMatcher}
import org.eclipse.jgit.internal.storage.file.FileRepository
import org.eclipse.jgit.lib.{ObjectId, ObjectReader}

import java.nio.charset.{Charset, StandardCharsets}
import java.nio.file.{Files, Path}
import scala.jdk.StreamConverters._
import scala.util.{Try, Using}

class LfsBlobConverter(
  lfsGlobExpression: String,
  repo: FileRepository
) extends TreeBlobModifier {

  val lfsObjectsDir: Path = repo.getDirectory.toPath.resolve(LFS.ObjectsPath)

  val threadLocalObjectDBResources = repo.getObjectDatabase.threadLocalResources

  val lfsGlob = TextMatcher(Glob, lfsGlobExpression)

  val lfsSuitableFiles: (FileName => Boolean) = f => lfsGlob(f.string)

  val gitAttributesLine = s"$lfsGlobExpression filter=lfs diff=lfs merge=lfs -text"

  implicit val UTF_8: Charset = StandardCharsets.UTF_8

  val lfsPointerMemo = MemoUtil.concurrentCleanerMemo[ObjectId]()
  
  override def apply(dirtyBlobs: TreeBlobs) = {
    val cleanedBlobs = super.apply(dirtyBlobs)
    if (cleanedBlobs == dirtyBlobs) cleanedBlobs else ensureGitAttributesSetFor(cleanedBlobs)
  }

  def ensureGitAttributesSetFor(cleanedBlobs: TreeBlobs): TreeBlobs = {
    implicit lazy val inserter = threadLocalObjectDBResources.inserter()

    val newGitAttributesId = cleanedBlobs.entryMap.get(GitAttributesFileName).fold {
      storeBlob(gitAttributesLine)
    } {
      case (_, oldGitAttributesId) =>
        val objectLoader = threadLocalObjectDBResources.reader().open(oldGitAttributesId)
        Using(ByteSource.wrap(objectLoader.getCachedBytes).asCharSource(UTF_8).lines()) { oldAttributesStream =>
          val oldAttributes = oldAttributesStream.toScala(Seq)
          if (oldAttributes.contains(gitAttributesLine)) oldGitAttributesId else {
            storeBlob((oldAttributes :+ gitAttributesLine).mkString("\n"))
          }
        }.get
    }
    cleanedBlobs.copy(entryMap = cleanedBlobs.entryMap + (GitAttributesFileName -> (RegularFile, newGitAttributesId)))
  }

  override def fix(entry: TreeBlobEntry) = {
    val cleanId = if (lfsSuitableFiles(entry.filename)) lfsPointerBlobIdForRealBlob(entry.objectId) else entry.objectId
    (entry.mode, cleanId)
  }

  val lfsPointerBlobIdForRealBlob: MemoFunc[ObjectId, ObjectId] = lfsPointerMemo { blobId: ObjectId =>
    implicit val reader = threadLocalObjectDBResources.reader()
    implicit lazy val inserter = threadLocalObjectDBResources.inserter()

    (for {
      blobSize <- blobId.sizeTry if blobSize > 512
      pointer <- tryStoringLfsFileFor(blobId)
    } yield storeBlob(pointer.bytes)).getOrElse(blobId)
  }

  def tryStoringLfsFileFor(blobId: ObjectId)(implicit r: ObjectReader): Try[Pointer] = {
    val loader = blobId.open
    
    val tmpFile: Path = Files.createTempFile(s"bfg.git-lfs.conv-${blobId.name}","dat")
    
    val pointer = pointerFor(loader, tmpFile)

    val lfsPath = lfsObjectsDir.resolve(pointer.path)

    createParentDirs(lfsPath.toFile)

    val ensureLfsFile = Try(if (!Files.exists(lfsPath)) Files.move(tmpFile, lfsPath)).recover {
      case _ if Files.exists(lfsPath) && Files.size(lfsPath) == loader.getSize =>
    }

    Try(Files.deleteIfExists(tmpFile))

    ensureLfsFile.map(_ => pointer)
  }

}


================================================
FILE: bfg-library/src/main/scala/com/madgag/git/bfg/cleaner/ObjectIdCleaner.scala
================================================
/*
 * Copyright (c) 2012, 2013 Roberto Tyley
 *
 * This file is part of 'BFG Repo-Cleaner' - a tool for removing large
 * or troublesome blobs from Git repositories.
 *
 * BFG Repo-Cleaner is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * BFG Repo-Cleaner is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see http://www.gnu.org/licenses/ .
 */

package com.madgag.git.bfg.cleaner

import com.madgag.collection.concurrent.ConcurrentMultiMap
import com.madgag.git._
import com.madgag.git.bfg.GitUtil._
import com.madgag.git.bfg.cleaner.protection.{ProtectedObjectCensus, ProtectedObjectDirtReport}
import com.madgag.git.bfg.model.{Tree, TreeSubtrees, _}
import com.madgag.git.bfg.{CleaningMapper, Memo, MemoFunc, MemoUtil}
import org.eclipse.jgit.lib.Constants._
import org.eclipse.jgit.lib._
import org.eclipse.jgit.revwalk.{RevCommit, RevTag, RevWalk}

object ObjectIdCleaner {

  case class Config(protectedObjectCensus: ProtectedObjectCensus,
                    objectIdSubstitutor: ObjectIdSubstitutor = ObjectIdSubstitutor.OldIdsPublic,
                    commitNodeCleaners: Seq[CommitNodeCleaner] = Seq.empty,
                    treeEntryListCleaners: Seq[Cleaner[Seq[Tree.Entry]]] = Seq.empty,
                    treeBlobsCleaners: Seq[Cleaner[TreeBlobs]] = Seq.empty,
                    treeSubtreesCleaners: Seq[Cleaner[TreeSubtrees]] = Seq.empty,
                    // messageCleaners? - covers both Tag and Commits
                    objectChecker: Option[ObjectChecker] = None) {

    lazy val commitNodeCleaner = CommitNodeCleaner.chain(commitNodeCleaners)

    lazy val treeEntryListCleaner = Function.chain(treeEntryListCleaners)

    lazy val treeBlobsCleaner = Function.chain(treeBlobsCleaners)

    lazy val treeSubtreesCleaner:Cleaner[TreeSubtrees] = Function.chain(treeSubtreesCleaners)
  }

}

/*
 * Knows how to clean an object, and what objects are protected...
 */
class ObjectIdCleaner(config: ObjectIdCleaner.Config, objectDB: ObjectDatabase, implicit val revWalk: RevWalk) extends CleaningMapper[ObjectId] {

  import config._

  val threadLocalResources = objectDB.threadLocalResources

  val changesByFilename = new ConcurrentMultiMap[FileName, (ObjectId, ObjectId)]
  val deletionsByFilename = new ConcurrentMultiMap[FileName, ObjectId]

  // want to enforce that once any value is returned, it is 'good' and therefore an identity-mapped key as well
  val memo: Memo[ObjectId, ObjectId] = MemoUtil.concurrentCleanerMemo(protectedObjectCensus.fixedObjectIds)

  val commitMemo: Memo[ObjectId, ObjectId] = MemoUtil.concurrentCleanerMemo()
  val tagMemo: Memo[ObjectId, ObjectId] = MemoUtil.concurrentCleanerMemo()

  val treeMemo: Memo[ObjectId, ObjectId] = MemoUtil.concurrentCleanerMemo(protectedObjectCensus.treeIds.toSet[ObjectId])

  def apply(objectId: ObjectId): ObjectId = memoClean(objectId)

  val memoClean = memo {
    uncachedClean
  }

  def cleanedObjectMap(): Map[ObjectId, ObjectId] =
    Seq(memoClean, cleanCommit, cleanTag, cleanTree).map(_.asMap()).reduce(_ ++ _)

  def uncachedClean: (ObjectId) => ObjectId = {
    objectId =>
      threadLocalResources.reader().open(objectId).getType match {
        case OBJ_COMMIT => cleanCommit(objectId)
        case OBJ_TREE => cleanTree(objectId)
        case OBJ_TAG => cleanTag(objectId)
        case _ => objectId // we don't currently clean isolated blobs... only clean within a tree context
      }
  }

  def getCommit(commitId: AnyObjectId): RevCommit = revWalk synchronized (commitId asRevCommit)

  def getTag(tagId: AnyObjectId): RevTag = revWalk synchronized (tagId asRevTag)

  val cleanCommit: MemoFunc[ObjectId, ObjectId] = commitMemo { commitId =>
    val originalRevCommit = getCommit(commitId)
    val originalCommit = Commit(originalRevCommit)

    val cleanedArcs = originalCommit.arcs cleanWith this
    val kit = new CommitNodeCleaner.Kit(threadLocalResources, originalRevCommit, originalCommit, cleanedArcs, apply)
    val updatedCommitNode = commitNodeCleaner.fixer(kit)(originalCommit.node)
    val updatedCommit = Commit(updatedCommitNode, cleanedArcs)

    if (updatedCommit != originalCommit) {
      val commitBytes = updatedCommit.toBytes
      objectChecker.foreach(_.checkCommit(commitBytes))
      threadLocalResources.inserter().insert(OBJ_COMMIT, commitBytes)
    } else {
      originalRevCommit
    }
  }

  val cleanBlob: Cleaner[ObjectId] = identity // Currently a NO-OP, we only clean at treeblob level

  val cleanTree: MemoFunc[ObjectId, ObjectId] = treeMemo { originalObjectId =>
    val entries = Tree.entriesFor(originalObjectId)(threadLocalResources.reader())
    val cleanedTreeEntries = treeEntryListCleaner(entries)

    val tree = Tree(cleanedTreeEntries)

    val originalBlobs = tree.blobs
    val fixedTreeBlobs = treeBlobsCleaner(originalBlobs)
    val cleanedSubtrees = TreeSubtrees(treeSubtreesCleaner(tree.subtrees).entryMap.map {
      case (name, treeId) => (name, cleanTree(treeId))
    }).withoutEmptyTrees

    val treeBlobsChanged = fixedTreeBlobs != originalBlobs
    if (entries == cleanedTreeEntries && !treeBlobsChanged && cleanedSubtrees == tree.subtrees) originalObjectId else {
      if (treeBlobsChanged) recordChange(originalBlobs, fixedTreeBlobs)

      val updatedTree = tree copyWith(cleanedSubtrees, fixedTreeBlobs)

      val treeFormatter = updatedTree.formatter
      objectChecker.foreach(_.checkTree(treeFormatter.toByteArray))
      treeFormatter.insertTo(threadLocalResources.inserter())
    }
  }

  def recordChange(originalBlobs: TreeBlobs, fixedTreeBlobs: TreeBlobs): Unit = {
    val changedFiles: Set[TreeBlobEntry] = originalBlobs.entries.toSet -- fixedTreeBlobs.entries.toSet
    for (TreeBlobEntry(filename, _, oldId) <- changedFiles) {
      fixedTreeBlobs.objectId(filename) match {
        case Some(newId) => changesByFilename.addBinding(filename, (oldId, newId))
        case None => deletionsByFilename.addBinding(filename, oldId)
      }
    }
  }

  case class TreeBlobChange(oldId: ObjectId, newIdOpt: Option[ObjectId], filename: FileName)

  val cleanTag: MemoFunc[ObjectId, ObjectId] = tagMemo { id =>
    val originalTag = getTag(id)

    replacement(originalTag.getObject).map {
      cleanedObj =>
        val tb = new TagBuilder
        tb.setTag(originalTag.getTagName)
        tb.setObjectId(cleanedObj, originalTag.getObject.getType)
        tb.setTagger(originalTag.getTaggerIdent)
        tb.setMessage(objectIdSubstitutor.replaceOldIds(originalTag.getFullMessage, threadLocalResources.reader(), apply))
        val cleanedTag: ObjectId = threadLocalResources.inserter().insert(tb)
        objectChecker.foreach(_.checkTag(tb.build()))
        cleanedTag
    }.getOrElse(originalTag)
  }

  lazy val protectedDirt: Seq[ProtectedObjectDirtReport] = {
    protectedObjectCensus.protectorRevsByObject.map {
      case (protectedRevObj, refNames) =>
        val originalContentObject = treeOrBlobPointedToBy(protectedRevObj).merge
        val replacementTreeOrBlob = uncachedClean.replacement(originalContentObject)
        ProtectedObjectDirtReport(protectedRevObj, originalContentObject, replacementTreeOrBlob)
    }.toList
  }

  def stats() = Map("apply"->memoClean.stats(), "tree" -> cleanTree.stats(), "commit" -> cleanCommit.stats(), "tag" -> cleanTag.stats())

