fix(store): N+1 attachments, FTS5 escaping, epic progress, orphan tags, dead columns

- Fix N+1 attachment queries in list() for knowledge, tasks, epics, skills
- Add nextOrder() to epics (was hardcoded 1000)
- Scope LEFT JOIN subqueries by project_id in docs/code listFiles
- Escape FTS5 query text (preserve AND/OR/NOT/NEAR operators)
- Epic progress: exclude cancelled from total, only count done
- Add kind='file' filter to files vector/hybrid search
- Fix resolveEdges to handle duplicate symbol names (remove LIMIT 1)
- Replace N+1 orphan tag cleanup with single DELETE...NOT EXISTS
- Remove dead file_count column from schema and FileNode type

Author: prih

src/store/sqlite/lib/entity-helpers.ts

@@ -20,14 +20,16 @@ export class EntityHelpers {
     this.db.prepare(`DELETE FROM edges WHERE project_id = ? AND to_graph = ? AND to_id = ? AND from_graph = 'tags' AND kind = 'tagged'`)
       .run(this.projectId, graph, entityId);
 
-    // Clean up orphaned tags (tags with no remaining edges)
-    for (const old of oldTagIds) {
-      const edgeCount = num((this.db.prepare(
-        `SELECT COUNT(*) AS c FROM edges WHERE project_id = ? AND from_graph = 'tags' AND from_id = ? AND kind = 'tagged'`
-      ).get(this.projectId, num(old.from_id)) as { c: bigint }).c);
-      if (edgeCount === 0) {
-        this.db.prepare('DELETE FROM tags WHERE id = ? AND project_id = ?').run(num(old.from_id), this.projectId);
-      }
+    // Clean up orphaned tags in one query
+    if (oldTagIds.length > 0) {
+      const ids = oldTagIds.map(o => num(o.from_id));
+      const ph = ids.map(() => '?').join(',');
+      this.db.prepare(`
+        DELETE FROM tags WHERE project_id = ? AND id IN (${ph})
+        AND NOT EXISTS (
+          SELECT 1 FROM edges WHERE project_id = tags.project_id AND from_graph = 'tags' AND from_id = tags.id AND kind = 'tagged'
+        )
+      `).run(this.projectId, ...ids);
     }
 
     // Insert new tags

src/store/sqlite/lib/search.ts

@@ -4,6 +4,19 @@ import { num } from './bigint';
 
 const RRF_K = 60;
 
+/**
+ * Escape user text for FTS5 MATCH — wrap each token in double quotes.
+ * Preserves FTS5 operators (AND, OR, NOT, NEAR) when used explicitly.
+ */
+function ftsEscape(text: string): string {
+  const FTS5_OPS = new Set(['AND', 'OR', 'NOT', 'NEAR']);
+  return text
+    .split(/\s+/)
+    .filter(t => t.length > 0)
+    .map(t => FTS5_OPS.has(t) ? t : `"${t.replace(/"/g, '""')}"`)
+    .join(' ');
+}
+
 /**
  * Configuration for hybrid search on a specific entity table.
  * Each store provides its own config pointing to its FTS5 and vec0 tables.
@@ -54,7 +67,7 @@ export function hybridSearch(
       JOIN ${config.parentTable} p ON p.${config.parentIdColumn} = fts.rowid AND p.project_id = ? ${extraJoin}
       WHERE ${config.ftsTable} MATCH ?
       LIMIT ?
-    `).all(projectId, query.text, topK) as Array<{ id: bigint; rn: bigint }>;
+    `).all(projectId, ftsEscape(query.text), topK) as Array<{ id: bigint; rn: bigint }>;
 
     ftsRanked = rows.map(r => ({ id: num(r.id), rn: num(r.rn) }));
   }

src/store/sqlite/migrations/v001.ts

@@ -377,7 +377,6 @@ CREATE TABLE files (
   language    TEXT,
   mime_type   TEXT,
   size        INTEGER NOT NULL DEFAULT 0,
-  file_count  INTEGER NOT NULL DEFAULT 0,
   mtime       INTEGER NOT NULL DEFAULT 0,
   UNIQUE(project_id, file_path)
 );

