maint(brain): add orphan node pruning script#92
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Move extractor_state from <data_dir>/extractor_state/<name>.json into an extractor_state table in brain.db so that state lifecycle matches DB lifecycle. Wiping the DB now also resets extractor progress, eliminating silent skip-all-reprocessing on reingest. - ExtractorRegistry.__init__ accepts optional db_path; creates extractor_state table (name TEXT PK, state_json TEXT, updated_at TEXT) - _save_state / _load_state use DB when db_path is set, JSON otherwise - Backwards-compat shim: on first load, if DB row is missing, import from legacy JSON file and migrate into DB - CLI (cmd_ingest) passes db_path to registry - Four new tests: DB persistence, DB lifecycle matches DB wipe, JSON fallback, legacy shim import Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
159 active nodes (4.8%) have no edges in derivation_edges. These accumulate from extraction runs that don't link new nodes to existing ones. Left alone they waste embedding space and dilute retrieval. `scripts/prune_orphans.py` reports orphan count, domain/type breakdown, and 5 sample nodes. Pass `--execute` to set decayed=1 on all orphans. Defaults to dry-run; reads DB path from core.config or falls back to data/graph.db relative to cashew root.
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159 active nodes (4.8% of 3,295) have no edges in
derivation_edges.These accumulate from extraction runs that don't link new nodes to
existing ones. Left alone they waste embedding space and dilute retrieval
quality over time.
scripts/prune_orphans.pyqueries for nodes whereidappears inneither
parent_idnorchild_idof any edge and prints a report:total count, breakdown by domain and node_type, and 5 sample nodes.
Run
--executeto setdecayed=1on all orphan nodes (reversible, nota delete). Defaults to
--dry-runif no flag is given. DB path is readfrom
core.config.get_db_path()with a fallback todata/graph.dbrelative to the cashew root.
Current orphan distribution: bunny 96, raj 62, user 1. Top types: fact
43, observation 36, commitment 35, derived 22.