}


================================================
FILE: bfg-library/src/main/scala/com/madgag/git/bfg/cleaner/ObjectIdSubstitutor.scala
================================================
/*
 * Copyright (c) 2012, 2013 Roberto Tyley
 *
 * This file is part of 'BFG Repo-Cleaner' - a tool for removing large
 * or troublesome blobs from Git repositories.
 *
 * BFG Repo-Cleaner is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * BFG Repo-Cleaner is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see http://www.gnu.org/licenses/ .
 */

package com.madgag.git.bfg.cleaner

import com.madgag.git._
import com.madgag.git.bfg.GitUtil._
import com.madgag.git.bfg.cleaner.ObjectIdSubstitutor._
import org.eclipse.jgit.lib.{AbbreviatedObjectId, ObjectId, ObjectReader}

class CommitMessageObjectIdsUpdater(objectIdSubstitutor: ObjectIdSubstitutor) extends CommitNodeCleaner {

  override def fixer(kit: CommitNodeCleaner.Kit) = commitNode => commitNode.copy(message = objectIdSubstitutor.replaceOldIds(commitNode.message, kit.threadLocalResources.reader(), kit.mapper))

}

object ObjectIdSubstitutor {

  object OldIdsPrivate extends ObjectIdSubstitutor {
    def format(oldIdText: String, newIdText: String) = newIdText
  }

  object OldIdsPublic extends ObjectIdSubstitutor {
    def format(oldIdText: String, newIdText: String) = s"$newIdText [formerly $oldIdText]"
  }

  val hexRegex = """\b\p{XDigit}{10,40}\b""".r // choose minimum size based on size of project??

}

trait ObjectIdSubstitutor {

  def format(oldIdText: String, newIdText: String): String

  // slow!
  def replaceOldIds(message: String, reader: ObjectReader, mapper: Cleaner[ObjectId]): String = {
    val substitutionOpts = for {
      m: String <- hexRegex.findAllIn(message).toSet
      objectId <- reader.resolveExistingUniqueId(AbbreviatedObjectId.fromString(m)).toOption
    } yield mapper.replacement(objectId).map(newId => m -> format(m, reader.abbreviate(newId, m.length).name))

    val substitutions = substitutionOpts.flatten.toMap
    if (substitutions.isEmpty) message else hexRegex.replaceSomeIn(message, m => substitutions.get(m.matched))
  }
}

================================================
FILE: bfg-library/src/main/scala/com/madgag/git/bfg/cleaner/RepoRewriter.scala
================================================
/*
 * Copyright (c) 2012 Roberto Tyley
 *
 * This file is part of 'BFG Repo-Cleaner' - a tool for removing large
 * or troublesome blobs from Git repositories.
 *
 * BFG Repo-Cleaner is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * BFG Repo-Cleaner is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see http://www.gnu.org/licenses/ .
 */

package com.madgag.git.bfg.cleaner

import com.madgag.git._
import com.madgag.git.bfg.Timing
import org.eclipse.jgit.lib.{ObjectId, ProgressMonitor, RefDatabase}
import org.eclipse.jgit.revwalk.RevSort._
import org.eclipse.jgit.revwalk.{RevCommit, RevWalk}
import org.eclipse.jgit.transport.ReceiveCommand

import scala.jdk.CollectionConverters._
import scala.collection.parallel.CollectionConverters._
import scala.concurrent.ExecutionContext.Implicits.global
import scala.concurrent.Future

/*
Encountering a blob ->
BIG-BLOB-DELETION : Either 'good' or 'delete'   - or possibly replace, with a different filename (means tree-level)
PASSWORD-REMOVAL : Either 'good' or 'replace'

Encountering a tree ->
BIG-BLOB-DELETION : Either 'good' or 'replace'   - possibly adding with a different placeholder blob entry
PASSWORD-REMOVAL : Either 'good' or 'replace' - replacing one blob entry with another

So if we encounter a tree, we are unlikely to want to remove that tree entirely...
SHOULD WE JUST DISALLOW THAT?
Obviously, a Commit HAS to have a tree, so it's dangerous to allow a None response to tree transformation

An objectId must be either GOOD or BAD, and we must never translate *either* kind of id into a BAD

User-customisation interface: TreeBlobs => TreeBlobs

User gets no say in adding, renaming, removing directories

TWO MAIN USE CASES FOR HISTORY-CHANGING ARE:
1: GETTING RID OF BIG BLOBS
2: REMOVING PASSWORDS IN HISTORICAL FILES

possible other use-case: fixing committer names - and possibly removing passwords from commits? (could possibly just be done with rebase)

Why else would you want to rewrite HISTORY? Many other changes (ie putting a directory one down) need only be applied
in a new commit, we don't care about history.

When updating a Tree, the User has no right to muck with sub-trees. They can only alter the blob contents.
 */

object RepoRewriter {

  def rewrite(repo: org.eclipse.jgit.lib.Repository, objectIdCleanerConfig: ObjectIdCleaner.Config): Map[ObjectId, ObjectId] = {
    implicit val refDatabase: RefDatabase = repo.getRefDatabase

    assert(refDatabase.hasRefs, "Can't find any refs in repo at " + repo.getDirectory.getAbsolutePath)

    val reporter: Reporter = new CLIReporter(repo)
    implicit val progressMonitor: ProgressMonitor = reporter.progressMonitor

    val allRefs = refDatabase.getRefs().asScala

    def createRevWalk: RevWalk = {

      val revWalk = new RevWalk(repo)

      revWalk.sort(TOPO) // crucial to ensure we visit parents BEFORE children, otherwise blow stack
      revWalk.sort(REVERSE, true) // we want to start with the earliest commits and work our way up...

      val startCommits = allRefs.map(_.targetObjectId.asRevObject(revWalk)).collect { case c: RevCommit => c }

      revWalk.markStart(startCommits.asJavaCollection)
      revWalk
    }

    implicit val revWalk = createRevWalk
    implicit val reader = revWalk.getObjectReader

    reporter.reportRefsForScan(allRefs)

    reporter.reportObjectProtection(objectIdCleanerConfig)(repo.getObjectDatabase, revWalk)

    val objectIdCleaner = new ObjectIdCleaner(objectIdCleanerConfig, repo.getObjectDatabase, revWalk)

    val commits = revWalk.asScala.toSeq

    def clean(commits: Seq[RevCommit]): Unit = {
      reporter.reportCleaningStart(commits)

      Timing.measureTask("Cleaning commits", commits.size) {
        Future {
          commits.par.foreach {
            commit => objectIdCleaner(commit.getTree)
          }
        }

        commits.foreach {
          commit =>
            objectIdCleaner(commit)
            progressMonitor update 1
        }
      }
    }

    def updateRefsWithCleanedIds(): Unit = {
      val refUpdateCommands = for (ref <- repo.nonSymbolicRefs;
                                   (oldId, newId) <- objectIdCleaner.substitution(ref.getObjectId)
      ) yield new ReceiveCommand(oldId, newId, ref.getName)

      if (refUpdateCommands.isEmpty) {
        println("\nBFG aborting: No refs to update - no dirty commits found??\n")
      } else {
        reporter.reportRefUpdateStart(refUpdateCommands)

        Timing.measureTask("...Ref update", refUpdateCommands.size) {
          // Hack a fix for issue #23 : Short-cut the calculation that determines an update is NON-FF
          val quickMergeCalcRevWalk = new RevWalk(revWalk.getObjectReader) {
            override def isMergedInto(base: RevCommit, tip: RevCommit) =
              if (tip == objectIdCleaner(base)) false else super.isMergedInto(base, tip)
          }

          refDatabase.newBatchUpdate.setAllowNonFastForwards(true).addCommand(refUpdateCommands.asJavaCollection)
            .execute(quickMergeCalcRevWalk, progressMonitor)
        }

        reporter.reportResults(commits, objectIdCleaner)
      }
    }


    clean(commits)

    updateRefsWithCleanedIds()

    objectIdCleaner.stats()

    objectIdCleaner.cleanedObjectMap()
  }

}


================================================
FILE: bfg-library/src/main/scala/com/madgag/git/bfg/cleaner/Reporter.scala
================================================
package com.madgag.git.bfg.cleaner

import com.google.common.io.Files.asCharSink
import com.madgag.collection.concurrent.ConcurrentMultiMap
import com.madgag.git._
import com.madgag.git.bfg.cleaner.Reporter.dump
import com.madgag.git.bfg.cleaner.protection.{ProtectedObjectCensus, ProtectedObjectDirtReport}
import com.madgag.git.bfg.model.FileName
import com.madgag.text.Text._
import com.madgag.text.{ByteSize, Tables, Text}
import org.eclipse.jgit.diff.DiffEntry.ChangeType._
import org.eclipse.jgit.diff._
import org.eclipse.jgit.lib.FileMode._
import org.eclipse.jgit.lib._
import org.eclipse.jgit.revwalk.{RevCommit, RevWalk}
import org.eclipse.jgit.transport.ReceiveCommand

import java.nio.charset.StandardCharsets.UTF_8
import java.nio.file.Files.createDirectories
import java.nio.file.Path
import java.time.ZonedDateTime
import java.time.format.DateTimeFormatter
import scala.collection.immutable.SortedMap
import scala.jdk.CollectionConverters._


object Reporter {
  def dump(path: Path, iter: Iterable[String]): Unit = {
    val sink = asCharSink(path.toFile, UTF_8)

    sink.writeLines(iter.asJava, "\n")
  }
}

trait Reporter {

  val progressMonitor: ProgressMonitor

  def reportRefsForScan(allRefs: Iterable[Ref])(implicit objReader: ObjectReader): Unit

  def reportRefUpdateStart(refUpdateCommands: Iterable[ReceiveCommand]): Unit

  def reportObjectProtection(objectIdCleanerConfig: ObjectIdCleaner.Config)(implicit objectDB: ObjectDatabase, revWalk: RevWalk): Unit

  def reportCleaningStart(commits: Seq[RevCommit]): Unit

  def reportResults(commits: Seq[RevCommit], objectIdCleaner: ObjectIdCleaner): Unit
}

class CLIReporter(repo: Repository) extends Reporter {

  lazy val reportsDir: Path = {
    val now = ZonedDateTime.now()

    val topDirPath = repo.topDirectory.toPath.toAbsolutePath

    val reportsDir = topDirPath.resolveSibling(s"${topDirPath.getFileName}.bfg-report")

    val dateFormatter = DateTimeFormatter.ofPattern("uuuu-MM-dd")
    val timeFormatter = DateTimeFormatter.ofPattern("HH-mm-ss")

    val dir = reportsDir.resolve(now.format(dateFormatter)).resolve(now.format(timeFormatter))

    createDirectories(dir)
    dir
  }

  lazy val progressMonitor = new TextProgressMonitor

  def reportRefUpdateStart(refUpdateCommands: Iterable[ReceiveCommand]): Unit = {
    println(title("Updating " + plural(refUpdateCommands, "Ref")))

    val summaryTableCells = refUpdateCommands.map(update => (update.getRefName, update.getOldId.shortName, update.getNewId.shortName))

