feat(store): unified edges, single-table indexed stores, graph-prefixed schema

- Unified Edge type replaces Relation + CrossLink (one edges table)
- Code, Docs, Files: single table per graph with kind field
- Cleanup triggers on all entity tables (edges + attachments + vec0)
- Tags as entities with edges (kind='tagged'), inline in records
- Attachments: metadata only (url optional, no BLOB)
- CASCADE on all project_id FKs
- Search tests: keyword, vector, hybrid, project isolation
- All imports use @/ alias
- 31 tests passing

Author: prih

src/store/sqlite/migrations/v001.ts

@@ -34,24 +34,22 @@ CREATE TABLE team_members (
 );
 
 CREATE TABLE tags (
-  project_id INTEGER NOT NULL,
-  graph      TEXT NOT NULL,
-  entity_id  INTEGER NOT NULL,
-  tag        TEXT NOT NULL,
-  PRIMARY KEY (project_id, graph, entity_id, tag)
+  id         INTEGER PRIMARY KEY AUTOINCREMENT,
+  project_id INTEGER NOT NULL REFERENCES projects(id) ON DELETE CASCADE,
+  name       TEXT NOT NULL,
+  UNIQUE(project_id, name)
 );
-CREATE INDEX idx_tags_tag ON tags(tag);
-CREATE INDEX idx_tags_entity ON tags(graph, entity_id);
+CREATE INDEX idx_tags_project ON tags(project_id);
 
 CREATE TABLE attachments (
   id         INTEGER PRIMARY KEY AUTOINCREMENT,
-  project_id INTEGER NOT NULL,
+  project_id INTEGER NOT NULL REFERENCES projects(id) ON DELETE CASCADE,
   graph      TEXT NOT NULL,
   entity_id  INTEGER NOT NULL,
   filename   TEXT NOT NULL,
   mime_type  TEXT NOT NULL,
   size       INTEGER NOT NULL,
-  data       BLOB NOT NULL,
+  url        TEXT,
   added_at   INTEGER NOT NULL DEFAULT (unixepoch('now','subsec') * 1000),
   UNIQUE(project_id, graph, entity_id, filename)
 );
@@ -107,6 +105,14 @@ END;
 
 CREATE VIRTUAL TABLE knowledge_vec USING vec0(embedding float[${EMBEDDING_DIM}]);
 
+CREATE TRIGGER knowledge_cleanup AFTER DELETE ON knowledge BEGIN
+  DELETE FROM edges WHERE
+    (from_graph = 'knowledge' AND from_id = old.id AND project_id = old.project_id) OR
+    (to_graph = 'knowledge' AND to_id = old.id AND project_id = old.project_id);
+  DELETE FROM attachments WHERE graph = 'knowledge' AND entity_id = old.id AND project_id = old.project_id;
+  DELETE FROM knowledge_vec WHERE rowid = old.id;
+END;
+
 -- =============================================
 -- Tasks
 -- =============================================
@@ -150,6 +156,14 @@ END;
 
 CREATE VIRTUAL TABLE tasks_vec USING vec0(embedding float[${EMBEDDING_DIM}]);
 
+CREATE TRIGGER tasks_cleanup AFTER DELETE ON tasks BEGIN
+  DELETE FROM edges WHERE
+    (from_graph = 'tasks' AND from_id = old.id AND project_id = old.project_id) OR
+    (to_graph = 'tasks' AND to_id = old.id AND project_id = old.project_id);
+  DELETE FROM attachments WHERE graph = 'tasks' AND entity_id = old.id AND project_id = old.project_id;
+  DELETE FROM tasks_vec WHERE rowid = old.id;
+END;
+
 -- =============================================
 -- Epics
 -- =============================================
@@ -188,6 +202,14 @@ END;
 
 CREATE VIRTUAL TABLE epics_vec USING vec0(embedding float[${EMBEDDING_DIM}]);
 
+CREATE TRIGGER epics_cleanup AFTER DELETE ON epics BEGIN
+  DELETE FROM edges WHERE
+    (from_graph = 'epics' AND from_id = old.id AND project_id = old.project_id) OR
+    (to_graph = 'epics' AND to_id = old.id AND project_id = old.project_id);
+  DELETE FROM attachments WHERE graph = 'epics' AND entity_id = old.id AND project_id = old.project_id;
+  DELETE FROM epics_vec WHERE rowid = old.id;
+END;
+
 -- =============================================
 -- Skills
 -- =============================================
@@ -231,6 +253,14 @@ END;
 
 CREATE VIRTUAL TABLE skills_vec USING vec0(embedding float[${EMBEDDING_DIM}]);
 
