fix(server): checkpoints skip a project folder its parent repo ignores#14892

Projects nested inside a Git repository that ignores their directory currently fail baseline and turn checkpoint capture on every turn. This fixes #13712.

Capture uses the existing Git ignore classifier to distinguish an ignored directory from a staging failure. A wholly ignored project reports checkpointing as unsupported; baseline capture succeeds quietly and turn checkpoints become missing. If the directory contains tracked files, including newly staged files that have never been committed, capture records their current working contents without adding ignored new files. Scoped staged additions are seeded into the private checkpoint index, so unrelated staged changes stay out. Genuine Git failures keep their existing error handling. Nothing is force-added, and capture leaves the user's index untouched.

Maintainer takeover of #14892, preserving @JonasFocus's commits and merging main before rebuilding the tests and implementation. Thanks also to @ignaciorasetti for the earlier #13811 approach credited by the original author.

Verification:

• Three contributed behavior cases across two existing test files were rebuilt as five cases across the same files. The tracked-project fixture is shared across committed-only, staged-only, and mixed cases. All preexisting tests remain. The core Git driver and checkpoint service suites pass 68/68; the expanded focused run with VCS process and checkpoint store suites passes 120/120. The initial rebuild reproduced three failures against unchanged main; the staged-file review regression reproduced two failures before its fix.
• Tests cover ignored versus allowed siblings, committed and staged tracked edits after a directory becomes ignored, exclusion of ignored new files, absent unsupported refs, unchanged index bytes, and unsupported baseline/turn handling. Genuine clean-filter and timeout failures remain errors.
• Targeted lint, formatting, diff checks, and the server typecheck pass. No new diagnostic or ESLint suppressions were added.
• A headless integration probe ran the real checkpoint service, checkpoint store, VCS registry, and Git driver against disposable real repositories. The same probe loaded unchanged main for the before run and the rebuilt implementation for the after run:

The after run captured the expected edited file contents for all supported projects, excluded ignored secrets and unrelated staged changes, and preserved the original index bytes in all five cases. The ignored project emitted no capture warning. Additional actual-driver probes cover unusual filenames, intent-to-add, staged deletions, split and sparse indexes, manual index flags, unborn repositories, and failure propagation. This is a server behavior change, so proof is checkpoint status and Git tree output rather than screenshots. The probe used isolated fixture data and scoped subprocesses; no live userdata or provider agents were used.

Verification ran on headless Linux. Browser rendering, macOS, Windows, iOS, Android, Electron desktop, and relay/tunnel connections were not exercised.

Independent Opus and Sol whole-diff review ran for two rounds. Round one found that the private index could omit staged, uncommitted files in ignored directories. The shared regression fixture and scoped staged-addition import fix that issue; both reviewers found no blockers on the final revision.

Tests: Codex gpt-6-astra (high). Implementation: Codex gpt-6.1-sol (high). Reviews: Claude claude-opus-5-5 and Codex gpt-6-sol. Harnesses: Codex and Claude Code through T3 Code.