chore: reconcile SQLite shaping artifacts

[levifig]

Summary

• mark five SPEC-040 shaping ideas as absorbed by SPEC-040 in Markdown compatibility metadata
• preserve the worktree-only cwt/brave-joliot session before removing its redundant worktree
• keep the cleanup small after rescuing all worktree .agents trees under ~/.local/state/loaf/rescue/worktree-agents-20260531-012936

Verification

• git diff --check
• bin/loaf idea resolve --by SPEC-040
• bin/loaf state migrate markdown --apply

Note: bin/loaf state migrate markdown --apply --resume was rejected because those flags are mutually exclusive; reran with --apply only.