fix(store): BigInt consistency, indexes, CHECK constraints, safe JSON, tests

- Wrap vec0 insert rowid in BigInt() consistently across all stores
- Add compound indexes on edges (project_id, to/from_graph, to/from_id)
- Add updated_at indexes on knowledge, tasks, epics, skills
- Add assignee_id index on tasks
- Add CHECK constraints for status, priority, source, confidence in v001
- Add safeJson() helper for corrupted JSON fallback in skills/docs
- Replace correlated subqueries with LEFT JOIN in code/docs listFiles
- Add getUpdatedAt to EpicsStore interface + implementation
- Add hybrid search, pagination edge case, null/empty input tests

Author: prih

src/store/sqlite/lib/bigint.ts

@@ -7,3 +7,12 @@ export function num(v: bigint | number): number {
 export function now(): bigint {
   return BigInt(Date.now());
 }
+
+/** Safely parse JSON with a fallback for corrupted data */
+export function safeJson<T>(raw: string, fallback: T): T {
+  try {
+    return JSON.parse(raw) as T;
+  } catch {
+    return fallback;
+  }
+}

src/store/sqlite/migrations/v001.ts

@@ -67,8 +67,8 @@ CREATE TABLE edges (
   kind       TEXT NOT NULL,
   PRIMARY KEY (project_id, from_graph, from_id, to_graph, to_id, kind)
 );
-CREATE INDEX idx_edges_target ON edges(to_graph, to_id);
-CREATE INDEX idx_edges_source ON edges(from_graph, from_id);
+CREATE INDEX idx_edges_target ON edges(project_id, to_graph, to_id);
+CREATE INDEX idx_edges_source ON edges(project_id, from_graph, from_id);
 
 -- =============================================
 -- Knowledge (notes)
@@ -88,6 +88,7 @@ CREATE TABLE knowledge (
   UNIQUE(project_id, slug)
 );
 CREATE INDEX idx_knowledge_project ON knowledge(project_id);
+CREATE INDEX idx_knowledge_updated ON knowledge(project_id, updated_at);
 
 CREATE VIRTUAL TABLE knowledge_fts USING fts5(
   title, content, content=knowledge, content_rowid=id
@@ -123,8 +124,8 @@ CREATE TABLE tasks (
   slug          TEXT NOT NULL,
   title         TEXT NOT NULL,
   description   TEXT NOT NULL DEFAULT '',
-  status        TEXT NOT NULL DEFAULT 'backlog',
-  priority      TEXT NOT NULL DEFAULT 'medium',
+  status        TEXT NOT NULL DEFAULT 'backlog' CHECK(status IN ('backlog','todo','in_progress','review','done','cancelled')),
+  priority      TEXT NOT NULL DEFAULT 'medium' CHECK(priority IN ('critical','high','medium','low')),
   "order"       REAL NOT NULL DEFAULT 0,
   due_date      INTEGER,
   estimate      INTEGER,
@@ -139,6 +140,8 @@ CREATE TABLE tasks (
 );
 CREATE INDEX idx_tasks_project ON tasks(project_id);
 CREATE INDEX idx_tasks_status ON tasks(project_id, status, "order");
+CREATE INDEX idx_tasks_assignee ON tasks(assignee_id);
+CREATE INDEX idx_tasks_updated ON tasks(project_id, updated_at);
 
