@monoes/monograph 1.1.0 → 1.2.1

package/dist/src/storage/fts-store.js

@@ -1,32 +1,185 @@
 export function ftsSearch(db, query, limit, label) {
-    // Clean and sanitize the query for FTS5
-    const safeQuery = query.replace(/['"*]/g, ' ').trim();
+    // Sanitize: strip only characters that break FTS5 MATCH syntax (* still stripped,
+    // trigram handles substring natively; " is now preserved since trigram doesn't need it removed)
+    const safeQuery = query.replace(/[*]/g, ' ').trim();
     if (!safeQuery)
         return [];
-    // Add wildcard for prefix matching
-    const ftsPrefixQuery = safeQuery.split(/\s+/).map((term) => term + '*').join(' ');
-    let sql = `
+    // Trigram handles substring matching natively — no need to append * to each term
+    const ftsQuery = safeQuery.split(/\s+/).join(' ');
+    let matchSql = `
     SELECT n.id, n.name, n.norm_label, n.file_path, n.label,
-           nodes_fts.rank
+           n.start_line, n.end_line, nodes_fts.rank
     FROM nodes_fts
     JOIN nodes n ON n.rowid = nodes_fts.rowid
     WHERE nodes_fts MATCH ?
   `;
-    const params = [ftsPrefixQuery];
+    const matchParams = [ftsQuery];
     if (label) {
-        sql += ' AND n.label = ?';
-        params.push(label);
+        matchSql += ' AND n.label = ?';
+        matchParams.push(label);
     }
-    sql += ' ORDER BY nodes_fts.rank LIMIT ?';
-    params.push(limit);
-    const rows = db.prepare(sql).all(...params);
-    return rows.map((r) => ({
+    matchSql += ' ORDER BY nodes_fts.rank LIMIT ?';
+    matchParams.push(limit);
+    let matchRows = [];
+    try {
+        matchRows = db.prepare(matchSql).all(...matchParams);
+    }
+    catch {
+        // FTS MATCH can throw on malformed queries; fall through to LIKE path
+    }
+    // For short queries (≤2 chars) trigram requires at least 3 characters to fire, so
+    // supplement with a LIKE fallback to catch single/double-character matches.
+    if (safeQuery.length <= 2) {
+        const escapedQuery = safeQuery.replace(/%/g, '\\%').replace(/_/g, '\\_');
+        const likePattern = `%${escapedQuery}%`;
+        let likeSql = `
+      SELECT n.id, n.name, n.norm_label, n.file_path, n.label,
+             n.start_line, n.end_line, 0 AS rank
+      FROM nodes n
+      WHERE (n.name LIKE ? OR n.norm_label LIKE ? OR n.file_path LIKE ?)
+    `;
+        const likeParams = [likePattern, likePattern, likePattern];
+        if (label) {
+            likeSql += ' AND n.label = ?';
+            likeParams.push(label);
+        }
+        likeSql += ' LIMIT ?';
+        likeParams.push(limit);
+        const likeRows = db.prepare(likeSql).all(...likeParams);
+        // Merge: MATCH results first, append LIKE results not already present
+        const seenIds = new Set(matchRows.map((r) => r.id));
+        for (const r of likeRows) {
+            if (!seenIds.has(r.id)) {
+                matchRows.push(r);
+                seenIds.add(r.id);
+            }
+        }
+    }
+    return matchRows.slice(0, limit).map((r) => ({
         id: r.id,
         name: r.name,
         normLabel: r.norm_label,
         filePath: r.file_path ?? null,
         label: r.label,
         rank: r.rank,
+        startLine: r.start_line ?? null,
+        endLine: r.end_line ?? null,
     }));
 }
+/**
+ * Computes an in-memory fuzzy sequence score for `query` against `name`.
+ * Walks through query chars left-to-right, finding each in `name` sequentially.
+ * Returns a score in [0, 1]: higher means a tighter match.
+ */
+function computeFuzzyScore(name, query) {
+    if (!query.length)
+        return 0;
+    const lname = name.toLowerCase();
+    const lquery = query.toLowerCase();
+    let nameIdx = 0;
+    let matched = 0;
+    let gapPenalty = 0;
+    let lastMatchPos = -1;
+    for (let qi = 0; qi < lquery.length; qi++) {
+        const ch = lquery[qi];
+        const pos = lname.indexOf(ch, nameIdx);
+        if (pos === -1)