src/store/sqlite/stores/code.ts

@@ -149,18 +149,20 @@ export class SqliteCodeStore implements CodeStore {
   // =========================================================================
 
   resolveEdges(edges: Array<{ fromName: string; toName: string; kind: string }>): void {
-    const findByName = this.db.prepare('SELECT id FROM code WHERE project_id = ? AND name = ? AND kind != \'file\' LIMIT 1');
+    const findByName = this.db.prepare("SELECT id FROM code WHERE project_id = ? AND name = ? AND kind != 'file'");
     const insertEdge = this.db.prepare(`
       INSERT OR IGNORE INTO edges (project_id, from_graph, from_id, to_graph, to_id, kind)
       VALUES (?, 'code', ?, 'code', ?, ?)
     `);
 
     const run = this.db.transaction(() => {
       for (const edge of edges) {
-        const fromRow = findByName.get(this.projectId, edge.fromName) as { id: bigint } | undefined;
-        const toRow = findByName.get(this.projectId, edge.toName) as { id: bigint } | undefined;
-        if (fromRow && toRow) {
-          insertEdge.run(this.projectId, num(fromRow.id), num(toRow.id), edge.kind);
+        const fromRows = findByName.all(this.projectId, edge.fromName) as Array<{ id: bigint }>;
+        const toRows = findByName.all(this.projectId, edge.toName) as Array<{ id: bigint }>;
+        for (const fromRow of fromRows) {
+          for (const toRow of toRows) {
+            insertEdge.run(this.projectId, num(fromRow.id), num(toRow.id), edge.kind);
+          }
         }
       }
     });
@@ -195,11 +197,11 @@ export class SqliteCodeStore implements CodeStore {
         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
+        SELECT file_id, COUNT(*) AS cnt FROM code WHERE project_id = ? AND kind != 'file' GROUP BY file_id
+      ) s ON 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>>;
+    `).all(this.projectId, ...params, limit, offset) as Array<Record<string, unknown>>;
 
     const total = num((this.db.prepare(`SELECT COUNT(*) AS c FROM code f WHERE ${where}`).get(...params) as { c: bigint }).c);
 

src/store/sqlite/stores/docs.ts

@@ -182,11 +182,11 @@ export class SqliteDocsStore implements DocsStore {
         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
+        SELECT file_id, COUNT(*) AS cnt FROM docs WHERE project_id = ? AND kind = 'chunk' GROUP BY file_id
+      ) ch ON 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>>;
+    `).all(this.projectId, ...params, limit, offset) as Array<Record<string, unknown>>;
 
     const total = num((this.db.prepare(`SELECT COUNT(*) AS c FROM docs d WHERE ${where}`).get(...params) as { c: bigint }).c);
 

src/store/sqlite/stores/epics.ts

@@ -9,6 +9,7 @@ import type {
   EpicListOptions,
   EpicStatus,
   TaskPriority,
+  AttachmentMeta,
   SearchQuery,
   SearchResult,
 } from '../../types';
@@ -38,7 +39,7 @@ export class SqliteEpicsStore implements EpicsStore {
   // Helpers
   // =========================================================================
 