 CREATE VIRTUAL TABLE tasks_fts USING fts5(
   title, description, content=tasks, content_rowid=id
@@ -174,8 +177,8 @@ CREATE TABLE epics (
   slug          TEXT NOT NULL,
   title         TEXT NOT NULL,
   description   TEXT NOT NULL DEFAULT '',
-  status        TEXT NOT NULL DEFAULT 'open',
-  priority      TEXT NOT NULL DEFAULT 'medium',
+  status        TEXT NOT NULL DEFAULT 'open' CHECK(status IN ('open','in_progress','done','cancelled')),
+  priority      TEXT NOT NULL DEFAULT 'medium' CHECK(priority IN ('critical','high','medium','low')),
   "order"       REAL NOT NULL DEFAULT 0,
   version       INTEGER NOT NULL DEFAULT 1,
   created_by_id INTEGER REFERENCES team_members(id) ON DELETE SET NULL,
@@ -185,6 +188,7 @@ CREATE TABLE epics (
   UNIQUE(project_id, slug)
 );
 CREATE INDEX idx_epics_project ON epics(project_id);
+CREATE INDEX idx_epics_updated ON epics(project_id, updated_at);
 
 CREATE VIRTUAL TABLE epics_fts USING fts5(
   title, description, content=epics, content_rowid=id
@@ -224,8 +228,8 @@ CREATE TABLE skills (
   triggers_json      TEXT NOT NULL DEFAULT '[]',
   input_hints_json   TEXT NOT NULL DEFAULT '[]',
   file_patterns_json TEXT NOT NULL DEFAULT '[]',
-  source             TEXT NOT NULL DEFAULT 'user',
-  confidence         REAL NOT NULL DEFAULT 1.0,
+  source             TEXT NOT NULL DEFAULT 'user' CHECK(source IN ('user','learned')),
+  confidence         REAL NOT NULL DEFAULT 1.0 CHECK(confidence >= 0.0 AND confidence <= 1.0),
   usage_count        INTEGER NOT NULL DEFAULT 0,
   last_used_at       INTEGER,
   version            INTEGER NOT NULL DEFAULT 1,
@@ -236,6 +240,7 @@ CREATE TABLE skills (
   UNIQUE(project_id, slug)
 );
 CREATE INDEX idx_skills_project ON skills(project_id);
+CREATE INDEX idx_skills_updated ON skills(project_id, updated_at);
 
 CREATE VIRTUAL TABLE skills_fts USING fts5(
   title, description, content=skills, content_rowid=id

src/store/sqlite/stores/code.ts

@@ -192,8 +192,12 @@ export class SqliteCodeStore implements CodeStore {
     const where = conditions.join(' AND ');
     const rows = this.db.prepare(`
       SELECT f.id, f.file_id, f.language, f.mtime,
-        (SELECT COUNT(*) FROM code c WHERE c.project_id = f.project_id AND c.file_id = f.file_id AND c.kind != 'file') AS symbol_count
-      FROM code f WHERE ${where}
+        COALESCE(s.cnt, 0) AS symbol_count
+      FROM code f
+      LEFT JOIN (
+        SELECT project_id, file_id, COUNT(*) AS cnt FROM code WHERE kind != 'file' GROUP BY project_id, file_id
+      ) s ON s.project_id = f.project_id AND s.file_id = f.file_id
+      WHERE ${where}
       ORDER BY f.file_id ASC LIMIT ? OFFSET ?
     `).all(...params, limit, offset) as Array<Record<string, unknown>>;
 

src/store/sqlite/stores/docs.ts

@@ -8,7 +8,7 @@ import type {
   PaginationOptions,
 } from '../../types';
 import { MetaHelper } from '../lib/meta';
-import { num } from '../lib/bigint';
+import { num, safeJson } from '../lib/bigint';
 import { hybridSearch, SearchConfig } from '../lib/search';
 
