GC: Repository corruption due to premature deletion of orphaned file

[syntonyze]

Version

7.6.0-SNAPSHOT

Operating System

Linux/Unix

Bug description

Run some traffic to a git repository (via Gerrit) and perform cyclic GCs via:

jgit --git-dir $REPO_PATH gc --preserve-oldpacks --no-pack-refs

Occasionally, the GC fails with MissingObjectException (See logs provided).
When analysing the problem, we notice that the previous run removed an "orphaned file" (possibly containing the missing object).

2026-02-26 04:29:45 +0100 [main] WARN org.eclipse.jgit.internal.storage.file.GC - Deleted orphaned file /path/repo.git/objects/pack/pack-c97999fd8c6889f32716a19cd50600b84b961606.idx

The associated packfile, however it can still be found on disk, and its creation time is the same time as the deleted orphaned file.

root@repo /path/repo.git/objects/pack # stat pack-c97999fd8c6889f32716a19cd50600b84b961606.pack
  File: pack-c97999fd8c6889f32716a19cd50600b84b961606.pack
  Size: 3445      	Blocks: 8          IO Block: 4096   regular file
Device: 10304h/66308d	Inode: 36226711    Links: 1
Access: (0444/-r--r--r--)  Uid: (    0/    root)   Gid: (    0/    root)
Access: 2026-02-26 04:29:45.925940419 +0100
Modify: 2026-02-26 04:29:45.901940626 +0100
Change: 2026-02-26 04:29:45.905940592 +0100
 Birth: 2026-02-26 04:29:45.901940626 +0100

Actual behavior

An IDX file is deleted because the related pack is not found on disk.

2026-02-26 04:29:45 +0100 [main] WARN org.eclipse.jgit.internal.storage.file.GC - Deleted orphaned file /path/repo.git/objects/pack/pack-c97999fd8c6889f32716a19cd50600b84b961606.idx

Expected behavior

Whilst I am not sure why the pack file cannot be found on disk (FS resolution, creation order?), I guess there would be a few things Jgit could do to make this logic more robust:

• At the very least it could re-try.
• Also, the idx file should not necessarily be removed, but moved to preserved and restored if necessary.
• Honour the prunePackExpire before removing it.

Relevant log output

Running: java_args='-Xss8m -Xms16g -Xmx16g' time /usr/local/bin/jgit-7.6.0-vanilla.sh --git-dir /path/repo.git gc --preserve-oldpacks --no-pack-refs
Counting objects:       220502
Finding sources:        100% (220502/220502)
Getting sizes:          100% (66371/66371)
Compressing objects:    100% (16269/16270)
Writing objects:        100% (220502/220502)
Selecting commits:      100% (45727/45727)
Building bitmaps:       100% (2410/2410)
org.eclipse.jgit.api.errors.JGitInternalException: Garbage collection failed.
        at org.eclipse.jgit.api.GarbageCollectCommand.call(GarbageCollectCommand.java:254)
        at org.eclipse.jgit.pgm.Gc.run(Gc.java:66)
        at org.eclipse.jgit.pgm.TextBuiltin.execute(TextBuiltin.java:239)
        at org.eclipse.jgit.pgm.Main.execute(Main.java:247)
        at org.eclipse.jgit.pgm.Main.run(Main.java:135)
        at org.eclipse.jgit.pgm.Main.main(Main.java:106)
        at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103)
        at java.base/java.lang.reflect.Method.invoke(Method.java:580)
        at org.springframework.boot.loader.launch.Launcher.launch(Launcher.java:106)
        at org.springframework.boot.loader.launch.Launcher.launch(Launcher.java:64)
        at org.springframework.boot.loader.launch.JarLauncher.main(JarLauncher.java:40)
Caused by: org.eclipse.jgit.errors.MissingObjectException: Missing unknown c43c0d58a8de747eb2d48d9c491f01960c9824ba
        at org.eclipse.jgit.internal.storage.file.WindowCursor.open(WindowCursor.java:149)
        at org.eclipse.jgit.lib.ObjectReader$1.open(ObjectReader.java:295)
        at org.eclipse.jgit.revwalk.RevWalk$2.next(RevWalk.java:1311)
        at org.eclipse.jgit.internal.storage.pack.PackWriter.findObjectsToPack(PackWriter.java:2070)
        at org.eclipse.jgit.internal.storage.pack.PackWriter.preparePack(PackWriter.java:1021)
        at org.eclipse.jgit.internal.storage.pack.PackWriter.preparePack(PackWriter.java:937)
        at org.eclipse.jgit.internal.storage.file.GC.writePack(GC.java:1336)
        at org.eclipse.jgit.internal.storage.file.GC.repack(GC.java:911)
        at org.eclipse.jgit.internal.storage.file.GC.doGc(GC.java:320)
        at org.eclipse.jgit.internal.storage.file.GC.gc(GC.java:250)
        at org.eclipse.jgit.api.GarbageCollectCommand.call(GarbageCollectCommand.java:236)
        ... 10 more
Command exited with non-zero status 1

Other information

Repo config:

[core]
	repositoryformatversion = 0
	filemode = true
	bare = true
	logallrefupdates = false
[gc]
	pruneExpire = 360.minutes.ago
	prunePackExpire = 120.minutes.ago
	auto = 0
	autoPacklimit = 0