nlm-memory 0.9.1 → 0.10.0

package/migrations/014_sources_cursor.sql

@@ -0,0 +1,30 @@
+-- Migration 014: add 'cursor' to the sources.kind CHECK constraint.
+--
+-- SQLite does not support ALTER COLUMN to modify CHECK constraints in place.
+-- Standard approach: rename → recreate → copy → drop old.
+
+PRAGMA foreign_keys = OFF;
+
+CREATE TABLE sources_new (
+  id            INTEGER PRIMARY KEY AUTOINCREMENT,
+  kind          TEXT    NOT NULL CHECK (kind IN ('claude-code', 'hermes', 'hermes-agent', 'aider', 'cursor', 'opencode', 'pi', 'jsonl-generic', 'webhook')),
+  name          TEXT    NOT NULL UNIQUE,
+  path_or_url   TEXT,
+  runtime_label TEXT    NOT NULL,
+  parse_config  TEXT    NOT NULL DEFAULT '{}',
+  enabled       INTEGER NOT NULL DEFAULT 1,
+  token         TEXT,
+  created_at    TEXT    NOT NULL DEFAULT (datetime('now')),
+  updated_at    TEXT    NOT NULL DEFAULT (datetime('now'))
+);
+
+INSERT INTO sources_new SELECT id, kind, name, path_or_url, runtime_label, parse_config, enabled, token, created_at, updated_at FROM sources;
+
+DROP TABLE sources;
+ALTER TABLE sources_new RENAME TO sources;
+
+CREATE INDEX IF NOT EXISTS idx_sources_enabled ON sources(enabled) WHERE enabled = 1;
+
+PRAGMA foreign_keys = ON;
+
+INSERT OR IGNORE INTO schema_migrations (version, name) VALUES (14, '014_sources_cursor');

package/migrations/015_sources_windsurf.sql

@@ -0,0 +1,30 @@
+-- Migration 015: add 'windsurf' to the sources.kind CHECK constraint.
+--
+-- SQLite does not support ALTER COLUMN to modify CHECK constraints in place.
+-- Standard approach: rename → recreate → copy → drop old.
+
+PRAGMA foreign_keys = OFF;
+
+CREATE TABLE sources_new (
+  id            INTEGER PRIMARY KEY AUTOINCREMENT,
+  kind          TEXT    NOT NULL CHECK (kind IN ('claude-code', 'hermes', 'hermes-agent', 'aider', 'cursor', 'windsurf', 'opencode', 'pi', 'jsonl-generic', 'webhook')),
+  name          TEXT    NOT NULL UNIQUE,
+  path_or_url   TEXT,
+  runtime_label TEXT    NOT NULL,
+  parse_config  TEXT    NOT NULL DEFAULT '{}',
+  enabled       INTEGER NOT NULL DEFAULT 1,
+  token         TEXT,
+  created_at    TEXT    NOT NULL DEFAULT (datetime('now')),
+  updated_at    TEXT    NOT NULL DEFAULT (datetime('now'))
+);
+
+INSERT INTO sources_new SELECT id, kind, name, path_or_url, runtime_label, parse_config, enabled, token, created_at, updated_at FROM sources;
+
+DROP TABLE sources;
+ALTER TABLE sources_new RENAME TO sources;
+
+CREATE INDEX IF NOT EXISTS idx_sources_enabled ON sources(enabled) WHERE enabled = 1;
+
+PRAGMA foreign_keys = ON;
+
+INSERT OR IGNORE INTO schema_migrations (version, name) VALUES (15, '015_sources_windsurf');

