latticesql 0.16.0 → 0.16.2

package/README.md

@@ -376,15 +376,21 @@ db.defineEntityContext('agents', {
   // Files inside each entity's directory
   files: {
     'AGENT.md': {
-      source: { type: 'self' },                        // entity's own row
-      render: ([r]) => `# ${r.name as string}\n\n${r.bio as string ?? ''}`,
+      source: { type: 'self' }, // entity's own row
+      render: ([r]) => `# ${r.name as string}\n\n${(r.bio as string) ?? ''}`,
     },
     'TASKS.md': {
-      source: { type: 'hasMany', table: 'tasks', foreignKey: 'agent_id',
-                orderBy: 'created_at', orderDir: 'desc', limit: 20 },
+      source: {
+        type: 'hasMany',
+        table: 'tasks',
+        foreignKey: 'agent_id',
+        orderBy: 'created_at',
+        orderDir: 'desc',
+        limit: 20,
+      },
       render: (rows) => rows.map((r) => `- ${r.title as string}`).join('\n'),
-      omitIfEmpty: true,                               // skip if no tasks
-      budget: 4000,                                    // truncate at 4 000 chars
+      omitIfEmpty: true, // skip if no tasks
+      budget: 4000, // truncate at 4 000 chars
     },
     'SKILLS.md': {
       source: {
@@ -393,7 +399,7 @@ db.defineEntityContext('agents', {
         localKey: 'agent_id',
         remoteKey: 'skill_id',
         remoteTable: 'skills',
-        orderBy: 'name',                               // softDelete inherited from sourceDefaults
+        orderBy: 'name', // softDelete inherited from sourceDefaults
       },
       render: (rows) => rows.map((r) => `- ${r.name as string}`).join('\n'),
       omitIfEmpty: true,
@@ -426,14 +432,14 @@ context/
 
 **Source types:**
 
-| Type | What it queries |
-|---|---|
-| `{ type: 'self' }` | The entity row itself |
-| `{ type: 'hasMany', table, foreignKey, ... }` | Rows in `table` where `foreignKey = entityPk` |
-| `{ type: 'manyToMany', junctionTable, localKey, remoteKey, remoteTable, ... }` | Remote rows via a junction table |
-| `{ type: 'belongsTo', table, foreignKey, ... }` | Single parent row via FK on this entity (`null` FK → empty) |
-| `{ type: 'enriched', include: { ... } }` | Entity row + related data attached as `_key` JSON fields (v0.7+) |
-| `{ type: 'custom', query: (row, adapter) => Row[] }` | Fully custom synchronous query |
+| Type                                                                           | What it queries                                                  |
+| ------------------------------------------------------------------------------ | ---------------------------------------------------------------- |
+| `{ type: 'self' }`                                                             | The entity row itself                                            |
+| `{ type: 'hasMany', table, foreignKey, ... }`                                  | Rows in `table` where `foreignKey = entityPk`                    |
+| `{ type: 'manyToMany', junctionTable, localKey, remoteKey, remoteTable, ... }` | Remote rows via a junction table                                 |
+| `{ type: 'belongsTo', table, foreignKey, ... }`                                | Single parent row via FK on this entity (`null` FK → empty)      |
+| `{ type: 'enriched', include: { ... } }`                                       | Entity row + related data attached as `_key` JSON fields (v0.7+) |
+| `{ type: 'custom', query: (row, adapter) => Row[] }`                           | Fully custom synchronous query                                   |
 
 #### Source query options (v0.6+)
 
@@ -502,7 +508,7 @@ Set default query options for all relationship sources in an entity context:
 ```typescript
 db.defineEntityContext('agents', {
   slug: (row) => row.slug as string,
-  sourceDefaults: { softDelete: true },  // applied to all hasMany/manyToMany/belongsTo
+  sourceDefaults: { softDelete: true }, // applied to all hasMany/manyToMany/belongsTo
   files: {
     'TASKS.md': {
       // softDelete: true is inherited from sourceDefaults
@@ -548,6 +554,7 @@ Starts with the entity's own row and attaches related data as JSON string fields
 `EntityFileSpec.render` accepts declarative template objects in addition to functions. Three built-in templates:
 
 **entity-table** — heading + GFM table:
+
 ```typescript
 render: {
   template: 'entity-table',
@@ -562,6 +569,7 @@ render: {
 ```
 
 **entity-profile** — heading + field-value pairs + enriched JSON sections:
+
 ```typescript
 render: {
   template: 'entity-profile',
@@ -581,6 +589,7 @@ render: {
 ```
 
 **entity-sections** — per-row sections with metadata + body:
+
 ```typescript
 render: {
   template: 'entity-sections',
@@ -615,7 +624,7 @@ Register a post-write lifecycle hook that fires after `insert()`, `update()`, or
 db.defineWriteHook({
   table: 'agents',
   on: ['insert', 'update'],
-  watchColumns: ['team_id', 'division'],  // only fire when these change
+  watchColumns: ['team_id', 'division'], // only fire when these change
   handler: (ctx) => {
     // ctx.table, ctx.op, ctx.row, ctx.pk, ctx.changedColumns
     console.log(`${ctx.op} on ${ctx.table}: ${ctx.pk}`);
@@ -626,12 +635,12 @@ db.defineWriteHook({
 