+CREATE TRIGGER skills_cleanup AFTER DELETE ON skills BEGIN
+  DELETE FROM edges WHERE
+    (from_graph = 'skills' AND from_id = old.id AND project_id = old.project_id) OR
+    (to_graph = 'skills' AND to_id = old.id AND project_id = old.project_id);
+  DELETE FROM attachments WHERE graph = 'skills' AND entity_id = old.id AND project_id = old.project_id;
+  DELETE FROM skills_vec WHERE rowid = old.id;
+END;
+
 -- =============================================
 -- Code (one table — file nodes + symbol nodes, linked via edges)
 -- =============================================
@@ -275,6 +305,13 @@ END;
 
 CREATE VIRTUAL TABLE code_vec USING vec0(embedding float[${EMBEDDING_DIM}]);
 
+CREATE TRIGGER code_cleanup AFTER DELETE ON code BEGIN
+  DELETE FROM edges WHERE
+    (from_graph = 'code' AND from_id = old.id AND project_id = old.project_id) OR
+    (to_graph = 'code' AND to_id = old.id AND project_id = old.project_id);
+  DELETE FROM code_vec WHERE rowid = old.id;
+END;
+
 -- =============================================
 -- Docs (one table — file nodes + chunk nodes, linked via edges)
 -- =============================================
@@ -311,6 +348,13 @@ END;
 
 CREATE VIRTUAL TABLE docs_vec USING vec0(embedding float[${EMBEDDING_DIM}]);
 
+CREATE TRIGGER docs_cleanup AFTER DELETE ON docs BEGIN
+  DELETE FROM edges WHERE
+    (from_graph = 'docs' AND from_id = old.id AND project_id = old.project_id) OR
+    (to_graph = 'docs' AND to_id = old.id AND project_id = old.project_id);
+  DELETE FROM docs_vec WHERE rowid = old.id;
+END;
+
 -- =============================================
 -- Files (one table — file nodes + directory nodes, linked via edges)
 -- =============================================
@@ -335,5 +379,19 @@ CREATE INDEX idx_files_dir ON files(project_id, directory);
 CREATE INDEX idx_files_kind ON files(project_id, kind);
 
 CREATE VIRTUAL TABLE files_vec USING vec0(embedding float[${EMBEDDING_DIM}]);
+
+CREATE TRIGGER files_cleanup AFTER DELETE ON files BEGIN
+  DELETE FROM edges WHERE
+    (from_graph = 'files' AND from_id = old.id AND project_id = old.project_id) OR
+    (to_graph = 'files' AND to_id = old.id AND project_id = old.project_id);
+  DELETE FROM files_vec WHERE rowid = old.id;
+END;
+
+-- Tags cleanup: when a tag is deleted, remove its edges
+CREATE TRIGGER tags_cleanup AFTER DELETE ON tags BEGIN
+  DELETE FROM edges WHERE
+    (from_graph = 'tags' AND from_id = old.id AND project_id = old.project_id) OR
+    (to_graph = 'tags' AND to_id = old.id AND project_id = old.project_id);
+END;
 `,
 };

src/store/types/attachments.ts

@@ -1,34 +1,28 @@
 import type { GraphName } from './common';
 
 // ---------------------------------------------------------------------------
-// Attachments Store (shared across all graphs)
+// Attachments Store (metadata registry, files stored externally)
 // ---------------------------------------------------------------------------
 
 export interface AttachmentMeta {
   filename: string;
   mimeType: string;
   size: number;
+  /** Optional external URL (S3, CDN). If absent — file is in mirror directory */
+  url?: string;
   addedAt: number;
 }
 
-export interface AttachmentRecord extends AttachmentMeta {
-  graph: GraphName;
-  entityId: number;
-}
-
 export interface AttachmentsStore {
-  /** Add an attachment to an entity */
-  add(graph: GraphName, entityId: number, filename: string, data: Buffer): AttachmentMeta;
+  /** Register an attachment */
+  add(graph: GraphName, entityId: number, meta: AttachmentMeta): void;
 
-  /** Remove an attachment from an entity */
+  /** Remove an attachment record */
   remove(graph: GraphName, entityId: number, filename: string): void;
 
-  /** Remove all attachments for an entity (e.g. on delete) */
+  /** Remove all attachment records for an entity */
   removeAll(graph: GraphName, entityId: number): void;
 