package/migrations/016_sources_codex.sql

@@ -0,0 +1,30 @@
+-- Migration 016: add 'codex' to the sources.kind CHECK constraint.
+--
+-- SQLite does not support ALTER COLUMN to modify CHECK constraints in place.
+-- Standard approach: rename → recreate → copy → drop old.
+
+PRAGMA foreign_keys = OFF;
+
+CREATE TABLE sources_new (
+  id            INTEGER PRIMARY KEY AUTOINCREMENT,
+  kind          TEXT    NOT NULL CHECK (kind IN ('claude-code', 'codex', 'hermes', 'hermes-agent', 'aider', 'cursor', 'windsurf', 'opencode', 'pi', 'jsonl-generic', 'webhook')),
+  name          TEXT    NOT NULL UNIQUE,
+  path_or_url   TEXT,
+  runtime_label TEXT    NOT NULL,
+  parse_config  TEXT    NOT NULL DEFAULT '{}',
+  enabled       INTEGER NOT NULL DEFAULT 1,
+  token         TEXT,
+  created_at    TEXT    NOT NULL DEFAULT (datetime('now')),
+  updated_at    TEXT    NOT NULL DEFAULT (datetime('now'))
+);
+
+INSERT INTO sources_new SELECT id, kind, name, path_or_url, runtime_label, parse_config, enabled, token, created_at, updated_at FROM sources;
+
+DROP TABLE sources;
+ALTER TABLE sources_new RENAME TO sources;
+
+CREATE INDEX IF NOT EXISTS idx_sources_enabled ON sources(enabled) WHERE enabled = 1;
+
+PRAGMA foreign_keys = ON;
+
+INSERT OR IGNORE INTO schema_migrations (version, name) VALUES (16, '016_sources_codex');

package/migrations/017_signals.sql

@@ -0,0 +1,31 @@
+-- Migration 017: signals - agent self-improvement telemetry lane.
+--
+-- Distinct from facts: append-only, idempotent on a deterministic id, no
+-- supersedence pointer, no embeddings. No FK to sessions; a signal can arrive
+-- before or without a session row, session_id is a soft link.
+
+CREATE TABLE IF NOT EXISTS signals (
+  id            TEXT PRIMARY KEY,
+  v             INTEGER NOT NULL DEFAULT 1,
+  install_scope TEXT NOT NULL,
+  kind          TEXT NOT NULL CHECK (kind IN ('gate', 'eval', 'review', 'test')),
+  producer      TEXT NOT NULL,
+  outcome       TEXT NOT NULL CHECK (outcome IN ('pass', 'fail', 'fix', 'exhausted')),
+  model         TEXT NOT NULL,
+  repo          TEXT NOT NULL,
+  step          TEXT,
+  detail        TEXT,
+  session_id    TEXT,
+  ts            TEXT NOT NULL,
+  created_at    TEXT NOT NULL DEFAULT (datetime('now'))
+);
+
+-- Aggregation hot path: failure-mode roll-up scoped to an install + repo/model.
+CREATE INDEX IF NOT EXISTS idx_signals_agg
+  ON signals(install_scope, repo, model, kind, step);
+
+-- Retention prune + recency window scans.
+CREATE INDEX IF NOT EXISTS idx_signals_ts
+  ON signals(ts);
+
+INSERT OR IGNORE INTO schema_migrations (version, name) VALUES (17, '017_signals');

package/migrations/018_repair_self_supersede.sql

@@ -0,0 +1,21 @@
+-- Migration 018: repair self-supersedence damage.
+--
+-- The SQLite scanOnce path set supersedes = prior.session_id with no self-id
+-- guard. Adapter session ids are deterministic, so a resumed (grown) transcript
+-- re-ingested under the SAME id and insertSession wrote a self-loop edge
+-- (id -> id, 'supersedes') then flipped that same row to status='superseded'.
+-- Result: a session that supersedes itself and is marked superseded with no
+-- real successor. The code fix guards both the scan path and insertSession;
+-- this migration repairs rows already damaged.
+
+DELETE FROM session_edges WHERE from_session = to_session AND kind = 'supersedes';
+
+-- Restore sessions wrongly marked superseded: a legitimately superseded row
+-- keeps a real incoming 'supersedes' edge (some other session -> it). Rows with
+-- no remaining incoming edge were only self-superseded and should be 'closed'.
+UPDATE sessions
+SET status = 'closed', updated_at = datetime('now')
+WHERE status = 'superseded'
+  AND id NOT IN (SELECT to_session FROM session_edges WHERE kind = 'supersedes');
+
+INSERT OR IGNORE INTO schema_migrations (version, name) VALUES (18, '018_repair_self_supersede');