+            break;
+        matched++;
+        if (lastMatchPos !== -1) {
+            gapPenalty += pos - lastMatchPos - 1;
+        }
+        lastMatchPos = pos;
+        nameIdx = pos + 1;
+    }
+    if (matched === 0)
+        return 0;
+    const matchRatio = matched / lquery.length;
+    const normalizedGap = gapPenalty / (lname.length || 1);
+    return matchRatio * (1 / (1 + normalizedGap));
+}
+/** Returns a small bonus based on node label to favour structural node types. */
+function computeNodeTypeBonus(label) {
+    if (label === 'File' || label === 'Module')
+        return 0.02;
+    if (label === 'Class')
+        return 0.01;
+    return 0;
+}
+/**
+ * Hybrid search combining three strategies:
+ *  1. FTS5 (trigram) BM25 match via `ftsSearch`
+ *  2. LIKE fallback for short queries (≤3 chars) or when FTS returns 0 results
+ *  3. In-memory fuzzy character-sequence scoring applied to all candidates
+ *
+ * Results are deduped by id (highest combinedScore wins), re-ranked, and
+ * trimmed to `limit`. The existing `ftsSearch` is left unchanged.
+ */
+export function hybridSearch(db, query, limit, label) {
+    const safeQuery = query.replace(/[*]/g, ' ').trim();
+    if (!safeQuery)
+        return [];
+    // id → best result so far
+    const best = new Map();
+    const upsert = (result) => {
+        const existing = best.get(result.id);
+        if (!existing || result.combinedScore > existing.combinedScore) {
+            best.set(result.id, result);
+        }
+    };
+    // ── Strategy 1: FTS5 BM25 ──────────────────────────────────────────────────
+    const ftsRows = ftsSearch(db, safeQuery, limit * 2, label);
+    for (const row of ftsRows) {
+        // FTS5 rank is negative; larger magnitude = better match. Map to (0,1) with higher = better.
+        const absRank = Math.abs(row.rank);
+        const ftsScore = absRank / (1 + absRank);
+        const fuzz = computeFuzzyScore(row.name, safeQuery);
+        const combined = ftsScore + fuzz + computeNodeTypeBonus(row.label);
+        upsert({ ...row, combinedScore: combined, matchStrategy: 'fts' });
+    }
+    // ── Strategy 2: LIKE fallback ──────────────────────────────────────────────
+    // Always run for short queries (≤3 chars) or when FTS returned nothing.
+    if (safeQuery.length <= 3 || ftsRows.length === 0) {
+        const escapedSafeQuery = safeQuery.replace(/%/g, '\\%').replace(/_/g, '\\_');
+        const likePattern = `%${escapedSafeQuery}%`;
+        let likeSql = `
+      SELECT n.id, n.name, n.norm_label, n.file_path, n.label,
+             n.start_line, n.end_line
+      FROM nodes n
+      WHERE (n.name LIKE ? OR n.norm_label LIKE ?)
+    `;
+        const likeParams = [likePattern, likePattern];
+        if (label) {
+            likeSql += ' AND n.label = ?';
+            likeParams.push(label);
+        }
+        likeSql += ' LIMIT ?';
+        likeParams.push(limit * 2);
+        const likeRows = db
+            .prepare(likeSql)
+            .all(...likeParams);
+        for (const r of likeRows) {
+            const name = r.name;
+            const lbl = r.label;
+            const fuzz = computeFuzzyScore(name, safeQuery);
+            const combined = 0.3 + fuzz + computeNodeTypeBonus(lbl);
+            upsert({
+                id: r.id,
+                name,
+                normLabel: r.norm_label,
+                filePath: r.file_path ?? null,
+                label: lbl,
+                rank: 0,
+                startLine: r.start_line ?? null,
+                endLine: r.end_line ?? null,
+                combinedScore: combined,
+                matchStrategy: 'like',
+            });
+        }
+    }
+    // ── Sort, dedupe (handled by Map), slice ───────────────────────────────────
+    return Array.from(best.values())
+        .sort((a, b) => b.combinedScore - a.combinedScore)
+        .slice(0, limit);
+}
 //# sourceMappingURL=fts-store.js.map

