chore: remove beads (bd) issue tracker from the repo (#668)

We weren't using beads as intended, and its git hooks were interfering with
commits (the pre-commit bd-sync hook aborted commits when the daemon flush
failed). Removes the only tracked artifact (.beads/issues.jsonl) and the
.gitignore entries. Local-only bits (the bd pre-commit/post-merge hooks, the
bd daemon, and the .beads/ working dir) are removed outside version control.

The real secret-scanning pre-commit hook that beads had displaced
(.git/hooks/pre-commit.backup) has been restored as the active hook.

Author: frankbria