package/migrations/019_split_replaces.sql

@@ -0,0 +1,117 @@
+-- nlm:no-wrap
+-- Migration 019: split the mechanical `replaces` relation out of `supersedes`.
+--
+-- Two relations were overloaded onto one edge kind ('supersedes') and one
+-- status ('superseded'): mechanical re-ingest of a grown transcript
+-- (supersede-on-resume) and operator-asserted epistemic overturn. This
+-- migration introduces edge kind 'replaces' + status 'replaced' for the
+-- mechanical case and reclassifies existing rows.
+--
+-- The mechanical signature is exact, no heuristics: an edge whose two sessions
+-- share the same transcript_path is a re-parse (replaces); different paths is
+-- operator supersedence (untouched). See
+-- docs/plans/2026-06-10-supersedence-split.md.
+--
+-- Widening the CHECK constraints on sessions.status and session_edges.kind
+-- requires a table rebuild (SQLite cannot ALTER a CHECK constraint, and
+-- better-sqlite3 forbids writable_schema edits). The rebuild runs under
+-- foreign_keys=OFF so dropping the old `sessions` table does not cascade-delete
+-- its dependents; the pragma is a no-op inside a transaction, hence nlm:no-wrap.
+
+PRAGMA foreign_keys = OFF;
+
+BEGIN;
+
+-- ── Rebuild sessions with the widened status CHECK ──────────────────────────
+DROP TRIGGER IF EXISTS sessions_ai;
+DROP TRIGGER IF EXISTS sessions_au;
+DROP TRIGGER IF EXISTS sessions_ad;
+
+CREATE TABLE sessions_new (
+  id                  TEXT PRIMARY KEY,
+  runtime             TEXT NOT NULL,
+  runtime_session_id  TEXT,
+  started_at          TEXT NOT NULL,
+  ended_at            TEXT,
+  duration_min        INTEGER,
+  label               TEXT NOT NULL,
+  summary             TEXT NOT NULL,
+  body                TEXT,
+  status              TEXT NOT NULL CHECK(status IN ('active','closed','superseded','replaced')),
+  transcript_kind     TEXT,
+  transcript_path     TEXT,
+  transcript_offset   INTEGER,
+  transcript_length   INTEGER,
+  created_at          TEXT NOT NULL DEFAULT (datetime('now')),
+  updated_at          TEXT NOT NULL DEFAULT (datetime('now'))
+);
+
+INSERT INTO sessions_new
+  (id, runtime, runtime_session_id, started_at, ended_at, duration_min,
+   label, summary, body, status, transcript_kind, transcript_path,
+   transcript_offset, transcript_length, created_at, updated_at)
+SELECT
+  id, runtime, runtime_session_id, started_at, ended_at, duration_min,
+  label, summary, body, status, transcript_kind, transcript_path,
+  transcript_offset, transcript_length, created_at, updated_at
+FROM sessions;
+
+DROP TABLE sessions;
+ALTER TABLE sessions_new RENAME TO sessions;
+
+CREATE INDEX IF NOT EXISTS idx_sessions_started_at ON sessions(started_at DESC);
+CREATE INDEX IF NOT EXISTS idx_sessions_status ON sessions(status);
+CREATE INDEX IF NOT EXISTS idx_sessions_runtime ON sessions(runtime);
+
+CREATE TRIGGER sessions_ai AFTER INSERT ON sessions BEGIN
+  INSERT INTO sessions_fts(rowid, label, summary, body)
+  VALUES (new.rowid, new.label, new.summary, new.body);
+END;
+CREATE TRIGGER sessions_au AFTER UPDATE ON sessions BEGIN
+  INSERT INTO sessions_fts(sessions_fts, rowid, label, summary, body)
+  VALUES('delete', old.rowid, old.label, old.summary, old.body);
+  INSERT INTO sessions_fts(rowid, label, summary, body)
+  VALUES (new.rowid, new.label, new.summary, new.body);
+END;
+CREATE TRIGGER sessions_ad AFTER DELETE ON sessions BEGIN
+  INSERT INTO sessions_fts(sessions_fts, rowid, label, summary, body)
+  VALUES('delete', old.rowid, old.label, old.summary, old.body);
+END;
+
+-- The rebuild reassigned rowids; rebuild the external-content FTS index so its
+-- rowid → session mapping matches the new sessions table.
+INSERT INTO sessions_fts(sessions_fts) VALUES('rebuild');
+
+-- ── Rebuild session_edges with the widened kind CHECK ───────────────────────
+CREATE TABLE session_edges_new (
+  from_session        TEXT NOT NULL REFERENCES sessions(id) ON DELETE CASCADE,
+  to_session          TEXT NOT NULL REFERENCES sessions(id) ON DELETE CASCADE,
+  kind                TEXT NOT NULL CHECK(kind IN ('supersedes','replaces','continues','branched_from','merged_from')),
+  PRIMARY KEY (from_session, to_session, kind)
+);
+
+INSERT INTO session_edges_new (from_session, to_session, kind)
+SELECT from_session, to_session, kind FROM session_edges;
+
+DROP TABLE session_edges;
+ALTER TABLE session_edges_new RENAME TO session_edges;
+
+CREATE INDEX IF NOT EXISTS idx_session_edges_from ON session_edges(from_session);
+CREATE INDEX IF NOT EXISTS idx_session_edges_to ON session_edges(to_session);
+CREATE INDEX IF NOT EXISTS idx_session_edges_kind ON session_edges(kind);
+
+-- ── Reclassify mechanical edges + predecessor rows ──────────────────────────
+UPDATE session_edges SET kind = 'replaces'
+WHERE kind = 'supersedes'
+  AND (SELECT transcript_path FROM sessions WHERE id = from_session)
+    = (SELECT transcript_path FROM sessions WHERE id = to_session);
+
+UPDATE sessions SET status = 'replaced', updated_at = datetime('now')
+WHERE status = 'superseded'
+  AND id IN (SELECT to_session FROM session_edges WHERE kind = 'replaces');
+
+INSERT OR IGNORE INTO schema_migrations (version, name) VALUES (19, '019_split_replaces');
+
+COMMIT;
+
+PRAGMA foreign_keys = ON;