    Tables.formatTable(("Ref", "Before", "After"), summaryTableCells.toSeq).map("\t" + _).foreach(println)

    println()
  }

  def reportRefsForScan(allRefs: Iterable[Ref])(implicit objReader: ObjectReader): Unit = {
    val refsByObjType = allRefs.groupBy {
      ref => objReader.open(ref.getObjectId).getType
    } withDefault Seq.empty

    refsByObjType.foreach {
      case (typ, refs) => println("Found " + refs.size + " " + Constants.typeString(typ) + "-pointing refs : " + abbreviate(refs.map(_.getName).toSeq, "...", 4).mkString(", "))
    }
  }


  // abort due to Dirty Tips on Private run - user needs to manually clean
  // warn due to Dirty Tips on Public run - it's not so serious if users publicise dirty tips.
  // if no protection
  def reportObjectProtection(objectIdCleanerConfig: ObjectIdCleaner.Config)(implicit objectDB: ObjectDatabase, revWalk: RevWalk): Unit = {
    println(title("Protected commits"))

    if (objectIdCleanerConfig.protectedObjectCensus.isEmpty) {
      println("You're not protecting any commits, which means the BFG will modify the contents of even *current* commits.\n\n" +
        "This isn't recommended - ideally, if your current commits are dirty, you should fix up your working copy and " +
        "commit that, check that your build still works, and only then run the BFG to clean up your history.")
    } else {
      println("These are your protected commits, and so their contents will NOT be altered:\n")

      val unprotectedConfig = objectIdCleanerConfig.copy(protectedObjectCensus = ProtectedObjectCensus.None)

      reportProtectedCommitsAndTheirDirt(objectIdCleanerConfig)
    }
  }

  case class DiffSideDetails(id: ObjectId, path: String, mode: FileMode, size: Option[Long])

  def reportProtectedCommitsAndTheirDirt(objectIdCleanerConfig: ObjectIdCleaner.Config)(implicit objectDB: ObjectDatabase, revWalk: RevWalk): Unit = {
    implicit val reader = revWalk.getObjectReader

    def diffDetails(d: DiffEntry) = {
      val side = DiffEntry.Side.OLD
      val id: ObjectId = d.getId(side).toObjectId
      DiffSideDetails(id, d.getPath(side), d.getMode(side), id.sizeOpt)
    }

    def fileInfo(d: DiffSideDetails) = {
      val extraInfo = (d.mode match {
        case GITLINK => Some("submodule")
        case _ => d.size.map(ByteSize.format(_))
      }).map(e => s"($e)")

      (d.path +: extraInfo.toSeq).mkString(" ")
    }

    val protectedDirtDir = reportsDir.resolve("protected-dirt")
    createDirectories(protectedDirtDir)

    val reports = ProtectedObjectDirtReport.reportsFor(objectIdCleanerConfig, objectDB)

    reports.foreach {
      report =>
        val protectorRevs = objectIdCleanerConfig.protectedObjectCensus.protectorRevsByObject(report.revObject)
        val objectTitle = s" * ${report.revObject.typeString} ${report.revObject.shortName} (protected by '${protectorRevs.mkString("', '")}')"

        report.dirt match {
          case None => println(objectTitle)
          case Some(diffEntries) =>
            if (diffEntries.isEmpty) {
              println(objectTitle + " - dirty")
            } else {
              println(objectTitle + " - contains " + plural(diffEntries, "dirty file") + " : ")
              abbreviate(diffEntries.view.map(diffDetails).map(fileInfo), "...").foreach {
                dirtyFile => println("\t- " + dirtyFile)
              }

              val protectorRefsFileNameSafe: String = protectorRevs.mkString("_").replace(
                protectedDirtDir.getFileSystem.getSeparator,
                "-"
              )
              val diffFile = protectedDirtDir.resolve(s"${report.revObject.shortName}-$protectorRefsFileNameSafe.csv")

              dump(diffFile, diffEntries.map {
                diffEntry =>
                  val de = diffDetails(diffEntry)

                  val modifiedLines = if (diffEntry.getChangeType == MODIFY) diffEntry.editList.map(changedLinesFor) else None

                  val elems = Seq(de.id.name, diffEntry.getChangeType.name, de.mode.name, de.path, de.size.getOrElse(""), modifiedLines.getOrElse(""))

                  elems.mkString(",")
              })
              }
            }
        }

    val dirtyReports = reports.filter(_.objectProtectsDirt)
    if (dirtyReports.nonEmpty) {

      println(s"""
      |WARNING: The dirty content above may be removed from other commits, but as
      |the *protected* commits still use it, it will STILL exist in your repository.
      |
      |Details of protected dirty content have been recorded here :
      |
      |${protectedDirtDir.toAbsolutePath.toString + protectedDirtDir.getFileSystem.getSeparator}
      |
      |If you *really* want this content gone, make a manual commit that removes it,
      |and then run the BFG on a fresh copy of your repo.
       """.stripMargin)
      // TODO would like to abort here if we are cleaning 'private' data.
    }
  }

  def changedLinesFor(edits: EditList): String = {
    edits.asScala.map {
      edit => Seq(edit.getBeginA + 1, edit.getEndA).distinct.mkString("-")
    }.mkString(";")
  }

  def reportCleaningStart(commits: Seq[RevCommit]): Unit = {
    println(title("Cleaning"))
    println("Found " + commits.size + " commits")
  }

  def reportResults(commits: Seq[RevCommit], objectIdCleaner: ObjectIdCleaner): Unit = {
    def reportTreeDirtHistory(): Unit = {

      val dirtHistoryElements = math.max(20, math.min(60, commits.size))
      def cut[A](xs: Seq[A], n: Int) = {
        val avgSize = xs.size.toFloat / n
        def startOf(unit: Int): Int = math.round(unit * avgSize)
        (0 until n).view.map(u => xs.slice(startOf(u), startOf(u + 1)))
      }
      val treeDirtHistory = cut(commits, dirtHistoryElements).map {
        case commits if commits.isEmpty => ' '
        case commits if (commits.exists(c => objectIdCleaner.isDirty(c.getTree))) => 'D'
        case commits if (commits.exists(objectIdCleaner.isDirty)) => 'm'
        case _ => '.'
      }.mkString
      def leftRight(markers: Seq[String]) = markers.mkString(" " * (treeDirtHistory.length - markers.map(_.size).sum))
      println(title("Commit Tree-Dirt History"))
      println("\t" + leftRight(Seq("Earliest", "Latest")))
      println("\t" + leftRight(Seq("|", "|")))
      println("\t" + treeDirtHistory)
      println("\n\tD = dirty commits (file tree fixed)")
      println("\tm = modified commits (commit message or parents changed)")
      println("\t. = clean commits (no changes to file tree)\n")

      val firstModifiedCommit = commits.find(objectIdCleaner.isDirty).map(_ -> "First modified commit")
      val lastDirtyCommit = commits.reverse.find(c => objectIdCleaner.isDirty(c.getTree)).map(_ -> "Last dirty commit")
      val items = for {
        (commit, desc) <- firstModifiedCommit ++ lastDirtyCommit
        (before, after) <- objectIdCleaner.substitution(commit)
      } yield (desc, before.shortName, after.shortName)
      Tables.formatTable(("", "Before", "After"), items.toSeq).map("\t" + _).foreach(println)
    }

    reportTreeDirtHistory()

    lazy val mapFile: Path = reportsDir.resolve("object-id-map.old-new.txt")
    lazy val cacheStatsFile: Path = reportsDir.resolve("cache-stats.txt")

    val changedIds = objectIdCleaner.cleanedObjectMap()

    def reportFiles[FI](
        fileData: ConcurrentMultiMap[FileName, FI],
        actionType: String,
        tableTitles: Product
      )(f: ((FileName,Set[FI])) => Product)(fi: FI => Seq[String]): Unit = {
      implicit val fileNameOrdering = Ordering[String].on[FileName](_.string)

      val dataByFilename = SortedMap[FileName, Set[FI]](fileData.toMap.toSeq: _*)
      if (dataByFilename.nonEmpty) {
        println(title(s"$actionType files"))
        Tables.formatTable(tableTitles, dataByFilename.map(f).toSeq).map("\t" + _).foreach(println)

        val actionFile = reportsDir.resolve(s"${actionType.toLowerCase}-files.txt")

        dump(actionFile, dataByFilename.flatMap {
          case (filename, changes) => changes.map(fi.andThen(fid => (fid :+ filename).mkString(" ")))
        })
      }
    }

    reportFiles(objectIdCleaner.changesByFilename, "Changed", ("Filename", "Before & After")) {
      case (filename, changes) => (filename, Text.abbreviate(changes.map {case (oldId, newId) => oldId.shortName+" ⇒ "+newId.shortName}, "...").mkString(", "))
    } { case (oldId, newId) => Seq(oldId.name, newId.name) }

    implicit val reader = objectIdCleaner.threadLocalResources.reader()

    reportFiles(objectIdCleaner.deletionsByFilename, "Deleted", ("Filename", "Git id")) {
      case (filename, oldIds) => (filename, Text.abbreviate(oldIds.map(oldId => oldId.shortName + oldId.sizeOpt.map(size => s" (${ByteSize.format(size)})").mkString), "...").mkString(", "))
    } { oldId => Seq(oldId.name, oldId.sizeOpt.mkString) }

    println(s"\n\nIn total, ${changedIds.size} object ids were changed. Full details are logged here:\n\n\t$reportsDir")

    dump(mapFile,SortedMap[AnyObjectId, ObjectId](changedIds.toSeq: _*).view.map { case (o,n) => s"${o.name} ${n.name}"})

    dump(cacheStatsFile,objectIdCleaner.stats().map(_.toString()))

    println("\nBFG run is complete! When ready, run: git reflog expire --expire=now --all && git gc --prune=now --aggressive")

