fix: prune stale install_meta skill/plugin rows whose files were deleted

[SherlockSalvatore]

Summary

Fixes #77. A skill or plugin whose files were deleted from disk (e.g. rm -rf ~/.claude) lingered forever as a ghost row in the Extensions list, still attributed to the agent it was installed under.

Root cause

sync_extensions and sync_extensions_for_agent exempted every row carrying install_meta from stale cleanup. That exemption is meant for CLI binaries, whose detection can transiently fail on startup (a CLI is resolved via PATH, which a GUI app may not fully inherit), so "missing from one scan" isn't proof it was removed. But the rule didn't look at the extension kind, so file-backed kinds (skill, plugin) were kept too — and a skill is a concrete file on disk, so "missing from scan" does mean the file is gone.

(Scanned MCP/hook entries carry no install_meta — they're entries in a shared config file — so they never hit this exemption and were already pruned by the normal path. This bug only affected skill/plugin.)

Fix

Narrow the exemption via a shared stale_row_should_prune predicate used by both sync paths:

• disabled rows → kept (intentionally absent from scans);
• CLI with install_meta → kept (flaky binary detection);
• file-backed install_meta rows → kept only while their source_path still exists on disk; pruned once the file is gone.

This removes ghosts after a real delete while still tolerating a transient scan gap (if the file is still on disk, the row is kept). Only the DB row is deleted — no on-disk files are touched. No schema change.

Test plan

• cargo test -p hk-core — 492 passing, incl. three new tests:
  • test_stale_row_should_prune_decision — the keep/prune decision matrix
  • test_sync_prunes_ghost_skill_when_files_deleted — global path: ghost pruned, live skill kept, CLI kept
  • test_sync_for_agent_prunes_ghost_skill_with_install_meta — same through the per-agent path
  • verified the ghost tests fail on the old behavior and pass on the new
• cargo clippy -p hk-core clean (no new warnings)

Before / After

Before (ghost row still listed under the agent):

After (ghost row gone after rescan):