package/migrations/020_collapse_duplicate_active_facts.sql

@@ -0,0 +1,45 @@
+-- Migration 020: collapse duplicate active facts (NLM #301).
+--
+-- The SQLite supersedence loop superseded only the single most-recent active
+-- prior per new fact (ORDER BY created_at DESC LIMIT 1). Once two facts for the
+-- same (subject, predicate) were simultaneously active — a multi-pass backfill,
+-- or an ON DELETE SET NULL un-supersede when a re-ingest deleted a chain head —
+-- every later ingest cleared only one, so the duplicate persisted. The code fix
+-- collapses ALL priors set-wise; this migration repairs the rows already stuck.
+--
+-- Within each conflicting (subject, predicate) group, the newest active fact
+-- (created_at, then id as a deterministic tiebreak) stays active; the older
+-- actives get superseded_by = that newest fact's id. Plain UPDATE — no table
+-- rebuild, so the runner's BEGIN/COMMIT wrapper is fine (no -- nlm:no-wrap).
+
+WITH winners AS (
+  SELECT subject, predicate, id AS winner_id
+  FROM (
+    SELECT
+      subject, predicate, id,
+      ROW_NUMBER() OVER (
+        PARTITION BY subject, predicate
+        ORDER BY created_at DESC, id DESC
+      ) AS rn
+    FROM facts
+    WHERE superseded_by IS NULL
+  )
+  WHERE rn = 1
+)
+UPDATE facts
+SET superseded_by = (
+  SELECT w.winner_id FROM winners w
+  WHERE w.subject = facts.subject AND w.predicate = facts.predicate
+)
+WHERE superseded_by IS NULL
+  AND id != (
+    SELECT w.winner_id FROM winners w
+    WHERE w.subject = facts.subject AND w.predicate = facts.predicate
+  )
+  AND EXISTS (
+    SELECT 1 FROM facts dup
+    WHERE dup.subject = facts.subject AND dup.predicate = facts.predicate
+      AND dup.superseded_by IS NULL AND dup.id != facts.id
+  );
+
+INSERT OR IGNORE INTO schema_migrations (version, name) VALUES (20, '020_collapse_duplicate_active_facts');

