index emptied between staging and commit resulting in `git commit` recording an empty tree

What happened?

Staging and then commiting files can sometimes result in a commit deleting the entire repository.

Example (commands run by a person in a terminal window in a dev container):

$ # make a change to the file hello-express/server.js
$ git status  # tree is normal
On branch main
Your branch is ahead of 'origin/main' by 4 commits.
  (use "git push" to publish your local commits)

Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git restore <file>..." to discard changes in working directory)
	modified:   hello-express/server.js

no changes added to commit (use "git add" and/or "git commit -a")

$ git status ; git add hello-express/server.js ; sleep 1 ; git status  # index is deleted while entire does its work
On branch main
Your branch is ahead of 'origin/main' by 4 commits.
  (use "git push" to publish your local commits)

Changes to be committed:
  (use "git restore --staged <file>..." to unstage)
	deleted:    .claude/rules/behavior.md
	deleted:    .claude/rules/knowledge-graph.md
	deleted:    .claude/rules/memory.md
	deleted:    .claude/settings.json
	deleted:    .claude/skills/graphify/.graphify_version
	deleted:    .claude/skills/graphify/SKILL.md
	deleted:    .claude/skills/graphify/references/add-watch.md
	deleted:    .claude/skills/graphify/references/exports.md
	deleted:    .claude/skills/graphify/references/extraction-spec.md
	deleted:    .claude/skills/graphify/references/github-and-merge.md
	deleted:    .claude/skills/graphify/references/hooks.md
	deleted:    .claude/skills/graphify/references/query.md
	deleted:    .claude/skills/graphify/references/transcribe.md
	deleted:    .claude/skills/graphify/references/update.md
	deleted:    .devcontainer/DISABLED_init-firewall.sh
	deleted:    .devcontainer/Dockerfile
	deleted:    .devcontainer/container-post-start-root.sh
	deleted:    .devcontainer/container-post-start-user.sh
	deleted:    .devcontainer/devcontainer.json
	deleted:    .entire/.gitignore
	deleted:    .entire/settings.json
	deleted:    .gitattributes
	deleted:    .githooks/commit-msg
	deleted:    .githooks/post-commit
	deleted:    .githooks/post-merge
	deleted:    .githooks/post-rewrite
	deleted:    .githooks/pre-push
	deleted:    .githooks/prepare-commit-msg
	deleted:    .gitignore
	deleted:    .mcp.json
	deleted:    CLAUDE.md
	deleted:    README.md
	deleted:    docs/agents/domain.md
	deleted:    docs/agents/issue-tracker.md
	deleted:    docs/agents/triage-labels.md
	deleted:    graphify-out/graph.json
	deleted:    hello-express/.gitignore
	deleted:    hello-express/package-lock.json
	deleted:    hello-express/package.json
	deleted:    hello-express/server.js
	deleted:    scripts/bootstrap-git-hooks.sh

Untracked files:
  (use "git add <file>..." to include in what will be committed)
	.claude/
	.devcontainer/
	.entire/
	.gitattributes
	.githooks/
	.gitignore
	.mcp.json
	CLAUDE.md
	README.md
	docs/
	graphify-out/
	hello-express/
	scripts/

On branch main
Your branch is ahead of 'origin/main' by 4 commits.
  (use "git push" to publish your local commits)

Changes to be committed:
  (use "git restore --staged <file>..." to unstage)
	modified:   hello-express/server.js


$ sleep 10 ; git status  # entire completes its work, tree goes back to normal
On branch main
Your branch is ahead of 'origin/main' by 4 commits.
  (use "git push" to publish your local commits)

Changes to be committed:
  (use "git restore --staged <file>..." to unstage)
	modified:   hello-express/server.js


$ 

To work around this problem, both people and agents need to insert a long enough delay between the git add and git commit, or check the status and only proceed to the commit if/when the number of files to be committed matches what we expect to be committed.

If the empty tree accidentally gets committed, git reset --mixed HEAD~1 can be used to revert back to the last good commit.

Steps to reproduce

This does not happen every time, but can be reproduced in a small number of attempts (under 5). Note I'm running in a container with limited CPU and RAM, which may trigger the problem more than a less resource-constrained environment.

1. Modify a file in the repo
2. git status shows everything is as expected
3. git add NAME_OF_FILE ; sleep 1 ; git status shows the problem (does not happen every time)
4. git status after a few more seconds shows the problem has resolved itself. But if either a person or an agent runs git commit while the problem still exists (between steps 3 and 4), then all files are deleted from the git tree.