package/dist/src/storage/fts-store.js.map

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package/dist/src/storage/node-store.d.ts

@@ -2,8 +2,39 @@ import type Database from 'better-sqlite3';
 import type { MonographNode } from '../types.js';
 export declare function insertNode(db: Database.Database, node: MonographNode): void;
 export declare function insertNodes(db: Database.Database, nodes: MonographNode[]): void;
+/** Batch-fetch multiple nodes by ID using a single SQL IN query. Batches at 50 IDs. */
+export declare function getNodesByIds(db: Database.Database, ids: string[]): MonographNode[];
 export declare function getNode(db: Database.Database, id: string): MonographNode | undefined;
 export declare function getNodesForFile(db: Database.Database, filePath: string): MonographNode[];
 export declare function deleteNodesForFile(db: Database.Database, filePath: string): void;
 export declare function countNodes(db: Database.Database): number;
+export interface PropertyDef {
+    ident: string;
+    type: string;
+    cardinality: string;
+    viewContext: string;
+    closedValues: string[] | null;
+    description: string | null;
+    queryable: boolean;
+}
+/** List all registered property definitions */
+export declare function listProperties(db: Database.Database): PropertyDef[];
+/** Get a single property definition */
+export declare function getProperty(db: Database.Database, ident: string): PropertyDef | null;
+/** Register or update a custom property */
+export declare function upsertProperty(db: Database.Database, def: PropertyDef): void;
+/**
+ * Query nodes by a typed property value extracted from their JSON properties column.
+ * For queryable properties only.
+ * @param ident - property ident (e.g. 'layer', 'tags', 'ua_type')
+ * @param value - value to match (exact for closed/text, numeric comparison for number)
+ * @param comparator - '=' | 'LIKE' | '>' | '<' (default '=')
+ */
+export declare function queryByProperty(db: Database.Database, ident: string, value: string | number | boolean, comparator?: '=' | 'LIKE' | '>' | '<', limit?: number): Array<{
+    id: string;
+    name: string;
+    label: string;
+    filePath: string | null;
+    propertyValue: unknown;
+}>;
 //# sourceMappingURL=node-store.d.ts.map

package/dist/src/storage/node-store.d.ts.map

@@ -1 +1 @@
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package/dist/src/storage/node-store.js

