Refactor: fail closed on read_dir entry I/O errors

[jon-devlapaz]

Summary

Several inventory walks drop directory-entry errors via filter_map(|e| e.ok()), which can silently omit skills or catalog rows under partial I/O failure.

Locations

• src/check.rs — project skill listing
• src/skills.rs — multi-skill discover under skills/
• src/catalog.rs — by-project catalog listing

Design target

Propagate read_dir / entry errors as explicit Error (existing map_io style) unless a documented skip reason already exists (symlinks, ignore names).

Acceptance

• Partial read failures fail the command with a path-bearing message
• Acceptance or unit coverage for at least one path if easily forced; otherwise document intentional remaining skips only
• No behavior change on healthy trees

Priority

Low — correctness hygiene; independent slice.