 **Options:**
 
-| Field | Type | Description |
-|---|---|---|
-| `table` | `string` | Table to watch |
-| `on` | `Array<'insert' \| 'update' \| 'delete'>` | Operations that trigger the hook |
-| `watchColumns` | `string[]` (optional) | Only fire on update when these columns changed |
-| `handler` | `(ctx: WriteHookContext) => void` | Synchronous handler |
+| Field          | Type                                      | Description                                    |
+| -------------- | ----------------------------------------- | ---------------------------------------------- |
+| `table`        | `string`                                  | Table to watch                                 |
+| `on`           | `Array<'insert' \| 'update' \| 'delete'>` | Operations that trigger the hook               |
+| `watchColumns` | `string[]` (optional)                     | Only fire on update when these columns changed |
+| `handler`      | `(ctx: WriteHookContext) => void`         | Synchronous handler                            |
 
 Hook errors are caught and routed to error handlers — they never crash the caller. Multiple hooks per table are supported.
 
@@ -677,9 +686,16 @@ Methods that work on **any table** — including tables created via raw DDL (not
 
 ```typescript
 // Upsert by natural key (not just UUID). Auto-handles org_id, updated_at, deleted_at.
-const id = await db.upsertByNaturalKey('agents', 'name', 'Alice', {
-  role: 'engineer', status: 'active',
-}, { sourceFile: 'agents.md', orgId: 'org-1' });
+const id = await db.upsertByNaturalKey(
+  'agents',
+  'name',
+  'Alice',
+  {
+    role: 'engineer',
+    status: 'active',
+  },
+  { sourceFile: 'agents.md', orgId: 'org-1' },
+);
 
 // Sparse update — only writes non-null fields.
 await db.enrichByNaturalKey('agents', 'name', 'Alice', { title: 'Senior Engineer' });
@@ -700,7 +716,11 @@ const alice = await db.getByNaturalKey('agents', 'name', 'Alice');
 await db.link('agent_skills', { agent_id: 'a1', skill_id: 's1', proficiency: 'expert' });
 
 // Link with upsert (INSERT OR REPLACE — updates existing)
-await db.link('agent_projects', { agent_id: 'a1', project_id: 'p1', role: 'lead' }, { upsert: true });
+await db.link(
+  'agent_projects',
+  { agent_id: 'a1', project_id: 'p1', role: 'lead' },
+  { upsert: true },
+);
 
 // Unlink (DELETE matching rows)
 await db.unlink('agent_projects', { agent_id: 'a1', project_id: 'p1' });
@@ -748,11 +768,19 @@ Declarative report builder — queries data within a time window, groups into se
 
 ```typescript
 const report = await db.buildReport({
-  since: '8h',   // or '24h', '7d', or ISO timestamp
+  since: '8h', // or '24h', '7d', or ISO timestamp
   sections: [
-    { name: 'tasks', query: { table: 'tasks', orderBy: 'created_at', orderDir: 'desc' }, format: 'count_and_list' },
+    {
+      name: 'tasks',
+      query: { table: 'tasks', orderBy: 'created_at', orderDir: 'desc' },
+      format: 'count_and_list',
+    },
     { name: 'events', query: { table: 'activity', groupBy: 'type' }, format: 'counts' },
-    { name: 'alerts', query: { table: 'activity', filters: [{ col: 'severity', op: 'lte', val: 2 }] }, format: 'list' },
+    {
+      name: 'alerts',
+      query: { table: 'activity', filters: [{ col: 'severity', op: 'lte', val: 2 }] },
+      format: 'list',
+    },
   ],
 });
 
