Organized collections store metadata under a hidden .dorgy/ folder at the collection root:

• .dorgy/state.json — current collection metadata (paths, hashes, document IDs, search status).
• .dorgy/history.jsonl — append-only operation history for automation and audits.
• .dorgy/chroma/ — Chromadb index storage for semantic search.
• .dorgy/search.json — manifest describing the search index (counts, timestamps, enablement flags).
• .dorgy/classifications.json — cached classification results.
• .dorgy/vision.json — cached image captions when vision is enabled.
• .dorgy/quarantine/ — destination for corrupted files when configured.
• .dorgy/needs-review/ — staging area for low-confidence classifications.
• .dorgy/watch.log — rolling log written by dorgy watch batches.
• .dorgy/dorgy.log — shared CLI log.
• .dorgy/orig.json — snapshot of the original file structure used by dorgy undo.

See SPEC.md for additional context and lifecycle rules.