 const GRAPH = 'docs';
@@ -37,7 +37,7 @@ export class SqliteDocsStore implements DocsStore {
       content: row.content as string,
       level: num(row.level as bigint),
       language: (row.language as string | null) ?? undefined,
-      symbols: JSON.parse(row.symbols_json as string),
+      symbols: safeJson<string[]>(row.symbols_json as string, []),
       mtime: num(row.mtime as bigint),
     };
   }
@@ -179,8 +179,12 @@ export class SqliteDocsStore implements DocsStore {
     const where = conditions.join(' AND ');
     const rows = this.db.prepare(`
       SELECT d.id, d.file_id, d.title, d.mtime,
-        (SELECT COUNT(*) FROM docs c WHERE c.project_id = d.project_id AND c.file_id = d.file_id AND c.kind = 'chunk') AS chunk_count
-      FROM docs d WHERE ${where}
+        COALESCE(ch.cnt, 0) AS chunk_count
+      FROM docs d
+      LEFT JOIN (
+        SELECT project_id, file_id, COUNT(*) AS cnt FROM docs WHERE kind = 'chunk' GROUP BY project_id, file_id
+      ) ch ON ch.project_id = d.project_id AND ch.file_id = d.file_id
+      WHERE ${where}
       ORDER BY d.file_id ASC LIMIT ? OFFSET ?
     `).all(...params, limit, offset) as Array<Record<string, unknown>>;
 

src/store/sqlite/stores/epics.ts

@@ -112,7 +112,7 @@ export class SqliteEpicsStore implements EpicsStore {
     `).run(this.projectId, slug, data.title, data.description ?? '', data.status ?? 'open', data.priority ?? 'medium', ORDER_GAP, authorId, authorId, ts, ts);
     const id = result.lastInsertRowid;
 
-    this.db.prepare('INSERT INTO epics_vec (rowid, embedding) VALUES (?, ?)').run(id, Buffer.from(new Float32Array(embedding).buffer));
+    this.db.prepare('INSERT INTO epics_vec (rowid, embedding) VALUES (?, ?)').run(BigInt(id as number | bigint), Buffer.from(new Float32Array(embedding).buffer));
 
     if (data.tags && data.tags.length > 0) this.helpers.setTags(GRAPH, num(id), data.tags);
 
@@ -235,6 +235,15 @@ export class SqliteEpicsStore implements EpicsStore {
     `).run(this.projectId, epicId, taskId);
   }
 
+  // =========================================================================
+  // Timestamps
+  // =========================================================================
+
+  getUpdatedAt(epicId: number): number | null {
+    const row = this.db.prepare('SELECT updated_at FROM epics WHERE id = ? AND project_id = ?').get(epicId, this.projectId) as { updated_at: bigint } | undefined;
+    return row ? num(row.updated_at) : null;
+  }
+
   // =========================================================================
   // Meta
   // =========================================================================

src/store/sqlite/stores/knowledge.ts

@@ -81,7 +81,7 @@ export class SqliteKnowledgeStore implements KnowledgeStore {
     const result = this.stmts.insert.run(this.projectId, slug, data.title, data.content, authorId, authorId, ts, ts);
     const id = result.lastInsertRowid;
 
-    this.stmts.insertVec.run(id, Buffer.from(new Float32Array(embedding).buffer));
+    this.stmts.insertVec.run(BigInt(id as number | bigint), Buffer.from(new Float32Array(embedding).buffer));
 
     if (data.tags && data.tags.length > 0) {
       this.helpers.setTags(GRAPH, num(id), data.tags);

src/store/sqlite/stores/skills.ts

@@ -13,7 +13,7 @@ import type {
 import { VersionConflictError } from '../../types';
 import { MetaHelper } from '../lib/meta';
 import { EntityHelpers } from '../lib/entity-helpers';
-import { num, now } from '../lib/bigint';
+import { num, now, safeJson } from '../lib/bigint';
 import { hybridSearch, SearchConfig } from '../lib/search';
 
