fix(cli): ignore all runtime artifact directories

[cookerpapa]

Fixes #611.

The shared runtime gitignore list omits eight directories written during batch execution. Newly initialized projects leave those artifacts unprotected, and doctor incorrectly reports that all runtime entries are present.

This adds the eight directories to the list already shared by init, doctor and tracked-artifact detection. Project configuration and agent prompt overrides remain trackable. The command reference explains how existing projects can add the missing entries and untrack artifacts already in the index.

Validation on Node 24 / Linux:

• Three new CLI regressions fail on the unmodified base and pass with this change. Real CLI subprocesses and temporary Git repositories verify generated ignore rules, doctor output with eight/seven/no entries missing, and detection of already-tracked runtime files.
• All 47 targeted CLI/pattern tests pass.
• The upstream CI test selection passes: 3,604 tests, no skips.
• Full suite: 4,099 passed, 6 failed. The unmodified base has the same six Windows-path/base-agent lookup failures in files already excluded by upstream CI.
• Typecheck, lint, format, CLI help and changed-document link checks pass. Doctor's relevant diagnostics were exercised without a pi installation; its overall health status is consequently nonzero in these fixtures.

Base: 293d9a833ba685d4c2291a1d68e9b68b0271e00a.