Canonicalize bead JSONL tracking

[jamestexas]

Summary

• Track/confirm .beads/beads.jsonl as the canonical bead content artifact.
• Route .beads/beads.jsonl through the beads-jsonl merge driver.
• Remove tracked legacy bd scaffold where present and update AGENTS.md bead guidance to rsry.
• Keep local bead DB/runtime state ignored.

Safety checks

• jq -s length .beads/beads.jsonl
• git check-attr merge -- .beads/beads.jsonl
• git diff --check HEAD~1..HEAD
• focused setup scan found no entire/entire-graph refs in git config, hooks, .beads setup files, .gitattributes, or AGENTS.md
• focused active-bd scan found no runnable bd guidance; only the canonical warning that there is no bd dolt push remains where AGENTS.md includes it

Note: branches were built from clean origin/main temp worktrees to avoid local dirty worktree state and local Entire hook files.