Update CLI reference docs — 4 subcommands missing

Update CLI reference docs — 4 subcommands missing.

Scope¶

docs/reference/cli.md is missing:

projio claude update-permissions — scopes Edit/Write in .claude/settings.json to project root, ensures MCP wildcards
projio skill new <name> — scaffold a new skill in .projio/skills/
projio skill list — list available skills
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.

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

[[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