  }

  def title(text: String) = s"\n$text\n" + ("-" * text.size) + "\n"
}

================================================
FILE: bfg-library/src/main/scala/com/madgag/git/bfg/cleaner/TreeBlobModifier.scala
================================================
/*
 * Copyright (c) 2012 Roberto Tyley
 *
 * This file is part of 'BFG Repo-Cleaner' - a tool for removing large
 * or troublesome blobs from Git repositories.
 *
 * BFG Repo-Cleaner is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * BFG Repo-Cleaner is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see http://www.gnu.org/licenses/ .
 */

package com.madgag.git.bfg.cleaner

import com.madgag.git.bfg.MemoUtil
import com.madgag.git.bfg.model.{TreeBlobEntry, _}
import org.eclipse.jgit.lib.ObjectId

trait TreeBlobModifier extends Cleaner[TreeBlobs] {

  val memoisedCleaner: Cleaner[TreeBlobEntry] = MemoUtil.concurrentCleanerMemo[TreeBlobEntry](Set.empty) {
    entry =>
      val (mode, objectId) = fix(entry)
      TreeBlobEntry(entry.filename, mode, objectId)
  }

  def fix(entry: TreeBlobEntry): (BlobFileMode, ObjectId) // implementing code can not safely know valid filename

  override def apply(treeBlobs: TreeBlobs) = treeBlobs.entries.map(memoisedCleaner)

}


================================================
FILE: bfg-library/src/main/scala/com/madgag/git/bfg/cleaner/commits.scala
================================================
/*
 * Copyright (c) 2012 Roberto Tyley
 *
 * This file is part of 'BFG Repo-Cleaner' - a tool for removing large
 * or troublesome blobs from Git repositories.
 *
 * BFG Repo-Cleaner is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * BFG Repo-Cleaner is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see http://www.gnu.org/licenses/ .
 */

package com.madgag.git.bfg.cleaner

import com.madgag.git.ThreadLocalObjectDatabaseResources
import com.madgag.git.bfg.model._
import org.eclipse.jgit.lib._
import org.eclipse.jgit.revwalk.RevCommit

object CommitNodeCleaner {

  class Kit(val threadLocalResources: ThreadLocalObjectDatabaseResources,
            val originalRevCommit: RevCommit,
            val originalCommit: Commit,
            val updatedArcs: CommitArcs,
            val mapper: Cleaner[ObjectId]) {

    val arcsChanged = originalCommit.arcs != updatedArcs

    def commitIsChanged(withThisNode: CommitNode) = arcsChanged || originalCommit.node != withThisNode
  }

  def chain(cleaners: Seq[CommitNodeCleaner]) = new CommitNodeCleaner {
    def fixer(kit: CommitNodeCleaner.Kit) = Function.chain(cleaners.map(_.fixer(kit)))
  }
}

trait CommitNodeCleaner {
  def fixer(kit: CommitNodeCleaner.Kit): Cleaner[CommitNode]
}

object FormerCommitFooter extends CommitNodeCleaner {
  val Key = "Former-commit-id"

  override def fixer(kit: CommitNodeCleaner.Kit) = modifyIf(kit.commitIsChanged) {
    _ add Footer(Key, kit.originalRevCommit.name)
  }

  def modifyIf[A](predicate: A => Boolean)(modifier: A => A): (A => A) = v => if (predicate(v)) modifier(v) else v
}


================================================
FILE: bfg-library/src/main/scala/com/madgag/git/bfg/cleaner/kit/BlobInserter.scala
================================================
/*
 * Copyright (c) 2012, 2013 Roberto Tyley
 *
 * This file is part of 'BFG Repo-Cleaner' - a tool for removing large
 * or troublesome blobs from Git repositories.
 *
 * BFG Repo-Cleaner is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * BFG Repo-Cleaner is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see http://www.gnu.org/licenses/ .
 */

package com.madgag.git.bfg.cleaner.kit

import java.io.InputStream

import org.eclipse.jgit.lib.Constants._
import org.eclipse.jgit.lib.{ObjectId, ObjectInserter}

class BlobInserter(objectInserter: ObjectInserter) {
  def insert(data: Array[Byte]): ObjectId = objectInserter.insert(OBJ_BLOB, data)

  def insert(length: Long, in: InputStream): ObjectId = objectInserter.insert(OBJ_BLOB, length, in)
}


================================================
FILE: bfg-library/src/main/scala/com/madgag/git/bfg/cleaner/package.scala
================================================
/*
 * Copyright (c) 2012, 2013 Roberto Tyley
 *
 * This file is part of 'BFG Repo-Cleaner' - a tool for removing large
 * or troublesome blobs from Git repositories.
 *
 * BFG Repo-Cleaner is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * BFG Repo-Cleaner is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see http://www.gnu.org/licenses/ .
 */

package com.madgag.git.bfg

package object cleaner {
  type Cleaner[V] = V => V
}


================================================
FILE: bfg-library/src/main/scala/com/madgag/git/bfg/cleaner/protection/ProtectedObjectCensus.scala
================================================
/*
 * Copyright (c) 2012 Roberto Tyley
 *
 * This file is part of 'BFG Repo-Cleaner' - a tool for removing large
 * or troublesome blobs from Git repositories.
 *
 * BFG Repo-Cleaner is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * BFG Repo-Cleaner is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see http://www.gnu.org/licenses/ .
 */

package com.madgag.git.bfg.cleaner.protection

import com.madgag.git._
import com.madgag.scala.collection.decorators._
import org.eclipse.jgit.lib.{ObjectId, Repository}
import org.eclipse.jgit.revwalk._

/**
 * PROTECTING TREES :
 * Want to leave the tree unchanged for all commits at the tips of refs the user thinks are important.
 * What if you think a Tag is important? Or a tree?
 *
 * If a tag points to a:
 * - commit - that commit may change, but it's tree must stay the same
 * - tree - who the fuck tags tree anyway? if I've been asked to protect it, that suggests that it's supposed to be inviolate
 * - blob - that blob will continue to be referenced by the repo, not disappear, but not be cleaned either, as we currently clean at TreeBlob level
 *
 * We can take a shortcut here by just pushing all hallowed trees straight into the memo collection
 * This does mean that we will never notice, or be able to report, if somebody sets a rule that 'cleans' (alters) a hallowed tree
 * It might also have somewhat unexpected consequences if someone hallows a very 'simple' directory that occurs often
 *
 *
 * PROTECTING BLOBS :
 * If a user wants to protect the tip of a ref, all blobs will be retained. There is no space-saving or secrets-kept
 * by deleting, tampering with those blobs elsewhere. And if you have some big-old blob like a jar that you have
 * used consistently throughout the history of your project, it benefits no-one to remove it- in fact it's actively
 * harmful.
 *
 * We explicitly protect blobs (rather than just allowing them to fall under the protection given to Trees) precisely
 * because these blobs may historically have existed in other directories (trees) that did not appear in the
 * protected tips, and so would not be protected by Tree protection.
 *
 *
 * PROTECTING TAGS & COMMITS :
 * This just means protecting the Trees & Blobs under those Tags and Commits, as specified above. Changing other
 * state - such as the message, or author, or referenced commit Ids (and consequently the object Id of the target
 * object itself) is very much up for grabs. I gotta change your history, or I've no business being here.
 */
object ProtectedObjectCensus {

  val None = ProtectedObjectCensus()

  def apply(revisions: Set[String])(implicit repo: Repository): ProtectedObjectCensus = {

    implicit val (revWalk, reader) = repo.singleThreadedReaderTuple

    val objectProtection = revisions.groupBy { revision =>
      Option(repo.resolve(revision)).getOrElse { throw new IllegalArgumentException(
          s"Couldn't find '$revision' in ${repo.topDirectory.getAbsolutePath} - are you sure that exists?"
      )}.asRevObject
    }

    // blobs come from direct blob references and tag references
    // trees come from direct tree references, commit & tag references

    val treeAndBlobProtection = objectProtection.keys.groupUp(treeOrBlobPointedToBy)(_.toSet) // use Either?

    val directBlobProtection = treeAndBlobProtection collect {
      case (Left(blob), p) => blob.getId -> p
    }
    val treeProtection = treeAndBlobProtection collect {
      case (Right(tree), p) => tree -> p
    }
    val indirectBlobProtection = treeProtection.keys.flatMap(tree => allBlobsUnder(tree).map(_ -> tree)).groupUp(_._1)(_.map(_._2).toSet)

    ProtectedObjectCensus(objectProtection, treeProtection, directBlobProtection, indirectBlobProtection)
  }
}

case class ProtectedObjectCensus(protectorRevsByObject: Map[RevObject, Set[String]] = Map.empty,
                            treeProtection: Map[RevTree, Set[RevObject]] = Map.empty,
                            directBlobProtection: Map[ObjectId, Set[RevObject]] = Map.empty,
                            indirectBlobProtection: Map[ObjectId, Set[RevTree]] = Map.empty) {

  val isEmpty = protectorRevsByObject.isEmpty

  lazy val blobIds: Set[ObjectId] = directBlobProtection.keySet ++ indirectBlobProtection.keySet

  lazy val treeIds = treeProtection.keySet

  // blobs only for completeness here
  lazy val fixedObjectIds: Set[ObjectId] = treeIds ++ blobIds
}


================================================
FILE: bfg-library/src/main/scala/com/madgag/git/bfg/cleaner/protection/ProtectedObjectDirtReport.scala
================================================
/*
 * Copyright (c) 2012, 2013 Roberto Tyley
 *
 * This file is part of 'BFG Repo-Cleaner' - a tool for removing large
 * or troublesome blobs from Git repositories.
 *
 * BFG Repo-Cleaner is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * BFG Repo-Cleaner is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see http://www.gnu.org/licenses/ .
 */

package com.madgag.git.bfg.cleaner.protection

import com.madgag.git._
import com.madgag.git.bfg.GitUtil._
import com.madgag.git.bfg.cleaner.ObjectIdCleaner
import org.eclipse.jgit.diff.DiffEntry
import org.eclipse.jgit.diff.DiffEntry.ChangeType._
import org.eclipse.jgit.lib.{ObjectDatabase, ObjectId}
import org.eclipse.jgit.revwalk.{RevObject, RevWalk}
import org.eclipse.jgit.treewalk.TreeWalk
import org.eclipse.jgit.treewalk.filter.TreeFilter

import scala.jdk.CollectionConverters._

object ProtectedObjectDirtReport {
  def reportsFor(objectIdCleanerConfig: ObjectIdCleaner.Config, objectDB: ObjectDatabase)(implicit revWalk: RevWalk) = {
    val uncaringCleaner: ObjectIdCleaner = new ObjectIdCleaner(
      objectIdCleanerConfig.copy(protectedObjectCensus = ProtectedObjectCensus.None),
      objectDB,
      revWalk
    )

    for (protectedRevObj <- objectIdCleanerConfig.protectedObjectCensus.protectorRevsByObject.keys) yield {
      val originalContentTreeOrBlob = treeOrBlobPointedToBy(protectedRevObj)
      val replacementTreeOrBlob = originalContentTreeOrBlob.fold(uncaringCleaner.cleanBlob.replacement, uncaringCleaner.cleanTree.replacement)
      ProtectedObjectDirtReport(protectedRevObj, originalContentTreeOrBlob.merge, replacementTreeOrBlob)
    }
  }
}