@@ -1,4 +1,4 @@
-import { toNormLabel } from '../types.js';
+import { toNormLabel, MonographError } from '../types.js';
 export function insertNode(db, node) {
     db.prepare(`
     INSERT OR REPLACE INTO nodes
@@ -7,14 +7,41 @@ export function insertNode(db, node) {
     VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
   `).run(node.id, node.label, node.name, node.normLabel ?? toNormLabel(node.name), node.filePath ?? null, node.startLine ?? null, node.endLine ?? null, node.communityId ?? null, node.isExported ? 1 : 0, node.language ?? null, node.properties ? JSON.stringify(node.properties) : null);
 }
+const INSERT_SQL = `
+    INSERT OR REPLACE INTO nodes
+      (id, label, name, norm_label, file_path, start_line, end_line,
+       community_id, is_exported, language, properties)
+    VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
+  `;
 export function insertNodes(db, nodes) {
+    if (nodes.length === 0)
+        return;
+    // Prepare once and reuse across all rows — avoids N redundant prepare calls
+    const stmt = db.prepare(INSERT_SQL);
     const insertMany = db.transaction((rows) => {
         for (const n of rows) {
-            insertNode(db, n);
+            stmt.run(n.id, n.label, n.name, n.normLabel ?? toNormLabel(n.name), n.filePath ?? null, n.startLine ?? null, n.endLine ?? null, n.communityId ?? null, n.isExported ? 1 : 0, n.language ?? null, n.properties ? JSON.stringify(n.properties) : null);
         }
     });
     insertMany(nodes);
 }
+/** Batch-fetch multiple nodes by ID using a single SQL IN query. Batches at 50 IDs. */
+export function getNodesByIds(db, ids) {
+    if (ids.length === 0)
+        return [];
+    const BATCH = 50;
+    const results = [];
+    for (let i = 0; i < ids.length; i += BATCH) {
+        const chunk = ids.slice(i, i + BATCH);
+        const placeholders = chunk.map(() => '?').join(',');
+        const rows = db
+            .prepare(`SELECT * FROM nodes WHERE id IN (${placeholders})`)
+            .all(...chunk);
+        for (const row of rows)
+            results.push(rowToNode(row));
+    }
+    return results;
+}
 export function getNode(db, id) {
     const row = db
         .prepare('SELECT * FROM nodes WHERE id = ?')
@@ -34,6 +61,72 @@ export function countNodes(db) {
     const row = db.prepare('SELECT COUNT(*) as n FROM nodes').get();
     return row.n;
 }
+function rowToPropDef(row) {
+    return {
+        ident: row.ident,
+        type: row.type,
+        cardinality: row.cardinality,
+        viewContext: row.view_context,
+        closedValues: row.closed_values ? JSON.parse(row.closed_values) : null,
+        description: row.description ?? null,
+        queryable: row.queryable === 1,
+    };
+}
+/** List all registered property definitions */
+export function listProperties(db) {
+    const rows = db.prepare('SELECT * FROM node_properties ORDER BY ident').all();
+    return rows.map(rowToPropDef);
+}
+/** Get a single property definition */
+export function getProperty(db, ident) {
+    const row = db.prepare('SELECT * FROM node_properties WHERE ident = ?').get(ident);
+    return row ? rowToPropDef(row) : null;
+}
+/** Register or update a custom property */
+export function upsertProperty(db, def) {
+    db.prepare(`
+    INSERT INTO node_properties (ident, type, cardinality, view_context, closed_values, description, queryable)
+    VALUES (?, ?, ?, ?, ?, ?, ?)
+    ON CONFLICT(ident) DO UPDATE SET
+      type = excluded.type,
+      cardinality = excluded.cardinality,
+      view_context = excluded.view_context,
+      closed_values = excluded.closed_values,
+      description = excluded.description,
+      queryable = excluded.queryable
+  `).run(def.ident, def.type, def.cardinality, def.viewContext, def.closedValues != null ? JSON.stringify(def.closedValues) : null, def.description ?? null, def.queryable ? 1 : 0);
+}
+/**
+ * Query nodes by a typed property value extracted from their JSON properties column.
+ * For queryable properties only.
+ * @param ident - property ident (e.g. 'layer', 'tags', 'ua_type')
+ * @param value - value to match (exact for closed/text, numeric comparison for number)
+ * @param comparator - '=' | 'LIKE' | '>' | '<' (default '=')
+ */
+export function queryByProperty(db, ident, value, comparator = '=', limit = 100) {
+    const propDef = getProperty(db, ident);
+    if (!propDef) {
+        throw new MonographError(`Unknown property: '${ident}'. Register it first with upsertProperty.`);
+    }
+    if (!propDef.queryable) {
+        throw new MonographError(`Property '${ident}' is not queryable (view_context may be 'never' or queryable=false).`);
+    }
+    const extractExpr = `json_extract(properties, '$.${ident}')`;
+    const rows = db.prepare(`
+    SELECT id, name, label, file_path, ${extractExpr} AS property_value
+    FROM nodes
+    WHERE properties IS NOT NULL
+      AND ${extractExpr} ${comparator} ?
+    LIMIT ?
+  `).all(value, limit);
+    return rows.map(r => ({
+        id: r.id,
+        name: r.name,
+        label: r.label,
+        filePath: r.file_path ?? null,
+        propertyValue: r.property_value,
+    }));
+}
 function rowToNode(row) {
     return {
         id: row.id,

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package/dist/src/storage/schema.d.ts

