tooling: add Beads workspace + beads agent skill

Checks in the portable parts of the Beads issue tracker that
this project now uses as its durable source of truth (per the
PLAN.md retirement). The Dolt DB internals (.beads/embeddeddolt/,
.beads/backup/, runtime sockets/locks/sync-state) stay
gitignored by .beads/.gitignore; what lands here are:

  .beads/.gitignore       — Beads-managed ignore rules
  .beads/README.md        — workspace README from bd init
  .beads/config.yaml      — workspace config (id, etc.)
  .beads/metadata.json    — workspace metadata
  .beads/issues.jsonl     — passive JSONL export of issues
  .beads/interactions.jsonl — passive log of state changes

The JSONL files are the human-readable / diffable surface; the
authoritative store remains the Dolt DB synced via refs/dolt/data
on the git remote (see Beads SYNC_CONCEPTS.md).

Also adds .agents/skills/beads/ — the beads agent skill that
tells subagents to use `bd` for task tracking instead of local
TODO files. Mirrors the rule already in CLAUDE.md but in a form
other agents and IDEs can pick up.

Closes the implementation side of bd-2nl (which removed the
.git/info/exclude rule that previously hid .beads/ from Git).