/**
 * The function of the ProtectedObjectDirtReport is tell the user that this is the stuff they've decided
 * to protect in their latest commits - it's the stuff The BFG /would/ remove if you hadn't told it to
 * hold back,
 *
 * @param revObject - the protected object (eg protected because it is the HEAD commit, or even by additional refs)
 * @param originalTreeOrBlob - the unmodified content-object referred to by the protected object (may be same object)
 * @param replacementTreeOrBlob - an option, populated if cleaning creates a replacement for the content-object
 */
case class ProtectedObjectDirtReport(revObject: RevObject, originalTreeOrBlob: RevObject, replacementTreeOrBlob: Option[ObjectId]) {
  val objectProtectsDirt: Boolean = replacementTreeOrBlob.isDefined

  def dirt(implicit revWalk: RevWalk): Option[Seq[DiffEntry]] = replacementTreeOrBlob.map { newId =>
    val tw = new TreeWalk(revWalk.getObjectReader)
    tw.setRecursive(true)
    tw.reset

    tw.addTree(originalTreeOrBlob.asRevTree)
    tw.addTree(newId.asRevTree)
    tw.setFilter(TreeFilter.ANY_DIFF)
    DiffEntry.scan(tw).asScala.filterNot(_.getChangeType == ADD).toSeq
  }
}


================================================
FILE: bfg-library/src/main/scala/com/madgag/git/bfg/cleaner/treeblobs.scala
================================================
/*
 * Copyright (c) 2012 Roberto Tyley
 *
 * This file is part of 'BFG Repo-Cleaner' - a tool for removing large
 * or troublesome blobs from Git repositories.
 *
 * BFG Repo-Cleaner is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * BFG Repo-Cleaner is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see http://www.gnu.org/licenses/ .
 */

package com.madgag.git.bfg.cleaner

import com.madgag.git.bfg.cleaner.kit.BlobInserter
import com.madgag.git.bfg.model.FileName.ImplicitConversions._
import com.madgag.git.bfg.model.{TreeBlobEntry, _}
import com.madgag.textmatching.TextMatcher
import org.eclipse.jgit.lib.ObjectId

class FileDeleter(fileNameMatcher: TextMatcher) extends Cleaner[TreeBlobs] {
  override def apply(tbs: TreeBlobs) = tbs.entries.filterNot(e => fileNameMatcher(e.filename))
}

class BlobRemover(blobIds: Set[ObjectId]) extends Cleaner[TreeBlobs] {
  override def apply(treeBlobs: TreeBlobs) = treeBlobs.entries.filter(e => !blobIds.contains(e.objectId))
}

class BlobReplacer(badBlobs: Set[ObjectId], blobInserter: => BlobInserter) extends Cleaner[TreeBlobs] {
  override def apply(treeBlobs: TreeBlobs) = treeBlobs.entries.map {
    case e if badBlobs.contains(e.objectId) =>
      TreeBlobEntry(FileName(e.filename + ".REMOVED.git-id"), RegularFile, blobInserter.insert(e.objectId.name.getBytes))
    case e => e
  }
}












================================================
FILE: bfg-library/src/main/scala/com/madgag/git/bfg/memo.scala
================================================
/*
 * Copyright (c) 2012 Roberto Tyley
 *
 * This file is part of 'BFG Repo-Cleaner' - a tool for removing large
 * or troublesome blobs from Git repositories.
 *
 * BFG Repo-Cleaner is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * BFG Repo-Cleaner is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see http://www.gnu.org/licenses/ .
 */

package com.madgag.git.bfg

import scala.jdk.CollectionConverters._
import com.google.common.cache.{CacheBuilder, CacheLoader, CacheStats, LoadingCache}
import com.madgag.git.bfg.cleaner._

trait Memo[K, V] {
  def apply(z: K => V): MemoFunc[K, V]
}

trait MemoFunc[K,V] extends (K => V) {
  def asMap(): Map[K,V]

  def stats(): CacheStats
}

object MemoUtil {

  def memo[K, V](f: (K => V) => MemoFunc[K, V]): Memo[K, V] = new Memo[K, V] {
    def apply(z: K => V) = f(z)
  }

  /**
   *
   * A caching wrapper for a function (V => V), backed by a no-eviction LoadingCache from Google Collections.
   */
  def concurrentCleanerMemo[V](fixedEntries: Set[V] = Set.empty[V]): Memo[V, V] = {
    memo[V, V] {
      (f: Cleaner[V]) =>
        lazy val permanentCache = loaderCacheFor(f)(fix)

        def fix(v: V): Unit = {
          // enforce that once any value is returned, it is 'good' and therefore an identity-mapped key as well
          permanentCache.put(v, v)
        }

        fixedEntries foreach fix

        new MemoFunc[V, V] {
          def apply(k: V) = permanentCache.get(k)

          def asMap() = permanentCache.asMap().asScala.view.filter {
            case (oldId, newId) => newId != oldId
          }.toMap

          override def stats(): CacheStats = permanentCache.stats()
        }
    }
  }

  def loaderCacheFor[K, V](calc: K => V)(postCalc: V => Unit): LoadingCache[K, V] =
    CacheBuilder.newBuilder.asInstanceOf[CacheBuilder[K, V]].recordStats().build(new CacheLoader[K, V] {
      def load(key: K): V = {
        val v = calc(key)
        postCalc(v)
        v
      }
    })
}


================================================
FILE: bfg-library/src/main/scala/com/madgag/git/bfg/model/Commit.scala
================================================
package com.madgag.git.bfg.model

import com.madgag.git._
import com.madgag.git.bfg.cleaner._
import org.eclipse.jgit.lib.Constants.OBJ_COMMIT
import org.eclipse.jgit.lib._
import org.eclipse.jgit.revwalk.RevCommit

import java.nio.charset.StandardCharsets.UTF_8
import java.nio.charset.{Charset, IllegalCharsetNameException, UnsupportedCharsetException}
import scala.jdk.CollectionConverters._

/*
 * Copyright (c) 2012, 2013 Roberto Tyley
 *
 * This file is part of 'BFG Repo-Cleaner' - a tool for removing large
 * or troublesome blobs from Git repositories.
 *
 * BFG Repo-Cleaner is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * BFG Repo-Cleaner is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see http://www.gnu.org/licenses/ .
 */


object Commit {
  def apply(revCommit: RevCommit): Commit = Commit(CommitNode(revCommit), revCommit.arcs)
}

case class Commit(node: CommitNode, arcs: CommitArcs) {
  def toBytes: Array[Byte] = {
    val c = new CommitBuilder
    c.setParentIds(arcs.parents.asJava)
    c.setTreeId(arcs.tree)

    c.setAuthor(node.author)
    c.setCommitter(node.committer)
    c.setEncoding(node.encoding)
    c.setMessage(node.message)

    c.toByteArray
  }

  lazy val id = new ObjectInserter.Formatter().idFor(OBJ_COMMIT, toBytes)

  override lazy val toString = s"commit[${id.shortName}${node.subject.map(s=> s" '${s.take(50)}'").getOrElse("")}]"
}

case class CommitArcs(parents: Seq[ObjectId], tree: ObjectId) {
  def cleanWith(cleaner: ObjectIdCleaner) = CommitArcs(parents map cleaner.cleanCommit, cleaner.cleanTree(tree))
}

object CommitNode {
  def apply(c: RevCommit): CommitNode = CommitNode(c.getAuthorIdent, c.getCommitterIdent, c.getFullMessage,
      try c.getEncoding catch {case e @ (_ : IllegalCharsetNameException | _ : UnsupportedCharsetException) => UTF_8})
}

case class CommitNode(author: PersonIdent, committer: PersonIdent, message: String, encoding: Charset = UTF_8) {
  lazy val subject = message.linesIterator.to(LazyList).headOption
  lazy val lastParagraphBreak = message.lastIndexOf("\n\n")
  lazy val messageWithoutFooters = if (footers.isEmpty) message else (message take lastParagraphBreak)
  lazy val footers: List[Footer] = message.drop(lastParagraphBreak).linesIterator.collect {
    case Footer.FooterPattern(key, value) => Footer(key, value)
  }.toList

  def add(footer: Footer) = copy(message = message + "\n" + (if (footers.isEmpty) "\n" else "") + footer.toString)
}


================================================
FILE: bfg-library/src/main/scala/com/madgag/git/bfg/model/Footer.scala
================================================
/*
 * Copyright (c) 2012, 2013 Roberto Tyley
 *
 * This file is part of 'BFG Repo-Cleaner' - a tool for removing large
 * or troublesome blobs from Git repositories.
 *
 * BFG Repo-Cleaner is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * BFG Repo-Cleaner is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see http://www.gnu.org/licenses/ .
 */

package com.madgag.git.bfg.model

object Footer {
  // ^[A-Za-z0-9-]+:
  val FooterPattern = """([\p{Alnum}-]+): *(.*)""".r

  def apply(footerLine: String): Option[Footer] = footerLine match {
    case FooterPattern(key, value) => Some(Footer(key, value))
    case _ => None
  }
}

case class Footer(key: String, value: String) {
  override lazy val toString = key + ": " + value
}


================================================
FILE: bfg-library/src/main/scala/com/madgag/git/bfg/model/package.scala
================================================
/*
 * Copyright (c) 2012, 2013 Roberto Tyley
 *
 * This file is part of 'BFG Repo-Cleaner' - a tool for removing large
 * or troublesome blobs from Git repositories.
 *
 * BFG Repo-Cleaner is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * BFG Repo-Cleaner is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see http://www.gnu.org/licenses/ .
 */

package com.madgag.git.bfg

import org.eclipse.jgit.revwalk.RevCommit

import java.nio.file.Path


package object model {
  implicit class RichRevCommit(revCommit: RevCommit) {
    lazy val arcs: CommitArcs = CommitArcs(revCommit.getParents.toIndexedSeq, revCommit.getTree)
  }

  implicit class RichPath(path: Path) {
    def resolve(pathSegments: Seq[String]): Path = pathSegments.foldLeft(path)(_ resolve _)
  }
}