Entire CLI version

Entire CLI 0.10.2 Go version: go1.26.6 OS/Arch: linux/arm64

OS and architecture

Linux 6.12.76-linuxkit aarch64 GNU/Linux

Agent

Claude Code

Terminal

Zed

Logs / debug output

{"time":"2026-08-22T11:37:36.121720177-04:00","level":"INFO","msg":"turn-start","session_id":"cf0a7299-d289-44c6-a782-37d5e5419e19","component":"lifecycle","agent":"claude-code","event":"TurnStart","session_id":"cf0a7299-d289-44c6-a782-37d5e5419e19","session_ref":"/home/node/.claude/projects/-workspace/cf0a7299-d289-44c6-a782-37d5e5419e19.jsonl","model":""}
{"time":"2026-08-22T11:37:36.158698511-04:00","level":"INFO","msg":"phase transition","session_id":"cf0a7299-d289-44c6-a782-37d5e5419e19","component":"session","agent":"claude-code","session_id":"cf0a7299-d289-44c6-a782-37d5e5419e19","event":"TurnStart","from":"idle","to":"active"}
{"time":"2026-08-22T11:40:02.648421467-04:00","level":"INFO","msg":"prepare-commit-msg: agent commit trailer added","session_id":"cf0a7299-d289-44c6-a782-37d5e5419e19","component":"checkpoint","strategy":"manual-commit","source":"message","checkpoint_id":"01M0N221PRZM8XPS7ZGCZWWFJW","session_id":"cf0a7299-d289-44c6-a782-37d5e5419e19"}
{"time":"2026-08-22T11:40:04.690928177-04:00","level":"INFO","msg":"session condensed","session_id":"cf0a7299-d289-44c6-a782-37d5e5419e19","component":"checkpoint","strategy":"manual-commit","session_id":"cf0a7299-d289-44c6-a782-37d5e5419e19","checkpoint_id":"01M0N221PRZM8XPS7ZGCZWWFJW","checkpoints_condensed":2,"transcript_lines":392}
{"time":"2026-08-22T11:40:04.70602176-04:00","level":"INFO","msg":"post-commit: carried forward remaining files","session_id":"cf0a7299-d289-44c6-a782-37d5e5419e19","component":"checkpoint","session_id":"cf0a7299-d289-44c6-a782-37d5e5419e19","remaining_files":1}
{"time":"2026-08-22T11:40:04.710591718-04:00","level":"INFO","msg":"shadow branch deleted","session_id":"cf0a7299-d289-44c6-a782-37d5e5419e19","component":"checkpoint","strategy":"manual-commit","shadow_branch":"entire/7d296d6-e3b0c4"}
{"time":"2026-08-22T11:40:04.71061976-04:00","level":"WARN","msg":"perf","session_id":"cf0a7299-d289-44c6-a782-37d5e5419e19","component":"perf","op":"post-commit","duration_ms":2009,"slow":true,"steps.open_repository_and_head_ms":2,"steps.find_sessions_for_worktree_ms":2,"steps.resolve_commit_trees_ms":6,"steps.process_sessions_ms":1991,"steps.process_sessions.0_ms":1991,"steps.process_sessions.0.resolve_shadow_branch_ms":0,"steps.process_sessions.0.check_session_content_ms":535,"steps.process_sessions.0.transition_and_condense_ms":1437,"steps.process_sessions.0.extract_session_data_ms":1089,"steps.process_sessions.0.redact_transcript_ms":252,"steps.process_sessions.0.calculate_session_attribution_ms":0,"steps.process_sessions.0.write_committed_v1_ms":84,"steps.process_sessions.0.write_committed_v1.chunk_transcript_ms":0,"steps.process_sessions.0.write_committed_v1.chunk_transcript.write_transcript_blobs_ms":33,"steps.process_sessions.0.write_committed_v1.chunk_transcript.write_transcript_blobs.write_transcript_content_hash_ms":2,"steps.process_sessions.0.write_committed_v1.write_compact_transcript_ms":35,"steps.process_sessions.0.carry_forward_files_ms":15,"steps.process_sessions.0.write_carry_forward_shadow_ms":13,"steps.cleanup_shadow_branches_ms":1,"hook_type":"git"}
{"time":"2026-08-22T11:41:33.629912343-04:00","level":"INFO","msg":"prepare-commit-msg: agent commit trailer added","session_id":"cf0a7299-d289-44c6-a782-37d5e5419e19","component":"checkpoint","strategy":"manual-commit","source":"message","checkpoint_id":"01M0N24THXB9W0FZFZ23YZWDK0","session_id":"cf0a7299-d289-44c6-a782-37d5e5419e19"}