@@ -771,11 +799,13 @@ import { createSQLiteStateStore } from 'latticesql';
 
 db.defineWriteback({
   file: './agents/*/SESSION.md',
-  stateStore: createSQLiteStateStore(db.db),  // persists offsets in SQLite
+  stateStore: createSQLiteStateStore(db.db), // persists offsets in SQLite
   parse: (content, offset) => myParser(content, offset),
-  persist: async (entry, filePath) => { /* ... */ },
+  persist: async (entry, filePath) => {
+    /* ... */
+  },
   dedupeKey: (entry) => entry.id,
-  onArchive: (filePath) => archiveFile(filePath),  // lifecycle hook
+  onArchive: (filePath) => archiveFile(filePath), // lifecycle hook
 });
 ```
 
@@ -1046,9 +1076,9 @@ stop();
 const stop = await db.watch('./context', {
   interval: 10_000,
   cleanup: {
-    removeOrphanedDirectories: true,  // delete dirs for deleted entities
-    removeOrphanedFiles: true,        // delete stale relationship files
-    protectedFiles: ['SESSION.md'],   // never delete these
+    removeOrphanedDirectories: true, // delete dirs for deleted entities
+    removeOrphanedFiles: true, // delete stale relationship files
+    protectedFiles: ['SESSION.md'], // never delete these
     dryRun: false,
   },
   onCleanup: (r) => {
@@ -1074,15 +1104,15 @@ const result = await db.reconcile('./context', {
   removeOrphanedDirectories: true,
   removeOrphanedFiles: true,
   protectedFiles: ['SESSION.md'],
-  reverseSync: true,                    // default; set false to skip, 'dry-run' to preview
-  dryRun: false,                        // set true to preview without deleting
+  reverseSync: true, // default; set false to skip, 'dry-run' to preview
+  dryRun: false, // set true to preview without deleting
   onOrphan: (path, kind) => console.log(`would remove ${kind}: ${path}`),
 });
 
-console.log(result.filesWritten);           // files written this cycle
-console.log(result.cleanup.directoriesRemoved);  // orphaned dirs removed
-console.log(result.cleanup.warnings);            // dirs left in place (user files)
-console.log(result.reverseSync);                 // { filesScanned, filesChanged, updatesApplied, errors }
+console.log(result.filesWritten); // files written this cycle
+console.log(result.cleanup.directoriesRemoved); // orphaned dirs removed
+console.log(result.cleanup.warnings); // dirs left in place (user files)
+console.log(result.reverseSync); // { filesScanned, filesChanged, updatesApplied, errors }
 ```
 
 `ReconcileResult` extends `RenderResult` with `cleanup` and `reverseSync` fields:
@@ -1278,9 +1308,9 @@ Generate a GitHub-Flavoured Markdown table from rows with explicit column config
 import { markdownTable } from 'latticesql';
 
 const md = markdownTable(rows, [
-  { key: 'name',   header: 'Name' },
+  { key: 'name', header: 'Name' },
   { key: 'status', header: 'Status', format: (v) => String(v || '—') },
-  { key: 'name',   header: 'Detail', format: (v, row) => `[view](${row.slug}/DETAIL.md)` },
+  { key: 'name', header: 'Detail', format: (v, row) => `[view](${row.slug}/DETAIL.md)` },
 ]);
 // | Name | Status | Detail |
 // | --- | --- | --- |
@@ -1296,8 +1326,8 @@ Generate a URL-safe slug from a display name — lowercases, strips diacritics,
 ```typescript
 import { slugify } from 'latticesql';
 
-slugify('My Agent Name');  // 'my-agent-name'
-slugify('Jose Garcia');    // 'jose-garcia'
+slugify('My Agent Name'); // 'my-agent-name'
+slugify('Jose Garcia'); // 'jose-garcia'
 ```
 
 ### `truncate(content, maxChars, notice?)`
@@ -1332,7 +1362,7 @@ db.defineEntityContext('projects', {
   files: {
     'PROJECT.md': {
       source: { type: 'self' },
-      render: ([r]) => `# ${r.name as string}\n\n${r.description as string ?? ''}`,
+      render: ([r]) => `# ${r.name as string}\n\n${(r.description as string) ?? ''}`,
     },
   },
 });
@@ -1358,7 +1388,7 @@ await db.delete('projects', 'old-id');
 
 const result = await db.reconcile('./ctx', {
   removeOrphanedDirectories: true,
-  protectedFiles: ['NOTES.md'],   // agents wrote these — keep them
+  protectedFiles: ['NOTES.md'], // agents wrote these — keep them
 });
 // result.cleanup.directoriesRemoved → ['/.../ctx/projects/old-project']
 ```
@@ -1373,7 +1403,9 @@ Declare files that agents write inside entity directories. Lattice will never de
 db.defineEntityContext('agents', {
   slug: (r) => r.slug as string,
   protectedFiles: ['SESSION.md', 'NOTES.md'],
-  files: { /* ... */ },
+  files: {
+    /* ... */
+  },
 });
 ```
 