@@ -1,8 +1,14 @@
-export declare const CREATE_NODES = "\nCREATE TABLE IF NOT EXISTS nodes (\n  id TEXT PRIMARY KEY,\n  label TEXT NOT NULL,\n  name TEXT NOT NULL,\n  norm_label TEXT NOT NULL DEFAULT '',\n  file_path TEXT,\n  start_line INTEGER,\n  end_line INTEGER,\n  community_id INTEGER,\n  is_exported INTEGER NOT NULL DEFAULT 0,\n  language TEXT,\n  properties TEXT\n)";
-export declare const CREATE_EDGES = "\nCREATE TABLE IF NOT EXISTS edges (\n  id TEXT PRIMARY KEY,\n  source_id TEXT NOT NULL,\n  target_id TEXT NOT NULL,\n  relation TEXT NOT NULL,\n  confidence TEXT NOT NULL DEFAULT 'EXTRACTED',\n  confidence_score REAL NOT NULL DEFAULT 1.0,\n  FOREIGN KEY (source_id) REFERENCES nodes(id),\n  FOREIGN KEY (target_id) REFERENCES nodes(id)\n)";
+export declare const CREATE_NODES = "\nCREATE TABLE IF NOT EXISTS nodes (\n  id TEXT PRIMARY KEY,\n  label TEXT NOT NULL,\n  name TEXT NOT NULL,\n  norm_label TEXT NOT NULL DEFAULT '',\n  file_path TEXT,\n  start_line INTEGER,\n  end_line INTEGER,\n  community_id INTEGER,\n  is_exported INTEGER NOT NULL DEFAULT 0,\n  language TEXT,\n  properties TEXT,\n  embedding TEXT\n)";
+export declare const CREATE_EDGES = "\nCREATE TABLE IF NOT EXISTS edges (\n  id TEXT PRIMARY KEY,\n  source_id TEXT NOT NULL,\n  target_id TEXT NOT NULL,\n  relation TEXT NOT NULL,\n  confidence TEXT NOT NULL DEFAULT 'EXTRACTED',\n  confidence_score REAL NOT NULL DEFAULT 1.0,\n  weight REAL NOT NULL DEFAULT 1.0,\n  reason TEXT,\n  evidence TEXT,\n  FOREIGN KEY (source_id) REFERENCES nodes(id),\n  FOREIGN KEY (target_id) REFERENCES nodes(id)\n)";
 export declare const CREATE_COMMUNITIES = "\nCREATE TABLE IF NOT EXISTS communities (\n  id INTEGER PRIMARY KEY,\n  label TEXT,\n  size INTEGER NOT NULL DEFAULT 0,\n  cohesion_score REAL NOT NULL DEFAULT 0.0\n)";
 export declare const CREATE_INDEX_META = "\nCREATE TABLE IF NOT EXISTS index_meta (\n  key TEXT PRIMARY KEY,\n  value TEXT NOT NULL\n)";
-export declare const CREATE_NODES_FTS = "\nCREATE VIRTUAL TABLE IF NOT EXISTS nodes_fts USING fts5(\n  id UNINDEXED,\n  name,\n  norm_label,\n  file_path,\n  label UNINDEXED,\n  content='nodes',\n  content_rowid='rowid'\n)";
+export declare const CREATE_NODES_FTS = "\nCREATE VIRTUAL TABLE IF NOT EXISTS nodes_fts USING fts5(\n  id UNINDEXED,\n  name,\n  norm_label,\n  file_path,\n  label UNINDEXED,\n  content='nodes',\n  content_rowid='rowid',\n  tokenize='trigram'\n)";
+export declare const CREATE_EMBEDDINGS = "\nCREATE TABLE IF NOT EXISTS embeddings (\n  node_id TEXT PRIMARY KEY,\n  vector BLOB NOT NULL\n)";
+export declare const CREATE_WIKI_PAGES = "\nCREATE TABLE IF NOT EXISTS wiki_pages (\n  community_id TEXT PRIMARY KEY,\n  content TEXT NOT NULL,\n  generated_at TEXT NOT NULL\n)";
 export declare const CREATE_INDEXES: string[];
