Flat vault enforcement: scan_vault now only picks up .md files at the vault root and inside protected folders (type/, config/, attachments/, _themes/, theme/). Files in arbitrary subfolders are no longer indexed. This prevents stray files from being included and enforces the flat vault convention where all notes live at the root. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>