@@ -1417,18 +1449,18 @@ target: agent-id-here
 reason: Updating status after deployment completed.
 ---
 status: active
-last_task: piut-deploy
+last_task: api-deploy
 ===
 ```
 
-| Header | Required | Description |
-|--------|----------|-------------|
-| `type` | Yes | Must be `write` |
-| `timestamp` | Yes | ISO 8601 |
-| `op` | Yes | `create`, `update`, or `delete` |
-| `table` | Yes | Target table name |
-| `target` | For update/delete | Record primary key |
-| `reason` | Encouraged | Human-readable reason (audit trail) |
+| Header      | Required          | Description                         |
+| ----------- | ----------------- | ----------------------------------- |
+| `type`      | Yes               | Must be `write`                     |
+| `timestamp` | Yes               | ISO 8601                            |
+| `op`        | Yes               | `create`, `update`, or `delete`     |
+| `table`     | Yes               | Target table name                   |
+| `target`    | For update/delete | Record primary key                  |
+| `reason`    | Encouraged        | Human-readable reason (audit trail) |
 
 **Body**: `key: value` pairs — one field per line. Field names are validated against the table schema before any write is applied.
 
@@ -1449,15 +1481,16 @@ for (const entry of result.entries) {
 ```
 
 **`SessionWriteEntry`:**
+
 ```ts
 interface SessionWriteEntry {
-  id: string;                       // content-addressed ID
-  timestamp: string;                // ISO 8601
+  id: string; // content-addressed ID
+  timestamp: string; // ISO 8601
   op: 'create' | 'update' | 'delete';
   table: string;
-  target?: string;                  // required for update/delete
+  target?: string; // required for update/delete
   reason?: string;
-  fields: Record<string, string>;  // empty for delete
+  fields: Record<string, string>; // empty for delete
 }
 ```
 

package/dist/cli.js

@@ -47,13 +47,13 @@ function buildParsedConfig(raw, sourceName, configDir) {
   const dbPath = resolve(configDir, config.db);
   const tables = [];
   for (const [entityName, entityDef] of Object.entries(config.entities)) {
-    const definition = entityToTableDef(entityName, entityDef, configDir);
+    const definition = entityToTableDef(entityName, entityDef);
     tables.push({ name: entityName, definition });
   }
   const entityContexts = parseEntityContexts(config.entityContexts);
   return { dbPath, tables, entityContexts };
 }
-function entityToTableDef(entityName, entity, configDir) {
+function entityToTableDef(entityName, entity) {
   const rawFields = entity.fields;
   if (!rawFields || typeof rawFields !== "object" || Array.isArray(rawFields)) {
     throw new Error(`Lattice: entity "${entityName}" must have a "fields" object`);
@@ -77,7 +77,7 @@ function entityToTableDef(entityName, entity, configDir) {
   }
   const primaryKey = entity.primaryKey ?? pkFromField;
   const render = parseEntityRender(entity.render);
-  const outputFile = resolve(configDir, entity.outputFile);
+  const outputFile = entity.outputFile;
   return {
     columns,
     render,
@@ -528,7 +528,9 @@ var SchemaManager = class {
     if (this._entityContexts.has(name)) {
       const cols = adapter.all(`PRAGMA table_info("${name}")`);
       const hasDeletedAt = cols.some((c) => c.name === "deleted_at");
-      return adapter.all(`SELECT * FROM "${name}"${hasDeletedAt ? " WHERE deleted_at IS NULL" : ""}`);
+      return adapter.all(
+        `SELECT * FROM "${name}"${hasDeletedAt ? " WHERE deleted_at IS NULL" : ""}`
+      );
     }
     throw new Error(`Unknown table: "${name}"`);
   }
@@ -1100,7 +1102,14 @@ var RenderEngine = class {
       const slugs = new Set(rows.map((row) => def.slug(row)));
       currentSlugsByTable.set(table, slugs);
     }
-    return cleanupEntityContexts(outputDir, entityContexts, currentSlugsByTable, prevManifest, options, newManifest);
+    return cleanupEntityContexts(
+      outputDir,
+      entityContexts,
+      currentSlugsByTable,
+      prevManifest,
+      options,
+      newManifest
+    );
   }
   /**
    * Render all entity context definitions.
@@ -1215,7 +1224,6 @@ var ReverseSyncEngine = class {
         }
       }
       if (reverseSyncFiles.size === 0) continue;
-      const entityPk = this._schema.getPrimaryKey(table)[0] ?? "id";
       const allRows = this._schema.queryTable(this._adapter, table);
       const slugToRow = /* @__PURE__ */ new Map();
       for (const row of allRows) {
@@ -1247,7 +1255,7 @@ var ReverseSyncEngine = class {
             const updates = reverseSyncFn(currentContent, entityRow);
             if (updates.length === 0) continue;
             if (!dryRun) {
-              this._applyUpdates(updates, entityPk);
+              this._applyUpdates(updates);
             }
             result.updatesApplied += updates.length;
           } catch (err) {
@@ -1266,7 +1274,7 @@ var ReverseSyncEngine = class {
    * Each update is an independent UPDATE statement.
    * Wrapped in a transaction for atomicity.
    */
-  _applyUpdates(updates, _defaultPk) {
+  _applyUpdates(updates) {
     this._adapter.run("BEGIN");
     try {
       for (const update of updates) {
@@ -1283,10 +1291,7 @@ var ReverseSyncEngine = class {
         const setClause = setCols.map((c) => `"${c}" = ?`).join(", ");
         const whereClause = pkCols.map((c) => `"${c}" = ?`).join(" AND ");
         const sql = `UPDATE "${update.table}" SET ${setClause} WHERE ${whereClause}`;
-        const params = [
-          ...setCols.map((c) => update.set[c]),
-          ...pkCols.map((c) => update.pk[c])
-        ];
+        const params = [...setCols.map((c) => update.set[c]), ...pkCols.map((c) => update.pk[c])];
         this._adapter.run(sql, params);
       }
       this._adapter.run("COMMIT");
@@ -1356,8 +1361,12 @@ var InMemoryStateStore = class {
     return this._seen.get(filePath)?.has(key) ?? false;
   }
   markSeen(filePath, key) {
-    if (!this._seen.has(filePath)) this._seen.set(filePath, /* @__PURE__ */ new Set());
-    this._seen.get(filePath).add(key);
+    let seenSet = this._seen.get(filePath);
+    if (!seenSet) {
+      seenSet = /* @__PURE__ */ new Set();
+      this._seen.set(filePath, seenSet);
+    }
+    seenSet.add(key);
   }
 };
 