================================================
FILE: bfg-library/src/main/scala/com/madgag/git/bfg/timing.scala
================================================
/*
 * Copyright (c) 2012 Roberto Tyley
 *
 * This file is part of 'BFG Repo-Cleaner' - a tool for removing large
 * or troublesome blobs from Git repositories.
 *
 * BFG Repo-Cleaner is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * BFG Repo-Cleaner is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see http://www.gnu.org/licenses/ .
 */

package com.madgag.git.bfg

import java.lang.System._
import java.util.concurrent.TimeUnit.NANOSECONDS

import org.eclipse.jgit.lib.ProgressMonitor

object Timing {
  //  def measure[T](block: => T) = {
  //    val start = nanoTime
  //    val result = block
  //    val duration = nanoTime - start
  //    println("duration="+duration)
  //    result
  //  }

  def measureTask[T](taskName: String, workSize: Int)(block: => T)(implicit progressMonitor: ProgressMonitor) = {
    progressMonitor.beginTask(taskName, workSize)
    val start = nanoTime
    val result = block
    val duration = nanoTime - start
    progressMonitor.endTask()
    println(taskName + " completed in %,d ms.".format(NANOSECONDS.toMillis(duration)))
    result
  }
}


================================================
FILE: bfg-library/src/main/scala/com/madgag/inclusion/inclusion.scala
================================================
/*
 * Copyright (c) 2012, 2013 Roberto Tyley
 *
 * This file is part of 'BFG Repo-Cleaner' - a tool for removing large
 * or troublesome blobs from Git repositories.
 *
 * BFG Repo-Cleaner is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * BFG Repo-Cleaner is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see http://www.gnu.org/licenses/ .
 */

package com.madgag.inclusion

import scala.Function.const

case class IncExcExpression[-A](filters: Seq[Filter[A]]) {
  lazy val searchPath = (filters.headOption.map(_.impliedPredecessor).getOrElse(Include.everything) +: filters).reverse

  def includes(a: A): Boolean = searchPath.find(_.predicate(a)).get.included
}

sealed trait Filter[-A] {
  val included: Boolean

  val predicate: A => Boolean

  val impliedPredecessor: Filter[A]

  def isDefinedAt(a: A) = predicate(a)
}


object Include {
  def everything = Include(const(true))
}

object Exclude {
  def everything = Exclude(const(true))
}

case class Include[A](predicate: A => Boolean) extends Filter[A] {
  lazy val impliedPredecessor = Exclude.everything
  val included = true
}

case class Exclude[A](predicate: A => Boolean) extends Filter[A] {
  lazy val impliedPredecessor = Include.everything
  val included = false
}

================================================
FILE: bfg-library/src/main/scala/com/madgag/text/ByteSize.scala
================================================
/*
 * Copyright (c) 2012, 2013 Roberto Tyley
 *
 * This file is part of 'BFG Repo-Cleaner' - a tool for removing large
 * or troublesome blobs from Git repositories.
 *
 * BFG Repo-Cleaner is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * BFG Repo-Cleaner is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see http://www.gnu.org/licenses/ .
 */

package com.madgag.text

object ByteSize {

  import math._

  val magnitudeChars = Seq('B', 'K', 'M', 'G', 'T', 'P')
  val unit = 1024

  def parse(v: String): Long = magnitudeChars.indexOf(v.takeRight(1)(0).toUpper) match {
    case -1 => throw new IllegalArgumentException(s"Size unit is missing (ie ${magnitudeChars.mkString(", ")})")
    case index => v.dropRight(1).toLong << (index * 10)
  }

  def format(bytes: Long): String = {
    if (bytes < unit) s"$bytes B " else {
      val exp = (log(bytes.toDouble) / log(unit)).toInt
      val pre = magnitudeChars(exp)
      "%.1f %sB".format(bytes / pow(unit, exp), pre)
    }
  }

}


================================================
FILE: bfg-library/src/main/scala/com/madgag/text/Tables.scala
================================================
/*
 * Copyright (c) 2012, 2013 Roberto Tyley
 *
 * This file is part of 'BFG Repo-Cleaner' - a tool for removing large
 * or troublesome blobs from Git repositories.
 *
 * BFG Repo-Cleaner is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * BFG Repo-Cleaner is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see http://www.gnu.org/licenses/ .
 */

package com.madgag.text

object Tables {
  def formatTable(header: Product, data: Seq[Product], maxDataRows: Int = 16): Seq[String] = {
    val numColumns = data.head.productArity
    val sizes: Seq[Int] = (0 until numColumns).map(i => (data :+ header).map(_.productElement(i).toString.length).max)
    def padLine(l: Product): IndexedSeq[String] = {
      (0 until numColumns).map(c => l.productElement(c).toString.padTo(sizes(c), ' '))
    }

    val headerLine = padLine(header).mkString("   ")
    Text.abbreviate(headerLine +: "-" * headerLine.size +: data.map {
      l =>
        padLine(l).mkString(" | ")
    }, "...", maxDataRows+2).toSeq
  }
}


================================================
FILE: bfg-library/src/main/scala/com/madgag/text/text.scala
================================================
/*
 * Copyright (c) 2012, 2013 Roberto Tyley
 *
 * This file is part of 'BFG Repo-Cleaner' - a tool for removing large
 * or troublesome blobs from Git repositories.
 *
 * BFG Repo-Cleaner is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * BFG Repo-Cleaner is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see http://www.gnu.org/licenses/ .
 */

package com.madgag.text

object Text {

  def abbreviate[A](elems: Iterable[A], truncationToken: A, maxElements: Int = 3) = {
    val firstElems = elems.take(maxElements + 1)
    if (firstElems.size > maxElements) {
      firstElems.take(maxElements-1).toSeq :+ truncationToken
    } else {
      elems
    }
  }

  def plural[A](list: Iterable[A], noun: String) = s"${list.size} $noun${if (list.size == 1) "" else "s"}"
}


================================================
FILE: bfg-library/src/test/scala/com/madgag/git/LFSSpec.scala
================================================
/*
 * Copyright (c) 2015 Roberto Tyley
 *
 * This file is part of 'BFG Repo-Cleaner' - a tool for removing large
 * or troublesome blobs from Git repositories.
 *
 * BFG Repo-Cleaner is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * BFG Repo-Cleaner is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see http://www.gnu.org/licenses/ .
 */

package com.madgag.git

import com.madgag.git.LFS.Pointer
import com.madgag.git.test._
import org.eclipse.jgit.lib.Constants._
import org.eclipse.jgit.lib.ObjectInserter
import org.scalatest.OptionValues
import org.scalatest.flatspec.AnyFlatSpec
import org.scalatest.matchers.should.Matchers

import java.nio.file.Files
import java.nio.file.Files.createTempFile

class LFSSpec extends AnyFlatSpec with Matchers with OptionValues {
  "Our implementation of Git LFS Pointers" should "create pointers that have the same Git id as the ones produced by `git lfs pointer`" in {
    val pointer = LFS.Pointer("b2893eddd9b394bfb7efadafda2ae0be02c573fdd83a70f26c781a943f3b7016", 21616)

    val pointerObjectId = new ObjectInserter.Formatter().idFor(OBJ_BLOB, pointer.bytes)

    pointerObjectId shouldBe "1d90744cffd9e9f324870ed60b6d1258e56a39e1".asObjectId
  }

  it should "have the correctly sharded path" in {
    val pointer = LFS.Pointer("b2893eddd9b394bfb7efadafda2ae0be02c573fdd83a70f26c781a943f3b7016", 21616)

    pointer.path shouldBe Seq("b2", "89", "b2893eddd9b394bfb7efadafda2ae0be02c573fdd83a70f26c781a943f3b7016")
  }

  it should "calculate pointers correctly directly from the Git database, creating a temporary file" in {
    implicit val repo = unpackRepo("/sample-repos/example.git.zip")
    implicit val (revWalk, reader) = repo.singleThreadedReaderTuple

    val tmpFile = createTempFile(s"bfg.test.git-lfs",".conv")

    val pointer = LFS.pointerFor(abbrId("06d7").open, tmpFile)

    pointer shouldBe Pointer("5f70bf18a086007016e948b04aed3b82103a36bea41755b6cddfaf10ace3c6ef", 1024)

    Files.size(tmpFile) shouldBe 1024
  }
}

================================================
FILE: bfg-library/src/test/scala/com/madgag/git/bfg/GitUtilSpec.scala
================================================
/*
 * Copyright (c) 2012 Roberto Tyley
 *
 * This file is part of 'BFG Repo-Cleaner' - a tool for removing large
 * or troublesome blobs from Git repositories.
 *
 * BFG Repo-Cleaner is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * BFG Repo-Cleaner is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see http://www.gnu.org/licenses/ .
 */

package com.madgag.git.bfg

import com.madgag.git._
import com.madgag.git.test._
import org.eclipse.jgit.internal.storage.file.FileRepository
import org.scalatest.flatspec.AnyFlatSpec
import org.scalatest.matchers.should.Matchers

class GitUtilSpec extends AnyFlatSpec with Matchers {
  implicit val repo: FileRepository = unpackRepo("/sample-repos/example.git.zip")

  "reachable blobs" should "match expectations" in {
    implicit val (revWalk, reader) = repo.singleThreadedReaderTuple

    allBlobsReachableFrom(abbrId("475d") asRevCommit) shouldBe Set("d8d1", "34bd", "e69d", "c784", "d004").map(abbrId)
  }
}

================================================
FILE: bfg-library/src/test/scala/com/madgag/git/bfg/MessageFooterSpec.scala
================================================
/*
 * Copyright (c) 2012 Roberto Tyley
 *
 * This file is part of 'BFG Repo-Cleaner' - a tool for removing large
 * or troublesome blobs from Git repositories.
 *
 * BFG Repo-Cleaner is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * BFG Repo-Cleaner is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see http://www.gnu.org/licenses/ .
 */

package com.madgag.git.bfg

import com.madgag.git.bfg.model.{CommitNode, Footer}
import org.eclipse.jgit.lib.PersonIdent
import org.scalatest.flatspec.AnyFlatSpec
import org.scalatest.matchers.should.Matchers

class MessageFooterSpec extends AnyFlatSpec with Matchers {

  val person = new PersonIdent("Dave Eg", "dave@e.com")

  def commit(m: String) = CommitNode(person, person, m)

  "Message footers" should "append footer without new paragraph if footers already present" in {

    val updatedCommit = commit("Sub\n\nmessage\n\nSigned-off-by: Joe Eg <joe@e.com>") add Footer("Foo", "Bar")

    updatedCommit.message shouldBe "Sub\n\nmessage\n\nSigned-off-by: Joe Eg <joe@e.com>\nFoo: Bar"
  }

  it should "create paragraph break if no footers already present" in {

    val updatedCommit = commit("Sub\n\nmessage") add Footer("Foo", "Bar")

    updatedCommit.message shouldBe "Sub\n\nmessage\n\nFoo: Bar"
  }

  // def footersViaJGit(commit: RevCommit) = commit.getFooterLines.map(f => Footer(f.getKey, f.getValue)).toList
}

================================================
FILE: bfg-library/src/test/scala/com/madgag/git/bfg/TreeEntrySpec.scala
================================================
/*
 * Copyright (c) 2012 Roberto Tyley
 *
 * This file is part of 'BFG Repo-Cleaner' - a tool for removing large
 * or troublesome blobs from Git repositories.
 *
 * BFG Repo-Cleaner is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * BFG Repo-Cleaner is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see http://www.gnu.org/licenses/ .
 */

package com.madgag.git.bfg

import com.madgag.git.bfg.model.{FileName, Tree}
import org.eclipse.jgit.lib.FileMode
import org.eclipse.jgit.lib.FileMode._
import org.eclipse.jgit.lib.ObjectId.zeroId
import org.scalatest.flatspec.AnyFlatSpec
import org.scalatest.matchers.should.Matchers

class TreeEntrySpec extends AnyFlatSpec with Matchers {

  def a(mode: FileMode, name: String) = Tree.Entry(FileName(name), mode, zeroId)

