Update CLI reference docs — 4 subcommands missing

Update CLI reference docs — 4 subcommands missing.

Scope

docs/reference/cli.md is missing:

1. projio claude update-permissions — scopes Edit/Write in .claude/settings.json to project root, ensures MCP wildcards
2. projio skill new <name> — scaffold a new skill in .projio/skills/
3. projio skill list — list available skills
4. projio git untrack [--dry-run] — untrack files in projio gitignore block still tracked by git

Also: projio add docs should explicitly list claude as a valid package alongside biblio, notio, codio, indexio.

Approach

Read each command's implementation in src/projio/cli.py and add entries to cli.md matching existing format.

Related Notes

• issue-arash-20260331-172245-820267.md — Companion docs issue: MCP tools reference also has undocumented entries — both are doc-gap issues in the same projio reference suite
• issue-arash-20260331-171537-647473.md — Directly overlaps: covers projio add claude and projio claude update-permissions, the same subcommands that need docs here
• issue-arash-20260328-193353-406929.md — CLI subcommand output bug — fixing silent CLI and documenting CLI subcommands are related CLI health tasks

Batch Result

• status: done
• batch queue_id: 2dfdd2e244d7
• session: 4ff59117-10a7-42f1-8cbe-1b1300021fe4
• batch duration: 444.5s