Git LFS prune deletes staged objects #5636
Description
Describe the bug
Staged LFS files are deleted by git lfs prune. If I create a commit after that, the commit is broken and cannot be pushed. Even worse, if I have multiple local commits, I have permanently lost data. Note, --verify-remote does not prevent this
To Reproduce
Steps to reproduce the behavior:
git init
git lfs install
git lfs track myfile.data
git add .
git lfs prune
Verify that the LFS objects have been deleted from .git/lfs/objects
Expected behavior
Staged files should be retained in the same way as stashed or reachable files.
--verify-remote should check every file that is deleted, I guess?
System environment
macOS 13.4
Output of git lfs env
git-lfs/3.4.0 (GitHub; darwin arm64; go 1.20.6)
git version 2.42.0
Endpoint=https://github.com/jochenhz/lfs-bug.git/info/lfs (auth=basic)
LocalWorkingDir=/Users/jochenhunz/Downloads/gitlfs-bug/lfs-bug
LocalGitDir=/Users/jochenhunz/Downloads/gitlfs-bug/lfs-bug/.git
LocalGitStorageDir=/Users/jochenhunz/Downloads/gitlfs-bug/lfs-bug/.git
LocalMediaDir=/Users/jochenhunz/Downloads/gitlfs-bug/lfs-bug/.git/lfs/objects
LocalReferenceDirs=
TempDir=/Users/jochenhunz/Downloads/gitlfs-bug/lfs-bug/.git/lfs/tmp
ConcurrentTransfers=8
TusTransfers=false
BasicTransfersOnly=false
SkipDownloadErrors=false
FetchRecentAlways=false
FetchRecentRefsDays=7
FetchRecentCommitsDays=0
FetchRecentRefsIncludeRemotes=true
PruneOffsetDays=3
PruneVerifyRemoteAlways=false
PruneRemoteName=origin
LfsStorageDir=/Users/jochenhunz/Downloads/gitlfs-bug/lfs-bug/.git/lfs
AccessDownload=basic
AccessUpload=basic
DownloadTransfers=basic,lfs-standalone-file,ssh
UploadTransfers=basic,lfs-standalone-file,ssh
GIT_EXEC_PATH=/opt/homebrew/opt/git/libexec/git-core
git config filter.lfs.process = "git-lfs filter-process"
git config filter.lfs.smudge = "git-lfs smudge -- %f"
git config filter.lfs.clean = "git-lfs clean -- %f"