  "Tree entry ordering" should "match ordering used by Git" in {
    a(TREE, "agit-test-utils") should be < a(TREE, "agit")
  }
}

================================================
FILE: bfg-library/src/test/scala/com/madgag/git/bfg/cleaner/LfsBlobConverterSpec.scala
================================================
/*
 * Copyright (c) 2012, 2013 Roberto Tyley
 *
 * This file is part of 'BFG Repo-Cleaner' - a tool for removing large
 * or troublesome blobs from Git repositories.
 *
 * BFG Repo-Cleaner is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * BFG Repo-Cleaner is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see http://www.gnu.org/licenses/ .
 */

package com.madgag.git.bfg.cleaner

import com.madgag.diff.{After, Before, MapDiff}
import com.madgag.git.LFS.Pointer
import com.madgag.git._
import com.madgag.git.bfg.model.{BlobFileMode, FileName, Tree, TreeBlobs, _}
import com.madgag.git.test._
import com.madgag.scala.collection.decorators._
import org.eclipse.jgit.internal.storage.file.FileRepository
import org.eclipse.jgit.lib.ObjectId
import org.scalatest.concurrent.Eventually
import org.scalatest.flatspec.AnyFlatSpec
import org.scalatest.matchers.should.Matchers
import org.scalatest.{Inspectors, OptionValues}

import java.nio.file.Files.readAllBytes
import java.nio.file.{Files, Path}

class LfsBlobConverterSpec extends AnyFlatSpec with Matchers with OptionValues with Inspectors with Eventually {

  "LfsBlobConverter" should "successfully shift the blob to the LFS store" in {
    implicit val repo = unpackRepo("/sample-repos/example.git.zip")
    implicit val (revWalk, reader) = repo.singleThreadedReaderTuple

    val oldTreeBlobs = Tree(repo.resolve("early-release^{tree}")).blobs

    val newTreeBlobs = clean(oldTreeBlobs, "*ero*")

    val diff = oldTreeBlobs.diff(newTreeBlobs)

    diff.changed shouldBe Set(FileName("one-kb-zeros"))
    diff.unchanged should contain allOf(FileName("hero"), FileName("zero"))

    verifyPointersForChangedFiles(diff)
  }

  it should "not do damage if run twice - ie don't create a pointer for a pointer!" in {
    implicit val repo = unpackRepo("/sample-repos/example.git.zip")
    implicit val (revWalk, reader) = repo.singleThreadedReaderTuple

    val oldTreeBlobs = Tree(repo.resolve("early-release^{tree}")).blobs

    val treeBlobsAfterRun1 = clean(oldTreeBlobs, "*ero*")

    val firstDiff = oldTreeBlobs.diff(treeBlobsAfterRun1)

    firstDiff.changed shouldBe Set(FileName("one-kb-zeros"))

    val treeBlobsAfterRun2 = clean(treeBlobsAfterRun1, "*ero*")

    treeBlobsAfterRun1.diff(treeBlobsAfterRun2).changed shouldBe empty

    verifyPointersForChangedFiles(firstDiff) // Are the LFS files still intact?
  }


  def clean(oldTreeBlobs: TreeBlobs, glob: String)(implicit repo: FileRepository): TreeBlobs = {
    val converter = new LfsBlobConverter(glob, repo)
    converter(oldTreeBlobs)
  }

  def verifyPointerInsertedFor(fileName: FileName, diff: MapDiff[FileName, (BlobFileMode, ObjectId)])(implicit repo: FileRepository) = {
    implicit val (revWalk, reader) = repo.singleThreadedReaderTuple

    diff.changed should contain(fileName)

    val fileBeforeAndAfter = diff.changedMap(fileName)

    fileBeforeAndAfter(After)._1 shouldBe fileBeforeAndAfter(Before)._1

    val fileIds = fileBeforeAndAfter.mapV(_._2)

    val (originalFileId, pointerObjectId) = (fileIds(Before), fileIds(After))

    verifyPointerFileFor(originalFileId, pointerObjectId)
  }

  def verifyPointerFileFor(originalFileId: ObjectId, pointerObjectId: ObjectId)(implicit repo: FileRepository) = {
    implicit val (revWalk, reader) = repo.singleThreadedReaderTuple

    val pointer = Pointer.parse(pointerObjectId.open.getCachedBytes)

    val lfsStoredFile: Path = repo.getDirectory.toPath.resolve(Seq("lfs", "objects") ++ pointer.path)

    Files.exists(lfsStoredFile) shouldBe true

    Files.size(lfsStoredFile) shouldBe pointer.blobSize

    eventually { readAllBytes(lfsStoredFile).blobId } shouldBe originalFileId
  }

  def verifyPointersForChangedFiles(diff: MapDiff[FileName, (BlobFileMode, ObjectId)])(implicit repo: FileRepository) = {
    diff.only(Before) shouldBe empty
    diff.only(After).keys shouldBe Set(FileName(".gitattributes"))

    forAll(diff.changed) { fileName =>
      verifyPointerInsertedFor(fileName, diff)
    }
  }
}


================================================
FILE: bfg-library/src/test/scala/com/madgag/git/bfg/cleaner/ObjectIdCleanerSpec.scala
================================================
/*
 * Copyright (c) 2012, 2013 Roberto Tyley
 *
 * This file is part of 'BFG Repo-Cleaner' - a tool for removing large
 * or troublesome blobs from Git repositories.
 *
 * BFG Repo-Cleaner is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * BFG Repo-Cleaner is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see http://www.gnu.org/licenses/ .
 */

package com.madgag.git.bfg.cleaner

import com.madgag.git._
import com.madgag.git.bfg.cleaner.protection.ProtectedObjectCensus
import com.madgag.textmatching.Literal
import org.eclipse.jgit.lib.ObjectId
import org.eclipse.jgit.revwalk.RevCommit
import org.scalatest.Inspectors
import org.scalatest.flatspec.AnyFlatSpec
import org.scalatest.matchers.Matcher
import org.scalatest.matchers.should.Matchers

import scala.jdk.CollectionConverters._

class ObjectIdCleanerSpec extends AnyFlatSpec with Matchers {
  
  "cleaning" should "not have a StackOverflowError cleaning a repo with deep history" ignore new unpackedRepo("/sample-repos/deep-history.zip") {
    val dirtyCommitWithDeepHistory = "d88ac4f99511667fc0617ea026f3a0ce8a25fd07".asObjectId