+export declare const CREATE_NODE_PROPERTIES = "\nCREATE TABLE IF NOT EXISTS node_properties (\n  ident TEXT PRIMARY KEY,\n  type TEXT NOT NULL CHECK(type IN ('text','number','boolean','date','node-ref','closed')),\n  cardinality TEXT NOT NULL DEFAULT 'one' CHECK(cardinality IN ('one','many')),\n  view_context TEXT NOT NULL DEFAULT 'all' CHECK(view_context IN ('all','graph','query','never')),\n  closed_values TEXT,\n  description TEXT,\n  queryable INTEGER NOT NULL DEFAULT 1\n)";
+export declare const SEED_NODE_PROPERTIES = "\nINSERT OR IGNORE INTO node_properties (ident, type, cardinality, view_context, description, queryable) VALUES\n  ('ua_type',       'closed',  'one',  'query', 'Understand-Anything node type',        1),\n  ('summary',       'text',    'one',  'all',   'LLM-generated description',            1),\n  ('tags',          'text',    'many', 'all',   'Semantic tags from analysis',          1),\n  ('complexity',    'closed',  'one',  'query', 'Code complexity rating',               1),\n  ('layer',         'closed',  'one',  'graph', 'Architectural layer (community name)', 1),\n  ('community_id',  'number',  'one',  'query', 'Community cluster id',                 1),\n  ('language',      'text',    'one',  'query', 'Programming language',                 1),\n  ('is_exported',   'boolean', 'one',  'query', 'Whether symbol is exported',           1)";
+export declare const CREATE_SUPPRESSIONS = "\nCREATE TABLE IF NOT EXISTS suppressions (\n  id TEXT PRIMARY KEY,\n  file_path TEXT NOT NULL,\n  line INTEGER NOT NULL DEFAULT 0,\n  rule TEXT NOT NULL,\n  added_at TEXT NOT NULL,\n  last_seen_at TEXT\n)";
+export declare const CREATE_FILE_CACHE = "\n  CREATE TABLE IF NOT EXISTS file_cache (\n    file_path TEXT PRIMARY KEY,\n    content_hash TEXT NOT NULL,\n    last_parsed INTEGER NOT NULL,\n    node_count INTEGER NOT NULL DEFAULT 0,\n    edge_count INTEGER NOT NULL DEFAULT 0\n  )\n";
 export declare const FTS_SYNC_TRIGGERS = "\nCREATE TRIGGER IF NOT EXISTS nodes_fts_insert AFTER INSERT ON nodes BEGIN\n  INSERT INTO nodes_fts(rowid, id, name, norm_label, file_path, label)\n  VALUES (new.rowid, new.id, new.name, new.norm_label, new.file_path, new.label);\nEND;\nCREATE TRIGGER IF NOT EXISTS nodes_fts_delete AFTER DELETE ON nodes BEGIN\n  INSERT INTO nodes_fts(nodes_fts, rowid, id, name, norm_label, file_path, label)\n  VALUES ('delete', old.rowid, old.id, old.name, old.norm_label, old.file_path, old.label);\nEND;\nCREATE TRIGGER IF NOT EXISTS nodes_fts_update AFTER UPDATE ON nodes BEGIN\n  INSERT INTO nodes_fts(nodes_fts, rowid, id, name, norm_label, file_path, label)\n  VALUES ('delete', old.rowid, old.id, old.name, old.norm_label, old.file_path, old.label);\n  INSERT INTO nodes_fts(rowid, id, name, norm_label, file_path, label)\n  VALUES (new.rowid, new.id, new.name, new.norm_label, new.file_path, new.label);\nEND";
 //# sourceMappingURL=schema.d.ts.map

