fix(cli): surface and safely remediate gitignore conflicts

[Traderfuz]

Intent

gh-axi automatically surfaces tracked repository-.gitignore conflicts on dashboard and before PR creation; TTY asks once with yes/no/always; fixes only untrack via git rm --cached preserving local files; report-only/non-TTY unless explicit --fix-ignore-conflicts; local Always preference; no commit/push/delete by hygiene; reusable push-preflight boundary; tests/docs included.

What Changed

• Added reusable gitignore hygiene detection and remediation that surfaces tracked .gitignore conflicts on the dashboard and before pull request creation, with TTY prompts, an always preference, report-only non-TTY behavior, and explicit --fix-ignore-conflicts support.
• Remediation only untracks conflicting files with git rm --cached, preserving local files and avoiding commits, pushes, or deletes; shared preflight handling is wired through the CLI, dashboard, and PR commands.
• Added comprehensive tests and updated user-facing documentation, help examples, and installed skill guidance.

Risk Assessment

✅ Low: The changed hygiene detection, explicit and interactive repair paths, atomic index handling, dashboard/PR integration, and remediation guidance are consistent with the stated intent; no material source-verifiable defects were found.

Testing

Ran 173 focused behavioral tests across hygiene, dashboard, PR creation, CLI routing, and help surfaces. The tests passed, and the worktree remained clean; no UI artifact applies to this CLI-only change.

Pipeline

Updates from git push no-mistakes

✅ **intent** - passed

✅ No issues found.

✅ **Rebase** - passed

✅ No issues found.

🔧 **Review** - 1 issue found → auto-fixed ✅

• ⚠️ src/commands/home.ts:110 - The dashboard reports hygiene findings but suggests gh-axi hygiene, a command that does not exist. Users following the guidance receive an unknown-command error; point them to the supported dashboard invocation or explicit --fix-ignore-conflicts flow.

🔧 Fix: Fixed dashboard hygiene remediation command
✅ Re-checked - no issues remain.

✅ **Test** - passed

✅ No issues found.

• pnpm exec vitest run test/gitignore-hygiene.test.ts test/commands/home.test.ts test/commands/pr.test.ts test/cli.test.ts test/help-examples.test.ts
• Focused tests exercised temporary Git repositories, detection, report-only behavior, explicit repair, local-file preservation, Always preference, dashboard routing, and PR preflight wiring.
• git diff --check ...

✅ **Document** - passed

✅ No issues found.

✅ **Lint** - passed

✅ No issues found.

✅ **Push** - passed

✅ No issues found.

[Traderfuz]

Closing this PR because advisory session-start context hooks added three unrelated files (.dev-os/notepad.md, AGENTS.md, CLAUDE.md). The feature will be republished from a clean branch with those hooks paused and restored after validation.

[greptile-apps]

Confidence Score: 4/5

The repair path should be fixed before merging because invocation from a repository subdirectory can claim conflicts were repaired while leaving them tracked.

The new remediation passes root-relative findings to a cwd-relative git rm with --ignore-unmatch, then treats the requested path count as proof of success, producing a reachable false-success result.

Files Needing Attention: src/gitignore-hygiene.ts

_{Reviews (1): Last reviewed commit: "no-mistakes(document): Updated formattin..." | Re-trigger Greptile}

[greptile-apps]

Subdirectory Repairs Report Success

When repair runs from a repository subdirectory, these repository-root-relative paths are resolved against the current directory, so git rm --ignore-unmatch can remove nothing but still succeed, causing the command to report fixed while the conflicts remain tracked.