{"time":"2026-08-22T11:41:34.577849885-04:00","level":"INFO","msg":"attribution calculated","session_id":"cf0a7299-d289-44c6-a782-37d5e5419e19","component":"attribution","agent_lines":70,"human_added":270,"human_modified":0,"human_removed":0,"total_committed":340,"agent_percentage":8.31353919239905,"accumulated_user_added":0,"accumulated_user_removed":0,"files_touched":1}
{"time":"2026-08-22T11:41:34.688973802-04:00","level":"INFO","msg":"session condensed","session_id":"cf0a7299-d289-44c6-a782-37d5e5419e19","component":"checkpoint","strategy":"manual-commit","session_id":"cf0a7299-d289-44c6-a782-37d5e5419e19","checkpoint_id":"01M0N24THXB9W0FZFZ23YZWDK0","checkpoints_condensed":2,"transcript_lines":436}
{"time":"2026-08-22T11:41:34.70366226-04:00","level":"INFO","msg":"shadow branch deleted","session_id":"cf0a7299-d289-44c6-a782-37d5e5419e19","component":"checkpoint","strategy":"manual-commit","shadow_branch":"entire/82083e2-e3b0c4"}
{"time":"2026-08-22T11:42:03.310612218-04:00","level":"INFO","msg":"turn-end","session_id":"cf0a7299-d289-44c6-a782-37d5e5419e19","component":"lifecycle","agent":"claude-code","event":"TurnEnd","session_id":"cf0a7299-d289-44c6-a782-37d5e5419e19","session_ref":"/home/node/.claude/projects/-workspace/cf0a7299-d289-44c6-a782-37d5e5419e19.jsonl","model":""}
{"time":"2026-08-22T11:42:03.964946551-04:00","level":"INFO","msg":"no files modified during session, skipping checkpoint","session_id":"cf0a7299-d289-44c6-a782-37d5e5419e19","component":"lifecycle","agent":"claude-code"}
{"time":"2026-08-22T11:42:03.966716968-04:00","level":"INFO","msg":"phase transition","session_id":"cf0a7299-d289-44c6-a782-37d5e5419e19","component":"session","agent":"claude-code","session_id":"cf0a7299-d289-44c6-a782-37d5e5419e19","event":"TurnEnd","from":"active","to":"idle"}
{"time":"2026-08-22T11:42:03.966726426-04:00","level":"INFO","msg":"finalizing turn checkpoints with full transcript","session_id":"cf0a7299-d289-44c6-a782-37d5e5419e19","component":"checkpoint","agent":"claude-code","session_id":"cf0a7299-d289-44c6-a782-37d5e5419e19","checkpoint_count":2}
{"time":"2026-08-22T11:42:04.351615927-04:00","level":"INFO","msg":"finalize: checkpoint updated with full transcript","session_id":"cf0a7299-d289-44c6-a782-37d5e5419e19","component":"checkpoint","agent":"claude-code","checkpoint_id":"01M0N221PRZM8XPS7ZGCZWWFJW","session_id":"cf0a7299-d289-44c6-a782-37d5e5419e19"}
{"time":"2026-08-22T11:42:04.414681427-04:00","level":"INFO","msg":"finalize: checkpoint updated with full transcript","session_id":"cf0a7299-d289-44c6-a782-37d5e5419e19","component":"checkpoint","agent":"claude-code","checkpoint_id":"01M0N24THXB9W0FZFZ23YZWDK0","session_id":"cf0a7299-d289-44c6-a782-37d5e5419e19"}
{"time":"2026-08-22T11:59:49.696391086-04:00","level":"INFO","msg":"turn-start","session_id":"cf0a7299-d289-44c6-a782-37d5e5419e19","component":"lifecycle","agent":"claude-code","event":"TurnStart","session_id":"cf0a7299-d289-44c6-a782-37d5e5419e19","session_ref":"/home/node/.claude/projects/-workspace/cf0a7299-d289-44c6-a782-37d5e5419e19.jsonl","model":""}

Additional context

No response

Reproduce the reported sequence with git status, git add, a delay, and git commit in a constrained container, then trace the Git hook and checkpoint/post-commit flow named in the logs. Done means the index cannot transiently represent the whole repository as deleted during processing, so a normal commit never records an empty tree; add regression coverage for the observed race if the existing test layout identifies a suitable location.