-  private toRecord(row: Record<string, unknown>, tags?: string[], progress?: { total: number; done: number }): EpicRecord {
+  private toRecord(row: Record<string, unknown>, tags?: string[], progress?: { total: number; done: number }, attachments?: AttachmentMeta[]): EpicRecord {
     const id = num(row.id as bigint);
     return {
       id,
@@ -50,7 +51,7 @@ export class SqliteEpicsStore implements EpicsStore {
       tags: tags ?? this.helpers.fetchTags(GRAPH, id),
       order: num(row.order as bigint | number),
       progress: progress ?? this.computeProgress(id),
-      attachments: this.helpers.fetchAttachments(GRAPH, id),
+      attachments: attachments ?? this.helpers.fetchAttachments(GRAPH, id),
       createdAt: num(row.created_at as bigint),
       updatedAt: num(row.updated_at as bigint),
       version: num(row.version as bigint),
@@ -66,8 +67,8 @@ export class SqliteEpicsStore implements EpicsStore {
 
   private computeProgress(epicId: number): { total: number; done: number } {
     const row = this.db.prepare(`
-      SELECT COUNT(*) AS total,
-             COALESCE(SUM(CASE WHEN t.status IN ('done', 'cancelled') THEN 1 ELSE 0 END), 0) AS done
+      SELECT COALESCE(SUM(CASE WHEN t.status != 'cancelled' THEN 1 ELSE 0 END), 0) AS total,
+             COALESCE(SUM(CASE WHEN t.status = 'done' THEN 1 ELSE 0 END), 0) AS done
       FROM edges e
       JOIN tasks t ON t.id = e.to_id AND t.project_id = e.project_id
       WHERE e.project_id = ? AND e.from_graph = 'epics' AND e.from_id = ? AND e.to_graph = 'tasks' AND e.kind = 'belongs_to'
@@ -82,8 +83,9 @@ export class SqliteEpicsStore implements EpicsStore {
 
     const ph = epicIds.map(() => '?').join(',');
     const rows = this.db.prepare(`
-      SELECT e.from_id AS epic_id, COUNT(*) AS total,
-        COALESCE(SUM(CASE WHEN t.status IN ('done', 'cancelled') THEN 1 ELSE 0 END), 0) AS done
+      SELECT e.from_id AS epic_id,
+        COALESCE(SUM(CASE WHEN t.status != 'cancelled' THEN 1 ELSE 0 END), 0) AS total,
+        COALESCE(SUM(CASE WHEN t.status = 'done' THEN 1 ELSE 0 END), 0) AS done
       FROM edges e
       JOIN tasks t ON t.id = e.to_id AND t.project_id = e.project_id
       WHERE e.project_id = ? AND e.from_graph = 'epics' AND e.to_graph = 'tasks' AND e.kind = 'belongs_to'
@@ -109,7 +111,7 @@ export class SqliteEpicsStore implements EpicsStore {
     const result = this.db.prepare(`
       INSERT INTO epics (project_id, slug, title, description, status, priority, "order", version, created_by_id, updated_by_id, created_at, updated_at)
       VALUES (?, ?, ?, ?, ?, ?, ?, 1, ?, ?, ?, ?)
-    `).run(this.projectId, slug, data.title, data.description ?? '', data.status ?? 'open', data.priority ?? 'medium', ORDER_GAP, authorId, authorId, ts, ts);
+    `).run(this.projectId, slug, data.title, data.description ?? '', data.status ?? 'open', data.priority ?? 'medium', this.nextOrder(), authorId, authorId, ts, ts);
     const id = result.lastInsertRowid;
 
     this.db.prepare('INSERT INTO epics_vec (rowid, embedding) VALUES (?, ?)').run(BigInt(id as number | bigint), Buffer.from(new Float32Array(embedding).buffer));
@@ -198,9 +200,7 @@ export class SqliteEpicsStore implements EpicsStore {
 
     const results = rows.map(r => {
       const id = num(r.id as bigint);
-      const record = this.toRecord(r, tagsMap.get(id), progressMap.get(id));
-      record.attachments = attachMap.get(id) ?? [];
-      return record;
+      return this.toRecord(r, tagsMap.get(id), progressMap.get(id), attachMap.get(id) ?? []);
     });
 
     return { results, total };
@@ -210,6 +210,11 @@ export class SqliteEpicsStore implements EpicsStore {
     return hybridSearch(this.db, SEARCH_CONFIG, query, this.projectId);
   }
 