package/dist/src/storage/schema.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"schema.d.ts","sourceRoot":"","sources":["../../../src/storage/schema.ts"],"names":[],"mappings":"AAAA,eAAO,MAAM,YAAY,sVAcvB,CAAC;AAEH,eAAO,MAAM,YAAY,+ZAavB,CAAC;AAEH,eAAO,MAAM,kBAAkB,4KAM7B,CAAC;AAEH,eAAO,MAAM,iBAAiB,iGAI5B,CAAC;AAEH,eAAO,MAAM,gBAAgB,iNAU3B,CAAC;AAEH,eAAO,MAAM,iBAAiB,sGAI5B,CAAC;AAEH,eAAO,MAAM,iBAAiB,2IAK5B,CAAC;AAEH,eAAO,MAAM,cAAc,UAQ1B,CAAC;AAEF,eAAO,MAAM,sBAAsB,ubASjC,CAAC;AAEH,eAAO,MAAM,oBAAoB,21BAS0D,CAAC;AAE5F,eAAO,MAAM,mBAAmB,kNAQ9B,CAAC;AAEH,eAAO,MAAM,iBAAiB,mPAQ7B,CAAC;AAEF,eAAO,MAAM,iBAAiB,64BAc1B,CAAC"}

package/dist/src/storage/schema.js

@@ -10,7 +10,8 @@ CREATE TABLE IF NOT EXISTS nodes (
   community_id INTEGER,
   is_exported INTEGER NOT NULL DEFAULT 0,
   language TEXT,
-  properties TEXT
+  properties TEXT,
+  embedding TEXT
 )`;
 export const CREATE_EDGES = `
 CREATE TABLE IF NOT EXISTS edges (
@@ -20,6 +21,9 @@ CREATE TABLE IF NOT EXISTS edges (
   relation TEXT NOT NULL,
   confidence TEXT NOT NULL DEFAULT 'EXTRACTED',
   confidence_score REAL NOT NULL DEFAULT 1.0,
+  weight REAL NOT NULL DEFAULT 1.0,
+  reason TEXT,
+  evidence TEXT,
   FOREIGN KEY (source_id) REFERENCES nodes(id),
   FOREIGN KEY (target_id) REFERENCES nodes(id)
 )`;
@@ -43,7 +47,19 @@ CREATE VIRTUAL TABLE IF NOT EXISTS nodes_fts USING fts5(
   file_path,
   label UNINDEXED,
   content='nodes',
-  content_rowid='rowid'
+  content_rowid='rowid',
+  tokenize='trigram'
+)`;
+export const CREATE_EMBEDDINGS = `
+CREATE TABLE IF NOT EXISTS embeddings (
+  node_id TEXT PRIMARY KEY,
+  vector BLOB NOT NULL
+)`;
+export const CREATE_WIKI_PAGES = `
+CREATE TABLE IF NOT EXISTS wiki_pages (
+  community_id TEXT PRIMARY KEY,
+  content TEXT NOT NULL,
+  generated_at TEXT NOT NULL
 )`;
 export const CREATE_INDEXES = [
     `CREATE INDEX IF NOT EXISTS idx_nodes_file ON nodes(file_path)`,
@@ -54,6 +70,44 @@ export const CREATE_INDEXES = [
     `CREATE INDEX IF NOT EXISTS idx_edges_relation ON edges(relation)`,
     `CREATE INDEX IF NOT EXISTS idx_edges_confidence ON edges(confidence)`,
 ];
+export const CREATE_NODE_PROPERTIES = `
+CREATE TABLE IF NOT EXISTS node_properties (
+  ident TEXT PRIMARY KEY,
+  type TEXT NOT NULL CHECK(type IN ('text','number','boolean','date','node-ref','closed')),
+  cardinality TEXT NOT NULL DEFAULT 'one' CHECK(cardinality IN ('one','many')),
+  view_context TEXT NOT NULL DEFAULT 'all' CHECK(view_context IN ('all','graph','query','never')),
+  closed_values TEXT,
+  description TEXT,
+  queryable INTEGER NOT NULL DEFAULT 1
+)`;
+export const SEED_NODE_PROPERTIES = `
+INSERT OR IGNORE INTO node_properties (ident, type, cardinality, view_context, description, queryable) VALUES
+  ('ua_type',       'closed',  'one',  'query', 'Understand-Anything node type',        1),
+  ('summary',       'text',    'one',  'all',   'LLM-generated description',            1),
+  ('tags',          'text',    'many', 'all',   'Semantic tags from analysis',          1),
+  ('complexity',    'closed',  'one',  'query', 'Code complexity rating',               1),
+  ('layer',         'closed',  'one',  'graph', 'Architectural layer (community name)', 1),
+  ('community_id',  'number',  'one',  'query', 'Community cluster id',                 1),
+  ('language',      'text',    'one',  'query', 'Programming language',                 1),
+  ('is_exported',   'boolean', 'one',  'query', 'Whether symbol is exported',           1)`;
+export const CREATE_SUPPRESSIONS = `
+CREATE TABLE IF NOT EXISTS suppressions (
+  id TEXT PRIMARY KEY,
+  file_path TEXT NOT NULL,
+  line INTEGER NOT NULL DEFAULT 0,
+  rule TEXT NOT NULL,
+  added_at TEXT NOT NULL,
+  last_seen_at TEXT
+)`;
+export const CREATE_FILE_CACHE = `
+  CREATE TABLE IF NOT EXISTS file_cache (
+    file_path TEXT PRIMARY KEY,
+    content_hash TEXT NOT NULL,
+    last_parsed INTEGER NOT NULL,
+    node_count INTEGER NOT NULL DEFAULT 0,
+    edge_count INTEGER NOT NULL DEFAULT 0
+  )
+`;
 export const FTS_SYNC_TRIGGERS = `
 CREATE TRIGGER IF NOT EXISTS nodes_fts_insert AFTER INSERT ON nodes BEGIN
   INSERT INTO nodes_fts(rowid, id, name, norm_label, file_path, label)

package/dist/src/storage/schema.js.map

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package/dist/src/storage/suppressions.d.ts

