git-absorb clears skip-worktree (index entry flags reset; file becomes visible again)

[Koswu]

Summary

Running git absorb (with absorb.autoStageIfNothingStaged=true) clears the skip-worktree bit on index entries. After git absorb, files previously marked via git update-index --skip-worktree <path> become visible as normal modified files again (unstaged), even though they were still skip-worktree before running git absorb.

In my repo, the index entry flags get reset to 0.

Steps to reproduce

1. Create and commit a file:

   echo "base" > .absorb-skip-worktree-repro.txt
   git add .absorb-skip-worktree-repro.txt
   git commit -m "repro: add .absorb-skip-worktree-repro.txt"

2. Mark it as skip-worktree and modify it:

   git update-index --skip-worktree .absorb-skip-worktree-repro.txt
   echo "local-only change" >> .absorb-skip-worktree-repro.txt

3. Enable auto-stage and run absorb:

   git config absorb.autoStageIfNothingStaged true
   git reset # unstage everything
   git absorb

Evidence (before vs after)

Before git absorb

skip-worktree is set and the file is NOT reported by status:

$ git ls-files -v -- .absorb-skip-worktree-repro.txt
S .absorb-skip-worktree-repro.txt

$ git status --porcelain=v1 -- .absorb-skip-worktree-repro.txt
# (no output)

Also, index debug flags are non-zero (indicating flags were present):

$ git ls-files --debug -- .absorb-skip-worktree-repro.txt
.absorb-skip-worktree-repro.txt
  ...
  flags: 40004000

After git absorb

The file becomes visible again as an unstaged modification, and the index entry flags are reset:

$ git ls-files -v -- .absorb-skip-worktree-repro.txt
H .absorb-skip-worktree-repro.txt

$ git status --porcelain=v1 -- .absorb-skip-worktree-repro.txt
 M .absorb-skip-worktree-repro.txt

$ git diff --cached -- .absorb-skip-worktree-repro.txt
# (no output; it was NOT staged)

$ git diff -- .absorb-skip-worktree-repro.txt
diff --git a/.absorb-skip-worktree-repro.txt b/.absorb-skip-worktree-repro.txt
index df967b96a5..54dd57f7b2 100644
--- a/.absorb-skip-worktree-repro.txt
+++ b/.absorb-skip-worktree-repro.txt
@@ -1 +1,2 @@
 base
+local-only change ...

$ git ls-files --debug -- .absorb-skip-worktree-repro.txt
.absorb-skip-worktree-repro.txt
  ...
  flags: 0

Expected behavior

git absorb should not clear or modify the skip-worktree bit (or any other unrelated index entry flags). Files marked skip-worktree should remain skip-worktree after running git absorb.

Actual behavior

• Before git absorb:
  • git ls-files -v shows S .absorb-skip-worktree-repro.txt
  • git status does not report the file
• After git absorb:
  • git ls-files -v no longer shows S (in my case it showed H)
  • git status reports the file as modified (unstaged)
  • git diff --cached is empty (so it was not staged)
  • git ls-files --debug shows the index entry flags: 0 (flags got reset)

Environment

• git-absorb version: 0.8.0
• git version: 2.39.5
• OS: Debian GNU/Linux 12 (bookworm) (WSL2 kernel 6.6.87.2-microsoft-standard-WSL2 )

[tummychow]

two things:

• if you do this without git-absorb, does the flag get preserved? (ie make a change, git add it manually, git commit --fixup it manually, git rebase -i manually)
• if you do this with git-absorb, but without auto staging, does the flag get preserved? (ie make a change, git add it manually, git absorb)

also stating for the record: i'm not going to accept a pr that fixes this by shelling out to the git cli. if it can't be done in libgit2, then i'm going to find (or file) an upstream issue

[Koswu]

ok, I will file an upstream issue then

[tummychow]

oh we can leave this issue open, i have an upstream label for things that are blocked on libgit2. just drop the link to the upstream issue here