Replaces blanket `git add -A` in `commitOrAmendMergeWithFixes` with an
explicit allowlist of (squash-staged ∪ fix-agent-modified) paths, so
unrelated dirty files in the project root no longer get swept into a
task's squash commit. The in-merge fix agent now snapshots the working
tree before/after its session to capture exactly which files it touched.
Hardens the git invocations the allowlist relies on:
- All `git add` and `git checkout --ours/--theirs` calls switched from
shell-interpolated `execAsync` to `execFile` array form, eliminating
path-injection surface and batching per-file spawns into one call.
- `snapshotDirtyFiles` adopts `git -z` NUL-delimited parsing so paths
with embedded spaces or specials are handled correctly.
- Long allowlist debug logs are truncated to 20 entries with an overflow
marker.
Refused-to-stage paths emit a warn naming each file so the user can
audit what was filtered.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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