Remove tracked Beads metadata

[MaxGhenis]

Summary

• remove tracked .beads metadata from the repository
• keep GitHub issues/PRs as the source of truth instead of repo-local Beads state

Closes #391.

Tests

• Not run; metadata-only removal.

[vahid-ahmadi]

Suggestions / things to flag

• Local hooks aren't covered by this PR. Remove tracked Beads metadata #391 mentions "local Beads hooks can block normal commits." Anyone who installed Beads locally will still have .git/hooks/* entries and a daemon — the PR description should probably mention that contributors who previously ran bd init may need to bd uninstall (or just delete the local hook scripts) to fully stop the sync attempts. Worth a one-line note in the PR body.
• Stale clones. After merge, anyone with the directory locally will keep an untracked .beads/ folder containing *.db, daemon.lock, etc. Not a blocker, but a heads-up in the merge commit / release notes is friendly.
• PR body says "Tests: Not run" — appropriate here; this is metadata-only and CI's existing test suite is sufficient validation.