+  private nextOrder(): number {
+    const row = this.db.prepare(`SELECT MAX("order") AS m FROM epics WHERE project_id = ?`).get(this.projectId) as { m: bigint | null };
+    return row.m ? num(row.m) + ORDER_GAP : ORDER_GAP;
+  }
+
   // =========================================================================
   // Link / Unlink tasks
   // =========================================================================

src/store/sqlite/stores/files.ts

@@ -34,7 +34,6 @@ export class SqliteFilesStore implements FilesStore {
       language: (row.language as string | null),
       mimeType: (row.mime_type as string | null),
       size: num(row.size as bigint),
-      fileCount: num(row.file_count as bigint),
       mtime: num(row.mtime as bigint),
     };
   }
@@ -58,8 +57,8 @@ export class SqliteFilesStore implements FilesStore {
     const dirName = path.basename(dirPath) || dirPath;
 
     const result = this.db.prepare(`
-      INSERT INTO files (project_id, kind, file_path, file_name, directory, extension, size, file_count, mtime)
-      VALUES (?, 'directory', ?, ?, ?, '', 0, 0, 0)
+      INSERT INTO files (project_id, kind, file_path, file_name, directory, extension, size, mtime)
+      VALUES (?, 'directory', ?, ?, ?, '', 0, 0)
     `).run(this.projectId, dirPath, dirName, parentDir === dirPath ? '' : parentDir);
 
     return num(result.lastInsertRowid as bigint);
@@ -233,7 +232,7 @@ export class SqliteFilesStore implements FilesStore {
       const rows = this.db.prepare(`
         SELECT v.rowid AS id, v.distance
         FROM files_vec v
-        JOIN files p ON p.id = v.rowid AND p.project_id = ?
+        JOIN files p ON p.id = v.rowid AND p.project_id = ? AND p.kind = 'file'
         WHERE v.embedding MATCH ? AND v.k = ?
       `).all(this.projectId, embeddingBuf, topK * 3) as Array<{ id: bigint; distance: number }>;
 
@@ -261,7 +260,7 @@ export class SqliteFilesStore implements FilesStore {
         const rows = this.db.prepare(`
           SELECT v.rowid AS id, v.distance
           FROM files_vec v
-          JOIN files p ON p.id = v.rowid AND p.project_id = ?
+          JOIN files p ON p.id = v.rowid AND p.project_id = ? AND p.kind = 'file'
           WHERE v.embedding MATCH ? AND v.k = ?
         `).all(this.projectId, embeddingBuf, topK * 3) as Array<{ id: bigint; distance: number }>;
         rows.slice(0, topK).forEach((r, i) => vecResults.push({ id: num(r.id), rn: i + 1 }));

src/store/sqlite/stores/knowledge.ts

@@ -6,6 +6,7 @@ import type {
   NotePatch,
   NoteRecord,
   NoteDetail,
+  AttachmentMeta,
   PaginationOptions,
   SearchQuery,
   SearchResult,
@@ -51,15 +52,15 @@ export class SqliteKnowledgeStore implements KnowledgeStore {
     };
   }
 
-  private toRecord(row: Record<string, unknown>, tags?: string[]): NoteRecord {
+  private toRecord(row: Record<string, unknown>, tags?: string[], attachments?: AttachmentMeta[]): NoteRecord {
     const id = num(row.id as bigint);
     return {
       id,
       slug: row.slug as string,
       title: row.title as string,
       content: row.content as string,
       tags: tags ?? this.helpers.fetchTags(GRAPH, id),
-      attachments: this.helpers.fetchAttachments(GRAPH, id),
+      attachments: attachments ?? this.helpers.fetchAttachments(GRAPH, id),
       createdAt: num(row.created_at as bigint),
       updatedAt: num(row.updated_at as bigint),
       version: num(row.version as bigint),
@@ -166,9 +167,7 @@ export class SqliteKnowledgeStore implements KnowledgeStore {
 