 const GRAPH = 'skills';
@@ -42,10 +42,10 @@ export class SqliteSkillsStore implements SkillsStore {
       slug: row.slug as string,
       title: row.title as string,
       description: row.description as string,
-      steps: JSON.parse(row.steps_json as string),
-      triggers: JSON.parse(row.triggers_json as string),
-      inputHints: JSON.parse(row.input_hints_json as string),
-      filePatterns: JSON.parse(row.file_patterns_json as string),
+      steps: safeJson<string[]>(row.steps_json as string, []),
+      triggers: safeJson<string[]>(row.triggers_json as string, []),
+      inputHints: safeJson<string[]>(row.input_hints_json as string, []),
+      filePatterns: safeJson<string[]>(row.file_patterns_json as string, []),
       tags: tags ?? this.helpers.fetchTags(GRAPH, id),
       source: row.source as SkillRecord['source'],
       confidence: num(row.confidence as number),
@@ -84,7 +84,7 @@ export class SqliteSkillsStore implements SkillsStore {
     );
     const id = result.lastInsertRowid;
 
-    this.db.prepare('INSERT INTO skills_vec (rowid, embedding) VALUES (?, ?)').run(id, Buffer.from(new Float32Array(embedding).buffer));
+    this.db.prepare('INSERT INTO skills_vec (rowid, embedding) VALUES (?, ?)').run(BigInt(id as number | bigint), Buffer.from(new Float32Array(embedding).buffer));
 
     if (data.tags && data.tags.length > 0) this.helpers.setTags(GRAPH, num(id), data.tags);
 

src/store/sqlite/stores/tasks.ts

@@ -86,7 +86,7 @@ export class SqliteTasksStore implements TasksStore {
     );
     const id = result.lastInsertRowid;
 
-    this.db.prepare('INSERT INTO tasks_vec (rowid, embedding) VALUES (?, ?)').run(id, Buffer.from(new Float32Array(embedding).buffer));
+    this.db.prepare('INSERT INTO tasks_vec (rowid, embedding) VALUES (?, ?)').run(BigInt(id as number | bigint), Buffer.from(new Float32Array(embedding).buffer));
 
     if (data.tags && data.tags.length > 0) this.helpers.setTags(GRAPH_TASKS, num(id), data.tags);
 

src/store/types/epics.ts

@@ -64,4 +64,7 @@ export interface EpicsStore extends MetaMixin {
   search(query: SearchQuery): SearchResult[];
   linkTask(epicId: number, taskId: number): void;
   unlinkTask(epicId: number, taskId: number): void;
+
+  // --- Timestamps ---
+  getUpdatedAt(epicId: number): number | null;
 }

src/tests/store/contract/epics.test.ts

@@ -144,6 +144,40 @@ describe('EpicsStore contract', () => {
     expect(epics.get(epic.id)!.progress.total).toBe(1);
   });
 
+  // --- Hybrid search ---
+
+  it('hybrid search combines keyword and vector', () => {
+    epics.create({ title: 'MVP Release', description: 'Ship it' }, seedEmbedding(1));
+    epics.create({ title: 'Tech Debt', description: 'Cleanup' }, seedEmbedding(2));
+
+    const results = epics.search({ text: 'MVP', embedding: seedEmbedding(1), searchMode: 'hybrid' });
+    expect(results.length).toBeGreaterThan(0);
+  });
+
+  // --- Pagination edge cases ---
+
+  it('list with offset beyond total returns empty', () => {
+    epics.create({ title: 'Only', description: '' }, seedEmbedding(1));
+    const result = epics.list({ offset: 100 });
+    expect(result.results).toEqual([]);
+    expect(result.total).toBe(1);
+  });
+
+  // --- Null/empty input ---
+
+  it('creates epic with empty description', () => {
+    const epic = epics.create({ title: 'Minimal', description: '' }, seedEmbedding(1));
+    expect(epic.description).toBe('');
+  });
+
+  // --- Timestamps ---
+
+  it('getUpdatedAt works', () => {
+    const epic = epics.create({ title: 'T', description: '' }, seedEmbedding(1));
+    expect(epics.getUpdatedAt(epic.id)).toBe(epic.updatedAt);
+    expect(epics.getUpdatedAt(999)).toBeNull();
+  });
+
   // --- Meta ---
 
   it('meta is scoped', () => {