package/migrations/pg/001_initial.sql

@@ -0,0 +1,214 @@
+-- NLM PostgreSQL schema v1.
+-- Mirrors SQLite migrations/000–016 but uses PG idioms:
+--   - SERIAL / TEXT for PKs (no AUTOINCREMENT)
+--   - pgvector for embeddings instead of sqlite-vec
+--   - tsvector generated column + GIN for FTS5 equivalent
+--   - NOW() instead of datetime('now')
+--   - ON CONFLICT DO NOTHING / DO UPDATE instead of INSERT OR IGNORE / REPLACE
+
+CREATE EXTENSION IF NOT EXISTS vector;
+
+-- ── Sessions ────────────────────────────────────────────────────────────────
+CREATE TABLE IF NOT EXISTS sessions (
+  id                   TEXT PRIMARY KEY,
+  runtime              TEXT NOT NULL,
+  runtime_session_id   TEXT,
+  started_at           TEXT NOT NULL,
+  ended_at             TEXT,
+  duration_min         REAL,
+  label                TEXT NOT NULL,
+  summary              TEXT NOT NULL,
+  body                 TEXT,
+  status               TEXT NOT NULL CHECK (status IN ('active', 'closed', 'superseded')),
+  transcript_kind      TEXT,
+  transcript_path      TEXT,
+  transcript_offset    BIGINT,
+  transcript_length    BIGINT,
+  created_at           TIMESTAMPTZ NOT NULL DEFAULT NOW(),
+  updated_at           TIMESTAMPTZ NOT NULL DEFAULT NOW(),
+  fts_vector           TSVECTOR GENERATED ALWAYS AS (
+    setweight(to_tsvector('english', coalesce(label, '')), 'A') ||
+    setweight(to_tsvector('english', coalesce(summary, '')), 'B') ||
+    setweight(to_tsvector('english', coalesce(body, '')), 'C')
+  ) STORED
+);
+
+CREATE INDEX IF NOT EXISTS sessions_fts_idx ON sessions USING GIN(fts_vector);
+CREATE INDEX IF NOT EXISTS idx_sessions_started_at ON sessions(started_at);
+
+-- ── Session embeddings (chunks + map, mirrors SQLite architecture) ──────────
+CREATE TABLE IF NOT EXISTS session_embedding_chunks (
+  chunk_id   SERIAL PRIMARY KEY,
+  session_id TEXT NOT NULL REFERENCES sessions(id) ON DELETE CASCADE,
+  chunk_idx  INTEGER NOT NULL,
+  embedding  vector(768) NOT NULL
+);
+
+CREATE INDEX IF NOT EXISTS session_chunks_embedding_idx
+  ON session_embedding_chunks USING ivfflat (embedding vector_l2_ops)
+  WITH (lists = 100);
+
+CREATE TABLE IF NOT EXISTS session_chunk_map (
+  chunk_id   INTEGER NOT NULL REFERENCES session_embedding_chunks(chunk_id) ON DELETE CASCADE,
+  session_id TEXT NOT NULL REFERENCES sessions(id) ON DELETE CASCADE,
+  chunk_idx  INTEGER NOT NULL,
+  PRIMARY KEY (chunk_id)
+);
+
+CREATE INDEX IF NOT EXISTS idx_session_chunk_map_session ON session_chunk_map(session_id);
+
+-- ── Markers (decisions + open questions) ────────────────────────────────────
+CREATE TABLE IF NOT EXISTS markers (
+  id         SERIAL PRIMARY KEY,
+  session_id TEXT NOT NULL REFERENCES sessions(id) ON DELETE CASCADE,
+  kind       TEXT NOT NULL CHECK (kind IN ('decision', 'open')),
+  text       TEXT NOT NULL,
+  position   INTEGER NOT NULL DEFAULT 0
+);
+
+CREATE INDEX IF NOT EXISTS idx_markers_session ON markers(session_id);
+
+-- ── Entities ────────────────────────────────────────────────────────────────
+CREATE TABLE IF NOT EXISTS entities (
+  canonical          TEXT PRIMARY KEY,
+  type               TEXT NOT NULL DEFAULT 'candidate',
+  status             TEXT NOT NULL DEFAULT 'candidate',
+  source             TEXT NOT NULL DEFAULT 'auto-detected',
+  first_seen_session TEXT REFERENCES sessions(id) ON DELETE SET NULL,
+  last_seen_session  TEXT REFERENCES sessions(id) ON DELETE SET NULL,
+  session_count      INTEGER NOT NULL DEFAULT 0,
+  created_at         TIMESTAMPTZ NOT NULL DEFAULT NOW(),
+  updated_at         TIMESTAMPTZ NOT NULL DEFAULT NOW()
+);
+
+CREATE TABLE IF NOT EXISTS session_entities (
+  session_id        TEXT NOT NULL REFERENCES sessions(id) ON DELETE CASCADE,
+  entity_canonical  TEXT NOT NULL REFERENCES entities(canonical) ON DELETE CASCADE,
+  PRIMARY KEY (session_id, entity_canonical)
+);
+
+-- ── Session edges ────────────────────────────────────────────────────────────
+CREATE TABLE IF NOT EXISTS session_edges (
+  from_session TEXT NOT NULL REFERENCES sessions(id) ON DELETE CASCADE,
+  to_session   TEXT NOT NULL REFERENCES sessions(id) ON DELETE CASCADE,
+  kind         TEXT NOT NULL CHECK (kind IN ('supersedes', 'continues')),
+  created_at   TIMESTAMPTZ NOT NULL DEFAULT NOW(),
+  PRIMARY KEY (from_session, to_session, kind)
+);
+
+-- ── Facts ────────────────────────────────────────────────────────────────────
+CREATE TABLE IF NOT EXISTS facts (
+  id                 TEXT PRIMARY KEY,
+  kind               TEXT NOT NULL CHECK (kind IN ('decision', 'open', 'attribute')),
+  subject            TEXT NOT NULL,
+  predicate          TEXT NOT NULL,