     const results = rows.map(r => {
       const id = num(r.id as bigint);
-      const record = this.toRecord(r, tagsMap.get(id));
-      record.attachments = attachMap.get(id) ?? [];
-      return record;
+      return this.toRecord(r, tagsMap.get(id), attachMap.get(id) ?? []);
     });
 
     return { results, total };

src/store/sqlite/stores/skills.ts

@@ -7,6 +7,7 @@ import type {
   SkillRecord,
   SkillDetail,
   SkillListOptions,
+  AttachmentMeta,
   SearchQuery,
   SearchResult,
 } from '../../types';
@@ -35,7 +36,7 @@ export class SqliteSkillsStore implements SkillsStore {
   // CRUD
   // =========================================================================
 
-  private toRecord(row: Record<string, unknown>, tags?: string[]): SkillRecord {
+  private toRecord(row: Record<string, unknown>, tags?: string[], attachments?: AttachmentMeta[]): SkillRecord {
     const id = num(row.id as bigint);
     return {
       id,
@@ -51,7 +52,7 @@ export class SqliteSkillsStore implements SkillsStore {
       confidence: num(row.confidence as number),
       usageCount: num(row.usage_count as bigint),
       lastUsedAt: row.last_used_at ? num(row.last_used_at as bigint) : null,
-      attachments: this.helpers.fetchAttachments(GRAPH, id),
+      attachments: attachments ?? this.helpers.fetchAttachments(GRAPH, id),
       createdAt: num(row.created_at as bigint),
       updatedAt: num(row.updated_at as bigint),
       version: num(row.version as bigint),
@@ -172,9 +173,7 @@ export class SqliteSkillsStore implements SkillsStore {
 
     const results = rows.map(r => {
       const id = num(r.id as bigint);
-      const record = this.toRecord(r, tagsMap.get(id));
-      record.attachments = attachMap.get(id) ?? [];
-      return record;
+      return this.toRecord(r, tagsMap.get(id), attachMap.get(id) ?? []);
     });
 
     return { results, total };

src/store/sqlite/stores/tasks.ts

@@ -9,6 +9,7 @@ import type {
   TaskListOptions,
   TaskStatus,
   TaskPriority,
+  AttachmentMeta,
   SearchQuery,
   SearchResult,
 } from '../../types';
@@ -40,7 +41,7 @@ export class SqliteTasksStore implements TasksStore {
   // Task CRUD
   // =========================================================================
 
-  private toTaskRecord(row: Record<string, unknown>, tags?: string[]): TaskRecord {
+  private toTaskRecord(row: Record<string, unknown>, tags?: string[], attachments?: AttachmentMeta[]): TaskRecord {
     const id = num(row.id as bigint);
     return {
       id,
@@ -55,7 +56,7 @@ export class SqliteTasksStore implements TasksStore {
       estimate: row.estimate ? num(row.estimate as bigint) : null,
       completedAt: row.completed_at ? num(row.completed_at as bigint) : null,
       assigneeId: row.assignee_id ? num(row.assignee_id as bigint) : null,
-      attachments: this.helpers.fetchAttachments(GRAPH_TASKS, id),
+      attachments: attachments ?? this.helpers.fetchAttachments(GRAPH_TASKS, id),
       createdAt: num(row.created_at as bigint),
       updatedAt: num(row.updated_at as bigint),
       version: num(row.version as bigint),
@@ -178,9 +179,7 @@ export class SqliteTasksStore implements TasksStore {
 
     const results = rows.map(r => {
       const id = num(r.id as bigint);
-      const record = this.toTaskRecord(r, tagsMap.get(id));
-      record.attachments = attachMap.get(id) ?? [];
-      return record;
+      return this.toTaskRecord(r, tagsMap.get(id), attachMap.get(id) ?? []);
     });
 
     return { results, total };