   /** List attachments for an entity */
   list(graph: GraphName, entityId: number): AttachmentMeta[];
-
-  /** Get attachment file path (for serving) */
-  getPath(graph: GraphName, entityId: number, filename: string): string | null;
 }

src/store/types/knowledge.ts

@@ -8,12 +8,14 @@ import type { AttachmentMeta } from './attachments';
 export interface NoteCreate {
   title: string;
   content: string;
+  tags?: string[];
   authorId?: number;
 }
 
 export interface NotePatch {
   title?: string;
   content?: string;
+  tags?: string[];
 }
 
 export interface NoteRecord {

src/store/types/skills.ts

@@ -14,6 +14,7 @@ export interface SkillCreate {
   triggers?: string[];
   inputHints?: string[];
   filePatterns?: string[];
+  tags?: string[];
   source?: SkillSource;
   confidence?: number;
   authorId?: number;
@@ -26,6 +27,7 @@ export interface SkillPatch {
   triggers?: string[];
   inputHints?: string[];
   filePatterns?: string[];
+  tags?: string[];
   source?: SkillSource;
   confidence?: number;
 }

src/store/types/store.ts

@@ -5,7 +5,6 @@ import type { FilesStore } from './files';
 import type { KnowledgeStore } from './knowledge';
 import type { TasksStore } from './tasks';
 import type { SkillsStore } from './skills';
-import type { TagsStore } from './tags';
 import type { AttachmentsStore } from './attachments';
 import type { ProjectsStore } from './projects';
 import type { TeamStore } from './team';
@@ -23,7 +22,6 @@ export interface ProjectScopedStore {
   readonly knowledge: KnowledgeStore;
   readonly tasks: TasksStore;
   readonly skills: SkillsStore;
-  readonly tags: TagsStore;
   readonly attachments: AttachmentsStore;
 
   // --- Edges (unified graph edges — same-graph and cross-graph) ---

src/store/types/tags.ts

@@ -1,34 +1,12 @@
-import type { GraphName, PaginationOptions } from './common';
-
 // ---------------------------------------------------------------------------
-// Tags Store (shared across all graphs)
+// Tags (per-project entities, linked to other entities via edges)
+//
+// Tags are managed internally by each store's create/update methods.
+// No separate TagsStore — tags flow through Create/Patch/Record interfaces
+// and are stored in the `tags` table + `edges` table (kind='tagged').
 // ---------------------------------------------------------------------------
 
-export interface TagEntry {
-  tag: string;
-  /** How many entities use this tag (across all graphs) */
-  count: number;
-}
-
-export interface EntityTag {
-  graph: GraphName;
-  entityId: number;
-  tag: string;
-}
-
-export interface TagsStore {
-  /** Set tags for an entity (replaces previous tags) */
-  set(graph: GraphName, entityId: number, tags: string[]): void;
-
-  /** Get all tags for an entity */
-  get(graph: GraphName, entityId: number): string[];
-
-  /** Remove all tags for an entity (e.g. on delete) */
-  remove(graph: GraphName, entityId: number): void;
-
-  /** List all known tags with usage counts, optionally filtered by graph */
-  list(graph?: GraphName, pagination?: PaginationOptions): { results: TagEntry[]; total: number };
-
-  /** Find all entities that have a given tag, optionally filtered by graph */
-  findByTag(tag: string, graph?: GraphName, pagination?: PaginationOptions): { results: EntityTag[]; total: number };
+export interface TagRecord {
+  id: number;
+  name: string;
 }

src/store/types/tasks.ts

@@ -14,6 +14,7 @@ export interface TaskCreate {
   description: string;
   status?: TaskStatus;
   priority?: TaskPriority;
+  tags?: string[];
   dueDate?: number | null;
   estimate?: number | null;
   assigneeId?: number | null;
@@ -26,6 +27,7 @@ export interface TaskPatch {
   description?: string;
   status?: TaskStatus;
   priority?: TaskPriority;
+  tags?: string[];
   dueDate?: number | null;
   estimate?: number | null;
   assigneeId?: number | null;
@@ -75,6 +77,7 @@ export interface EpicCreate {
   description: string;
   status?: EpicStatus;
   priority?: TaskPriority;
+  tags?: string[];
   authorId?: number;
 }
 
@@ -83,6 +86,7 @@ export interface EpicPatch {
   description?: string;
   status?: EpicStatus;
   priority?: TaskPriority;
+  tags?: string[];
 }
 
 export interface EpicRecord {

src/tests/store/helpers.ts

@@ -1,7 +1,7 @@
 import { mkdtempSync, rmSync } from 'fs';
 import { tmpdir } from 'os';
 import { join } from 'path';
-import { SqliteStore } from '../../store';
+import { SqliteStore } from '@/store';
 
 export const TEST_DIM = 384;
 

src/tests/store/sqlite/bigint.test.ts

@@ -1,4 +1,4 @@
-import { num, now } from '../../../store/sqlite/lib/bigint';
+import { num, now } from '@/store/sqlite/lib/bigint';
 
 describe('BigInt helpers', () => {
   it('num converts BigInt to number', () => {

src/tests/store/sqlite/db.test.ts

@@ -3,7 +3,7 @@ import { existsSync } from 'fs';
 import { join } from 'path';
 import { mkdtempSync, rmSync } from 'fs';
 import { tmpdir } from 'os';
-import { SqliteStore } from '../../../store';
+import { SqliteStore } from '@/store';
 
 describe('SQLite DB lifecycle', () => {
   const factory = createSqliteStoreFactory();