@@ -0,0 +1,21 @@
+import type Database from 'better-sqlite3';
+export interface Suppression {
+    id: string;
+    filePath: string;
+    line: number;
+    rule: string;
+    addedAt: string;
+    lastSeenAt?: string;
+}
+export interface StaleSuppression extends Suppression {
+    reason: string;
+}
+export declare function addSuppression(db: Database.Database, filePath: string, line: number, rule: string): Suppression;
+export declare function listSuppressions(db: Database.Database, filePath?: string, rule?: string): Suppression[];
+export declare function removeSuppression(db: Database.Database, id: string): void;
+export declare function isSuppressed(db: Database.Database, filePath: string, line: number, rule: string): Suppression | null;
+export declare function findStaleSuppressions(db: Database.Database, activeFindings: Array<{
+    filePath: string;
+    rule: string;
+}>): StaleSuppression[];
+//# sourceMappingURL=suppressions.d.ts.map

package/dist/src/storage/suppressions.d.ts.map

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package/dist/src/storage/suppressions.js

@@ -0,0 +1,83 @@
+import { randomUUID } from 'crypto';
+// Add a suppression
+export function addSuppression(db, filePath, line, rule) {
+    const id = randomUUID();
+    const addedAt = new Date().toISOString();
+    db.prepare(`
+    INSERT INTO suppressions (id, file_path, line, rule, added_at, last_seen_at)
+    VALUES (?, ?, ?, ?, ?, NULL)
+  `).run(id, filePath, line, rule, addedAt);
+    return { id, filePath, line, rule, addedAt };
+}
+// List all suppressions (optionally filter by rule or file)
+export function listSuppressions(db, filePath, rule) {
+    let sql = `SELECT id, file_path, line, rule, added_at, last_seen_at FROM suppressions WHERE 1=1`;
+    const params = [];
+    if (filePath) {
+        sql += ` AND file_path = ?`;
+        params.push(filePath);
+    }
+    if (rule) {
+        sql += ` AND rule = ?`;
+        params.push(rule);
+    }
+    sql += ` ORDER BY added_at DESC`;
+    const rows = db.prepare(sql).all(...params);
+    return rows.map(r => ({
+        id: r.id,
+        filePath: r.file_path,
+        line: r.line,
+        rule: r.rule,
+        addedAt: r.added_at,
+        ...(r.last_seen_at != null ? { lastSeenAt: r.last_seen_at } : {}),
+    }));
+}
+// Remove a suppression
+export function removeSuppression(db, id) {
+    db.prepare(`DELETE FROM suppressions WHERE id = ?`).run(id);
+}
+// Check if a finding is suppressed
+// A suppression with line=0 is file-wide and matches any line for the same file+rule
+export function isSuppressed(db, filePath, line, rule) {
+    const row = db.prepare(`
+    SELECT id, file_path, line, rule, added_at, last_seen_at
+    FROM suppressions
+    WHERE file_path = ? AND rule = ? AND (line = 0 OR line = ?)
+    LIMIT 1
+  `).get(filePath, rule, line);
+    if (!row)
+        return null;
+    return {
+        id: row.id,
+        filePath: row.file_path,
+        line: row.line,
+        rule: row.rule,
+        addedAt: row.added_at,
+        ...(row.last_seen_at != null ? { lastSeenAt: row.last_seen_at } : {}),
+    };
+}
+// Find stale suppressions
+// A suppression is stale if:
+//   - the file no longer exists in the graph (reason: 'file_deleted')
+//   - the file exists but no active finding matches file+rule (reason: 'issue_resolved')
+export function findStaleSuppressions(db, activeFindings) {
+    const suppressions = listSuppressions(db);
+    if (suppressions.length === 0)
+        return [];
+    // Build a set of all file paths in the graph
+    const graphFiles = new Set(db.prepare(`SELECT DISTINCT file_path FROM nodes WHERE file_path IS NOT NULL`).all()
+        .map(r => r.file_path));
+    // Build a set of active finding keys: "filePath::rule"
+    const activeFindingKeys = new Set(activeFindings.map(f => `${f.filePath}::${f.rule}`));
+    const stale = [];
+    for (const s of suppressions) {
+        if (!graphFiles.has(s.filePath)) {
+            stale.push({ ...s, reason: 'file_deleted' });
+        }
+        else if (!activeFindingKeys.has(`${s.filePath}::${s.rule}`)) {
+            stale.push({ ...s, reason: 'issue_resolved' });
+        }
+    }
+    return stale;
+}
+//# sourceMappingURL=suppressions.js.map