help text: doctor, adf tidy --print-paths and adf vendor commands are missing or undocumented #363

Found during 2.0.0 release prep (#361).

• Root charter --help lists only charter doctor [--adf-only]. It is missing --ci, --format, and the hook-only --staged / --tidy-skipped flags from fix(hook): doctor gate only blocks on bloat in files the commit includes #360.
• charter adf --help lists --print-paths on the tidy line without describing it (feat(hook): pre-commit tidies only staged vendor files (#318 4/6) #356).
• Check the new adf vendor subcommands (status, set, init, restore, rename-legacy) and adf compile --mode against docs/cli-reference.md.

Fix the help text in place; adf.ts is near its LOC ceiling (1027/1041), so keep net lines at 0 there or move help strings out.