+  value              TEXT NOT NULL,
+  source_session_id  TEXT NOT NULL REFERENCES sessions(id) ON DELETE CASCADE,
+  source_quote       TEXT,
+  created_at         TEXT NOT NULL DEFAULT to_char(NOW() AT TIME ZONE 'UTC', 'YYYY-MM-DD"T"HH24:MI:SS"Z"'),
+  superseded_by      TEXT REFERENCES facts(id) ON DELETE SET NULL,
+  confidence         REAL NOT NULL CHECK (confidence >= 0.0 AND confidence <= 1.0)
+);
+
+CREATE INDEX IF NOT EXISTS idx_facts_subject_predicate_current
+  ON facts(subject, predicate) WHERE superseded_by IS NULL;
+CREATE INDEX IF NOT EXISTS idx_facts_subject_current
+  ON facts(subject) WHERE superseded_by IS NULL;
+CREATE INDEX IF NOT EXISTS idx_facts_session
+  ON facts(source_session_id);
+
+-- ── Fact embeddings ──────────────────────────────────────────────────────────
+CREATE TABLE IF NOT EXISTS fact_embeddings (
+  fact_id    TEXT PRIMARY KEY REFERENCES facts(id) ON DELETE CASCADE,
+  embedding  vector(768) NOT NULL
+);
+
+CREATE INDEX IF NOT EXISTS fact_embeddings_idx
+  ON fact_embeddings USING ivfflat (embedding vector_l2_ops)
+  WITH (lists = 100);
+
+-- ── Actions (event-sourced action log) ───────────────────────────────────────
+CREATE TABLE IF NOT EXISTS actions (
+  id           TEXT PRIMARY KEY,
+  timestamp    TEXT NOT NULL,
+  kind         TEXT NOT NULL,
+  subject_type TEXT NOT NULL,
+  subject_id   TEXT NOT NULL,
+  payload      TEXT,
+  actor        TEXT NOT NULL DEFAULT 'user',
+  runtime      TEXT,
+  reverted_by  TEXT REFERENCES actions(id),
+  created_at   TIMESTAMPTZ NOT NULL DEFAULT NOW()
+);
+
+CREATE INDEX IF NOT EXISTS idx_actions_subject ON actions(subject_type, subject_id);
+CREATE INDEX IF NOT EXISTS idx_actions_kind ON actions(kind);
+CREATE INDEX IF NOT EXISTS idx_actions_timestamp ON actions(timestamp DESC);
+
+-- ── Sources registry ─────────────────────────────────────────────────────────
+CREATE TABLE IF NOT EXISTS sources (
+  id             SERIAL PRIMARY KEY,
+  kind           TEXT NOT NULL CHECK (kind IN ('claude-code', 'codex', 'hermes', 'hermes-agent', 'aider', 'cursor', 'windsurf', 'opencode', 'pi', 'jsonl-generic', 'webhook')),
+  name           TEXT NOT NULL UNIQUE,
+  path_or_url    TEXT,
+  runtime_label  TEXT NOT NULL,
+  parse_config   TEXT NOT NULL DEFAULT '{}',
+  enabled        BOOLEAN NOT NULL DEFAULT TRUE,
+  token          TEXT,
+  created_at     TIMESTAMPTZ NOT NULL DEFAULT NOW(),
+  updated_at     TIMESTAMPTZ NOT NULL DEFAULT NOW()
+);
+
+-- ── Providers registry ───────────────────────────────────────────────────────
+CREATE TABLE IF NOT EXISTS providers (
+  id             SERIAL PRIMARY KEY,
+  kind           TEXT NOT NULL CHECK (kind IN ('deepseek', 'ollama', 'openai', 'anthropic', 'openrouter', 'openai-compatible')),
+  name           TEXT NOT NULL UNIQUE,
+  base_url       TEXT,
+  api_key        TEXT,
+  default_model  TEXT,
+  enabled        BOOLEAN NOT NULL DEFAULT TRUE,
+  created_at     TIMESTAMPTZ NOT NULL DEFAULT NOW(),
+  updated_at     TIMESTAMPTZ NOT NULL DEFAULT NOW()
+);
+
+-- ── Adapter state (per-runtime offsets for resumability) ─────────────────────
+CREATE TABLE IF NOT EXISTS adapter_state (
+  adapter_name       TEXT NOT NULL,
+  source_path        TEXT NOT NULL,
+  last_offset        BIGINT NOT NULL DEFAULT 0,
+  last_processed_at  TIMESTAMPTZ NOT NULL DEFAULT NOW(),
+  file_size          BIGINT,
+  session_id         TEXT,
+  failure_count      INTEGER NOT NULL DEFAULT 0,
+  PRIMARY KEY (adapter_name, source_path)
+);
+
+-- ── Schema migrations tracker ────────────────────────────────────────────────
+CREATE TABLE IF NOT EXISTS schema_migrations (
+  version     INTEGER PRIMARY KEY,
+  name        TEXT NOT NULL,
+  applied_at  TIMESTAMPTZ NOT NULL DEFAULT NOW()
+);
+
+INSERT INTO schema_migrations (version, name) VALUES (1, '001_initial')
+  ON CONFLICT DO NOTHING;
+
+-- Signals - agent self-improvement telemetry lane (mirror of SQLite 017).
+CREATE TABLE IF NOT EXISTS signals (
+  id            TEXT PRIMARY KEY,
+  v             INTEGER NOT NULL DEFAULT 1,
+  install_scope TEXT NOT NULL,
+  kind          TEXT NOT NULL CHECK (kind IN ('gate', 'eval', 'review', 'test')),
+  producer      TEXT NOT NULL,
+  outcome       TEXT NOT NULL CHECK (outcome IN ('pass', 'fail', 'fix', 'exhausted')),
+  model         TEXT NOT NULL,
+  repo          TEXT NOT NULL,
+  step          TEXT,
+  detail        TEXT,
+  session_id    TEXT,
+  ts            TEXT NOT NULL,
+  created_at    TEXT NOT NULL DEFAULT (now()::text)
+);
+CREATE INDEX IF NOT EXISTS idx_signals_agg ON signals(install_scope, repo, model, kind, step);
+CREATE INDEX IF NOT EXISTS idx_signals_ts ON signals(ts);

