* docs: add core commands reference and simplify README CLI section
- New docs/reference/core.md: reference for init (active options only,
copilot as main example), check, and version commands
- docs/toc.yml: add Core Commands under Reference
- README.md: replace verbose CLI Reference section (init options table,
30+ per-agent examples, deprecated flags, env vars) with links to
reference docs; use copilot as main example throughout
* docs: add CLI reference overview page
- New docs/reference/overview.md: explains each CLI surface area
(core, integrations, extensions, presets, workflows) with key
commands and links to detailed reference pages
- docs/toc.yml: add Overview as first item under Reference
- README.md: simplify CLI Reference to single link to overview page
* docs: remove command references from overview, keep paragraphs only