    val config = ObjectIdCleaner.Con
Download .txt
gitextract_c1a_g3a9/

├── .github/
│   ├── PULL_REQUEST_TEMPLATE.md
│   └── workflows/
│       ├── ci.yml
│       └── release.yml
├── .gitignore
├── .tool-versions
├── BUILD.md
├── CONTRIBUTING.md
├── LICENSE
├── README.md
├── backers.md
├── bfg/
│   ├── build.sbt
│   └── src/
│       ├── main/
│       │   └── scala/
│       │       └── com/
│       │           └── madgag/
│       │               └── git/
│       │                   └── bfg/
│       │                       └── cli/
│       │                           ├── CLIConfig.scala
│       │                           └── Main.scala
│       └── test/
│           └── scala/
│               └── com/
│                   └── madgag/
│                       └── git/
│                           └── bfg/
│                               └── cli/
│                                   ├── CLIConfigSpecs.scala
│                                   ├── MainSpec.scala
│                                   ├── MassiveNonFileObjectsRequiresOwnJvmSpec.scala
│                                   └── test/
│                                       └── unpackedRepo.scala
├── bfg-benchmark/
│   ├── build.sbt
│   ├── resources/
│   │   ├── jars/
│   │   │   └── grabJars.sh
│   │   └── repos/
│   │       ├── chromium-src/
│   │       │   └── commands/
│   │       │       └── issue-23/
│   │       │           └── bfg.txt
│   │       ├── gcc/
│   │       │   └── commands/
│   │       │       └── delete-file/
│   │       │           ├── bfg.txt
│   │       │           └── gfb.txt
│   │       ├── git/
│   │       │   └── commands/
│   │       │       └── delete-file/
│   │       │           ├── bfg.txt
│   │       │           └── gfb.txt
│   │       ├── github-gem/
│   │       │   └── commands/
│   │       │       └── delete-file/
│   │       │           ├── bfg.txt
│   │       │           └── gfb.txt
│   │       ├── intellij/
│   │       │   └── commands/
│   │       │       ├── delete-binary-resources/
│   │       │       │   └── bfg.txt
│   │       │       ├── delete-file/
│   │       │       │   ├── bfg.txt
│   │       │       │   └── gfb.txt
│   │       │       └── git-lfs-binary-resources/
│   │       │           └── bfg.txt
│   │       ├── jgit/
│   │       │   └── commands/
│   │       │       ├── delete-file/
│   │       │       │   ├── bfg.txt
│   │       │       │   └── gfb.txt
│   │       │       ├── replace-1-existing-string/
│   │       │       │   ├── bfg.txt
│   │       │       │   └── passwords.1-existing-string.txt
│   │       │       ├── replace-20-existing-strings/
│   │       │       │   ├── bfg.txt
│   │       │       │   └── passwords.20-existing-strings.txt
│   │       │       └── replace-500-existing-strings/
│   │       │           ├── bfg.txt
│   │       │           └── passwords.500-existing-strings.txt
│   │       ├── linux/
│   │       │   └── commands/
│   │       │       └── delete-file/
│   │       │           ├── bfg.txt
│   │       │           └── gfb.txt
│   │       ├── rails/
│   │       │   └── commands/
│   │       │       └── delete-file/
│   │       │           ├── bfg.txt
│   │       │           └── gfb.txt
│   │       └── wine/
│   │           └── commands/
│   │               └── delete-file/
│   │                   ├── bfg.txt
│   │                   └── gfb.txt
│   └── src/
│       ├── main/
│       │   └── scala/
│       │       ├── Benchmark.scala
│       │       ├── BenchmarkConfig.scala
│       │       ├── JavaVersion.scala
│       │       ├── lib/
│       │       │   ├── Repo.scala
│       │       │   └── Timing.scala
│       │       └── model/
│       │           ├── BFGJar.scala
│       │           ├── InvocableEngine.scala
│       │           ├── InvocableEngineSet.scala
│       │           └── Java.scala
│       └── test/
│           └── scala/
│               └── JavaVersionSpec.scala
├── bfg-library/
│   ├── build.sbt
│   └── src/
│       ├── main/
│       │   └── scala/
│       │       └── com/
│       │           └── madgag/
│       │               ├── collection/
│       │               │   └── concurrent/
│       │               │       ├── ConcurrentMultiMap.scala
│       │               │       └── ConcurrentSet.scala
│       │               ├── git/
│       │               │   ├── LFS.scala
│       │               │   └── bfg/
│       │               │       ├── GitUtil.scala
│       │               │       ├── cleaner/
│       │               │       │   ├── BlobCharsetDetector.scala
│       │               │       │   ├── BlobTextModifier.scala
│       │               │       │   ├── LfsBlobConverter.scala
│       │               │       │   ├── ObjectIdCleaner.scala
│       │               │       │   ├── ObjectIdSubstitutor.scala
│       │               │       │   ├── RepoRewriter.scala
│       │               │       │   ├── Reporter.scala
│       │               │       │   ├── TreeBlobModifier.scala
│       │               │       │   ├── commits.scala
│       │               │       │   ├── kit/
│       │               │       │   │   └── BlobInserter.scala
│       │               │       │   ├── package.scala
│       │               │       │   ├── protection/
│       │               │       │   │   ├── ProtectedObjectCensus.scala
│       │               │       │   │   └── ProtectedObjectDirtReport.scala
│       │               │       │   └── treeblobs.scala
│       │               │       ├── memo.scala
│       │               │       ├── model/
│       │               │       │   ├── Commit.scala
│       │               │       │   ├── Footer.scala
│       │               │       │   └── package.scala
│       │               │       └── timing.scala
│       │               ├── inclusion/
│       │               │   └── inclusion.scala
│       │               └── text/
│       │                   ├── ByteSize.scala
│       │                   ├── Tables.scala
│       │                   └── text.scala
│       └── test/
│           └── scala/
│               └── com/
│                   └── madgag/
│                       ├── git/
│                       │   ├── LFSSpec.scala
│                       │   └── bfg/
│                       │       ├── GitUtilSpec.scala
│                       │       ├── MessageFooterSpec.scala
│                       │       ├── TreeEntrySpec.scala
│                       │       ├── cleaner/
│                       │       │   ├── LfsBlobConverterSpec.scala
│                       │       │   ├── ObjectIdCleanerSpec.scala
│                       │       │   ├── ObjectIdSubstitutorSpec.scala
│                       │       │   ├── RepoRewriteSpec.scala
│                       │       │   └── TreeBlobModifierSpec.scala
│                       │       └── model/
│                       │           └── CommitSpec.scala
│                       └── text/
│                           └── ByteSizeSpecs.scala
├── bfg-test/
│   ├── build.sbt
│   └── src/
│       └── main/
│           └── scala/
│               └── com/
│                   └── madgag/
│                       └── git/
│                           └── bfg/
│                               └── test/
│                                   └── unpackedRepo.scala
├── build.sbt
├── project/
│   ├── build.properties
│   ├── dependencies.scala
│   └── plugins.sbt
└── version.sbt
Condensed preview — 100 files, each showing path, character count, and a content snippet. Download the .json file or copy for the full structured content (224K chars).
[
  {
    "path": ".github/PULL_REQUEST_TEMPLATE.md",
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    "preview": "I assert that this patch is my own work, and to [simplify the licensing of the BFG Repo-Cleaner](https://github.com/rtyl"
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    "path": ".github/workflows/ci.yml",
    "chars": 608,
    "preview": "name: CI\non:\n  workflow_dispatch:\n  pull_request:\n\n  # triggering CI default branch improves caching\n  # see https://doc"
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    "chars": 602,
    "preview": "name: Release\n\non:\n  workflow_dispatch:\n\njobs:\n  release:\n    uses: guardian/gha-scala-library-release-workflow/.github/"
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    "preview": "target\n*~\n.idea\n.idea_modules\n*.iml\n*.jar\nrepo.git.zip\n**/.project\n**/.classpath\n**/.settings\n.bsp\n\n.DS_Store\ntest-resul"
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    "preview": "The BFG is written in Scala, a modern functional language that runs on the JVM - so it\ncan run anywhere Java can.\n\nHere'"
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    "path": "CONTRIBUTING.md",
    "chars": 1553,
    "preview": "Issues and Questions\n--------------------\n\nIf you've found what looks like a bug, or have a feature request for the BFG,"
  },
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    "path": "LICENSE",
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    "preview": "                    GNU GENERAL PUBLIC LICENSE\n                       Version 3, 29 June 2007\n\n Copyright (C) 2007 Free "
  },
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    "path": "README.md",
    "chars": 994,
    "preview": "BFG Repo-Cleaner \n================\n\n[![CI](https://github.com/rtyley/bfg-repo-cleaner/actions/workflows/ci.yml/badge.svg"
  },
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    "path": "backers.md",
    "chars": 389,
    "preview": "Many thanks to supporters of the BFG!\n-----\n\nContribute towards the open-source development of the BFG on [**BountySourc"
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    "chars": 5753,
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    "path": "bfg/src/test/scala/com/madgag/git/bfg/cli/MassiveNonFileObjectsRequiresOwnJvmSpec.scala",
    "chars": 1743,
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    "path": "bfg-benchmark/resources/repos/intellij/commands/delete-binary-resources/bfg.txt",
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    "path": "bfg-benchmark/resources/repos/intellij/commands/git-lfs-binary-resources/bfg.txt",
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    "path": "bfg-benchmark/resources/repos/jgit/commands/delete-file/bfg.txt",
    "chars": 16,
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    "path": "bfg-benchmark/resources/repos/jgit/commands/delete-file/gfb.txt",
    "chars": 106,
    "preview": "--index-filter\ngit rm --cached --ignore-unmatch make_jgit.sh\n--prune-empty\n--tag-name-filter\ncat\n--\n--all\n"
  },
  {
    "path": "bfg-benchmark/resources/repos/jgit/commands/replace-1-existing-string/bfg.txt",
    "chars": 47,
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    "path": "bfg-benchmark/resources/repos/jgit/commands/replace-1-existing-string/passwords.1-existing-string.txt",
    "chars": 23,
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    "path": "bfg-benchmark/resources/repos/jgit/commands/replace-20-existing-strings/bfg.txt",
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    "path": "bfg-benchmark/resources/repos/jgit/commands/replace-20-existing-strings/passwords.20-existing-strings.txt",
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    "path": "bfg-library/src/test/scala/com/madgag/git/bfg/MessageFooterSpec.scala",
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    "preview": "/*\n * Copyright (c) 2012 Roberto Tyley\n *\n * This file is part of 'BFG Repo-Cleaner' - a tool for removing large\n * or t"
  },
  {
    "path": "bfg-library/src/test/scala/com/madgag/git/bfg/TreeEntrySpec.scala",
    "chars": 1375,
    "preview": "/*\n * Copyright (c) 2012 Roberto Tyley\n *\n * This file is part of 'BFG Repo-Cleaner' - a tool for removing large\n * or t"
  },
  {
    "path": "bfg-library/src/test/scala/com/madgag/git/bfg/cleaner/LfsBlobConverterSpec.scala",
    "chars": 4483,
    "preview": "/*\n * Copyright (c) 2012, 2013 Roberto Tyley\n *\n * This file is part of 'BFG Repo-Cleaner' - a tool for removing large\n "
  },
  {
    "path": "bfg-library/src/test/scala/com/madgag/git/bfg/cleaner/ObjectIdCleanerSpec.scala",
    "chars": 2759,
    "preview": "/*\n * Copyright (c) 2012, 2013 Roberto Tyley\n *\n * This file is part of 'BFG Repo-Cleaner' - a tool for removing large\n "
  },
  {
    "path": "bfg-library/src/test/scala/com/madgag/git/bfg/cleaner/ObjectIdSubstitutorSpec.scala",
    "chars": 2019,
    "preview": "/*\n * Copyright (c) 2012, 2013 Roberto Tyley\n *\n * This file is part of 'BFG Repo-Cleaner' - a tool for removing large\n "
  },
  {
    "path": "bfg-library/src/test/scala/com/madgag/git/bfg/cleaner/RepoRewriteSpec.scala",
    "chars": 7295,
    "preview": "/*\n * Copyright (c) 2012 Roberto Tyley\n *\n * This file is part of 'BFG Repo-Cleaner' - a tool for removing large\n * or t"
  },
  {
    "path": "bfg-library/src/test/scala/com/madgag/git/bfg/cleaner/TreeBlobModifierSpec.scala",
    "chars": 2078,
    "preview": "/*\n * Copyright (c) 2012 Roberto Tyley\n *\n * This file is part of 'BFG Repo-Cleaner' - a tool for removing large\n * or t"
  },
  {
    "path": "bfg-library/src/test/scala/com/madgag/git/bfg/model/CommitSpec.scala",
    "chars": 1341,
    "preview": "/*\n * Copyright (c) 2012, 2013 Roberto Tyley\n *\n * This file is part of 'BFG Repo-Cleaner' - a tool for removing large\n "
  },
  {
    "path": "bfg-library/src/test/scala/com/madgag/text/ByteSizeSpecs.scala",
    "chars": 1941,
    "preview": "/*\n * Copyright (c) 2012, 2013 Roberto Tyley\n *\n * This file is part of 'BFG Repo-Cleaner' - a tool for removing large\n "
  },
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    "path": "bfg-test/build.sbt",
    "chars": 93,
    "preview": "import Dependencies._\n\nlibraryDependencies ++= Seq(scalatest, jgit, scalaGit, scalaGitTest)\n\n"
  },
  {
    "path": "bfg-test/src/main/scala/com/madgag/git/bfg/test/unpackedRepo.scala",
    "chars": 4559,
    "preview": "package com.madgag.git.bfg.test\n\nimport com.madgag.git._\nimport com.madgag.git.test._\nimport org.eclipse.jgit.internal.s"
  },
  {
    "path": "build.sbt",
    "chars": 1253,
    "preview": "import ReleaseTransformations.*\nimport Dependencies.*\n\nThisBuild / organization := \"com.madgag\"\n\nThisBuild / scalaVersio"
  },
  {
    "path": "project/build.properties",
    "chars": 19,
    "preview": "sbt.version=1.10.7\n"
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  {
    "path": "project/dependencies.scala",
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    "preview": "import sbt._\n\nobject Dependencies {\n\n  val scalaGitVersion = \"5.0.3\"\n\n  val jgitVersionOverride = Option(System.getPrope"
  },
  {
    "path": "project/plugins.sbt",
    "chars": 321,
    "preview": "addSbtPlugin(\"com.github.sbt\" % \"sbt-release\" % \"1.4.0\")\n\naddSbtPlugin(\"org.xerial.sbt\" % \"sbt-sonatype\" % \"3.12.2\")\n\nad"
  },
  {
    "path": "version.sbt",
    "chars": 41,
    "preview": "ThisBuild / version := \"1.15.1-SNAPSHOT\"\n"
  }
]

About this extraction

This page contains the full source code of the rtyley/bfg-repo-cleaner GitHub repository, extracted and formatted as plain text for AI agents and large language models (LLMs). The extraction includes 100 files (203.9 KB), approximately 55.7k tokens. Use this with OpenClaw, Claude, ChatGPT, Cursor, Windsurf, or any other AI tool that accepts text input. You can copy the full output to your clipboard or download it as a .txt file.

Extracted by GitExtract — free GitHub repo to text converter for AI. Built by Nikandr Surkov.

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