package/migrations/pg/018_repair_self_supersede.sql

@@ -0,0 +1,16 @@
+-- PG parity for SQLite migration 018: repair self-supersedence damage.
+--
+-- One-shot repair, applied manually by an operator against a PG canonical
+-- store (PgStorage.init only runs 001_initial.sql, there is no version-gated
+-- runner on the PG side). Mirrors migrations/018_repair_self_supersede.sql.
+--
+-- Removes self-loop 'supersedes' edges (id -> id) written by the unguarded
+-- scan path, then restores sessions wrongly marked superseded — those left
+-- without any real incoming 'supersedes' edge.
+
+DELETE FROM session_edges WHERE from_session = to_session AND kind = 'supersedes';
+
+UPDATE sessions
+SET status = 'closed', updated_at = NOW()
+WHERE status = 'superseded'
+  AND id NOT IN (SELECT to_session FROM session_edges WHERE kind = 'supersedes');

package/migrations/pg/019_split_replaces.sql

@@ -0,0 +1,32 @@
+-- PG parity for SQLite migration 019: split the mechanical `replaces` relation
+-- out of `supersedes`.
+--
+-- One-shot repair, applied manually by an operator against a PG canonical store
+-- (PgStorage.init only runs 001_initial.sql; there is no version-gated runner on
+-- the PG side). Mirrors migrations/019_split_replaces.sql.
+--
+-- Widens the CHECK constraints on sessions.status and session_edges.kind to
+-- admit 'replaced' / 'replaces', then reclassifies existing mechanical edges:
+-- an edge whose two sessions share the same transcript_path is a re-parse
+-- (replaces); different paths is operator supersedence (untouched).
+
+BEGIN;
+
+ALTER TABLE sessions DROP CONSTRAINT IF EXISTS sessions_status_check;
+ALTER TABLE sessions ADD CONSTRAINT sessions_status_check
+  CHECK (status IN ('active', 'closed', 'superseded', 'replaced'));
+
+ALTER TABLE session_edges DROP CONSTRAINT IF EXISTS session_edges_kind_check;
+ALTER TABLE session_edges ADD CONSTRAINT session_edges_kind_check
+  CHECK (kind IN ('supersedes', 'replaces', 'continues'));
+
+UPDATE session_edges e SET kind = 'replaces'
+WHERE e.kind = 'supersedes'
+  AND (SELECT transcript_path FROM sessions WHERE id = e.from_session)
+    = (SELECT transcript_path FROM sessions WHERE id = e.to_session);
+
+UPDATE sessions SET status = 'replaced', updated_at = NOW()
+WHERE status = 'superseded'
+  AND id IN (SELECT to_session FROM session_edges WHERE kind = 'replaces');
+
+COMMIT;

