Prompt hooks take 40-55s on large worktrees: go-git worktree.Status() walks gitignored directories (git status: 0.02s; patched locally to 193ms)

Summary

On a large worktree, entire hooks claude-code user-prompt-submit takes 39–55 seconds per prompt, nearly all of it in capture_pre_prompt_state and init_session. The same worktree's git status --porcelain completes in 0.02s. Root cause (confirmed by patching, see bottom): three hot paths still use go-git's worktree.Status(), which stats and hashes every file on disk — including gitignored directories — while several sibling call sites were already converted to the native git CLI for exactly this reason (e.g. the comments in checkpoint/ephemeral.go and strategy/manual_commit_hooks.go:getStagedFiles).

Environment

• Entire CLI 0.7.8 (also reproduced on 0.7.7); patched build based on main @ 4398a44
• macOS 15 (Darwin 25.5.0), arm64
• go1.26.4 darwin/arm64
• Agent: Claude Code, manual-commit strategy
• Swift monorepo: 61GB on disk, ~686k files — ~34GB of that in nine gitignored SwiftPM .build/ directories. git status --porcelain returns 0–21 lines.

What we did / measured

Ran the hook directly with a captured payload, then entire doctor trace with ENTIRE_LOG_LEVEL=DEBUG:

user-prompt-submit  45954ms
  STEP                      DURATION
  capture_pre_prompt_state   24397ms
  init_session               21540ms

Debug log — the 24s sits between hook start and the state-capture line, which found only 21 untracked files:

16:58:26.465  DEBUG hook invoked  hook=user-prompt-submit
16:58:50.873  DEBUG captured state before prompt  untracked_files=21 transcript_offset=0
16:59:12.420  DEBUG perf op=user-prompt-submit duration_ms=45954 steps.capture_pre_prompt_state_ms=24397 steps.init_session_ms=21540

Profile is I/O bound (~3s user / ~24s sys). Reproduces on every prompt. Comparison on the identical worktree: git status --porcelain = 0.02s real.

Turn-end shows the same signature: every turn-end in the log is followed 20–50s later by committed changes to shadow branch (that path hits DetectFileChanges, see below).

Ruled out

• Metadata branch divergence (repaired; doctor green — no timing change). Side note: doctor's cherry-pick reconciliation aborts on chains >1000 commits ("commit chain exceeded 1000 commits without reaching root"), which may deserve its own issue.
• .entire/tmp growth (162MB → 8KB — no change)
• Version 0.7.7 → 0.7.8 (identical timings)
• Removing 7.2GB of the ignored build dirs shaved ~5s — time scales with ignored-dir bytes.

Root cause + validated patch

The three remaining go-git worktree.Status() call sites on the hook path:

1. cmd/entire/cli/state.go — getUntrackedFilesForState (→ capture_pre_prompt_state, 24.4s)
2. cmd/entire/cli/strategy/manual_commit_hooks.go — calculatePromptAttributionAtStart (→ init_session, 21.5s)
3. cmd/entire/cli/state.go — DetectFileChanges (→ the 20–50s turn-end shadow-branch commit delay)

We patched locally: one exported strategy.GitCLIStatus() helper that runs git status --porcelain=v1 -z -uall --no-renames and parses it into a go-git-compatible git.Status map (porcelain v1 status letters are byte-identical to go-git's StatusCode values), then swapped it into all three sites, plus a one-line test-scaffold fix (.git/refs/ so the native CLI recognizes the hand-rolled test repos).

Result on the same repo, same trace tooling:

user-prompt-submit  193ms          (was 45954ms — ~238x)
  capture_pre_prompt_state  102ms  (was 24397ms)
  init_session               79ms  (was 21540ms)

go test ./cmd/entire/cli ./cmd/entire/cli/strategy: 989 passed; the single failure (TestRunUninstall_Force_NothingInstalled) is pre-existing and environment-dependent (fails identically on pristine main when the CLI is installed on the machine).

Per CONTRIBUTING.md we're opening this issue first: happy to submit the PR (patch + tests, mise lint/test, checkpoint trailers) on maintainer approval.

Side note (macOS packaging)

The Homebrew cask binary for 0.7.8 is ad-hoc signed / not notarized and hangs in _dyld_start under Gatekeeper on macOS 15, even after removing com.apple.quarantine. The install-script binary runs fine. Probably warrants a separate issue.

Start with getUntrackedFilesForState and DetectFileChanges in cmd/entire/cli/state.go, then inspect calculatePromptAttributionAtStart in cmd/entire/cli/strategy/manual_commit_hooks.go and the existing Git CLI usage in sibling strategy code. Run go test ./cmd/entire/cli ./cmd/entire/cli/strategy, including the hand-rolled repository fixtures. Done means hook and turn-end paths avoid scanning ignored files while preserving status results and the existing tests pass.