feat(cli): close the accepted design gaps of skillx add (lock, update, commit refs) #166

Split out of #163, item 5. The hardening items of #163 are handled in their own PR; these are product decisions accepted for the first version of skillx add (#120), not defects, so they are tracked here instead of widening that PR.

1. Lock and update. Added skills (add:<name>) are not recorded in skillx.lock.json, skillx update skips them and sync --locked does not restore them. Decide whether an add entry belongs in a packages lock (source, commit, tree digest) so update can re-resolve it and sync --locked can restore it byte-exact.
2. Scope. add installs into one runtime skills directory (--runtime). There is no project-scope install and no install into several agents in one run.
3. Commit refs. @ref and /tree/<ref> take branch and tag names only. A commit SHA would need git init + git fetch --depth 1 origin <sha> instead of clone --branch, and the server must allow fetching a reachable SHA.

Current behaviour is documented in docs/cli-reference.md under skillx add.