package/migrations/pg/020_collapse_duplicate_active_facts.sql

@@ -0,0 +1,46 @@
+-- PG parity for SQLite migration 020: collapse duplicate active facts (#301).
+--
+-- One-shot repair, applied manually by an operator against a PG canonical store
+-- (PgStorage.init only runs 001_initial.sql; there is no version-gated runner on
+-- the PG side). Mirrors migrations/020_collapse_duplicate_active_facts.sql.
+--
+-- Within each conflicting (subject, predicate) group, the newest active fact
+-- (created_at, then id) stays active; the older actives get superseded_by set
+-- to that newest fact's id. The PG ingest path already collapsed all priors
+-- set-wise, so this only repairs rows the SQLite-era single-prior loop stranded
+-- in a corpus migrated to PG.
+
+BEGIN;
+
+WITH winners AS (
+  SELECT subject, predicate, id AS winner_id
+  FROM (
+    SELECT
+      subject, predicate, id,
+      ROW_NUMBER() OVER (
+        PARTITION BY subject, predicate
+        ORDER BY created_at DESC, id DESC
+      ) AS rn
+    FROM facts
+    WHERE superseded_by IS NULL
+  ) ranked
+  WHERE rn = 1
+),
+conflicts AS (
+  SELECT subject, predicate
+  FROM facts
+  WHERE superseded_by IS NULL
+  GROUP BY subject, predicate
+  HAVING COUNT(*) > 1
+)
+UPDATE facts f
+SET superseded_by = w.winner_id
+FROM winners w, conflicts c
+WHERE f.subject = w.subject
+  AND f.predicate = w.predicate
+  AND f.subject = c.subject
+  AND f.predicate = c.predicate
+  AND f.superseded_by IS NULL
+  AND f.id != w.winner_id;
+
+COMMIT;

package/nlm/index.js

@@ -412,7 +412,7 @@ async function main() {
     const mode = process.env["NLM_HOOK_MODE"] === "live" ? "live" : "shadow";
     const out = await runHook(
       { prompt, conversationId },
-      { mode, recall: (q) => recallOverHttp(q, "claude-code") }
+      { mode, recall: (q) => recallOverHttp(q, "claude-code", conversationId === "unknown" ? void 0 : conversationId) }
     );
     if (out) process.stdout.write(out);
   } catch {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "nlm-memory",
-  "version": "0.9.1",
+  "version": "0.10.0",
   "description": "Local-first non-linear memory operating system for AI operators.",
   "type": "module",
   "license": "Apache-2.0",
@@ -28,6 +28,7 @@
   ],
   "files": [
     "dist",
+    "migrations",
     "plugin",
     "plugin-hermes-agent",
     "nlm",

package/plugin/scripts/prompt-recall-hook.mjs

@@ -414,7 +414,7 @@ async function main() {
     const mode = process.env["NLM_HOOK_MODE"] === "live" ? "live" : "shadow";
     const out = await runHook(
       { prompt, conversationId },
-      { mode, recall: (q) => recallOverHttp(q, "claude-code") }
+      { mode, recall: (q) => recallOverHttp(q, "claude-code", conversationId === "unknown" ? void 0 : conversationId) }
     );
     if (out) process.stdout.write(out);
   } catch {

package/plugin/scripts/stop-hook.mjs

@@ -396,7 +396,7 @@ async function postCitationOverHttp(conversationId, citedId, kind, responsePrevi
       method: "POST",
       headers: hookAuthHeaders({ "content-type": "application/json" }),
       body: JSON.stringify({
-        conversation_id: conversationId,
+        ...conversationId !== "unknown" ? { conversation_id: conversationId } : {},
         cited_id: citedId,
         kind,
         response_preview: responsePreview