@@ -1774,19 +1783,32 @@ var Lattice = class {
       const entries = Object.entries(withConventions).filter(([k]) => k !== "id");
       if (entries.length === 0) return Promise.resolve(existing.id);
       const setCols = entries.map(([k]) => `"${k}" = ?`).join(", ");
-      this._adapter.run(`UPDATE "${table}" SET ${setCols} WHERE id = ?`, [...entries.map(([, v]) => v), existing.id]);
-      this._fireWriteHooks(table, "update", withConventions, existing.id, Object.keys(sanitized));
+      this._adapter.run(`UPDATE "${table}" SET ${setCols} WHERE id = ?`, [
+        ...entries.map(([, v]) => v),
+        existing.id
+      ]);
+      this._fireWriteHooks(
+        table,
+        "update",
+        withConventions,
+        existing.id,
+        Object.keys(sanitized)
+      );
       return Promise.resolve(existing.id);
     }
     const id = sanitized.id ?? uuidv4();
     const insertData = { ...withConventions, id, [naturalKeyCol]: naturalKeyVal };
     if (opts?.orgId && cols.has("org_id") && !insertData.org_id) insertData.org_id = opts.orgId;
     if (cols.has("deleted_at")) insertData.deleted_at = null;
-    if (cols.has("created_at") && !insertData.created_at) insertData.created_at = (/* @__PURE__ */ new Date()).toISOString();
+    if (cols.has("created_at") && !insertData.created_at)
+      insertData.created_at = (/* @__PURE__ */ new Date()).toISOString();
     const filtered = this._filterToSchemaColumns(table, insertData);
     const colNames = Object.keys(filtered).map((c) => `"${c}"`).join(", ");
     const placeholders = Object.keys(filtered).map(() => "?").join(", ");
-    this._adapter.run(`INSERT INTO "${table}" (${colNames}) VALUES (${placeholders})`, Object.values(filtered));
+    this._adapter.run(
+      `INSERT INTO "${table}" (${colNames}) VALUES (${placeholders})`,
+      Object.values(filtered)
+    );
     this._fireWriteHooks(table, "insert", filtered, id);
     return Promise.resolve(id);
   }
@@ -1803,14 +1825,25 @@ var Lattice = class {
     );
     if (!existing) return Promise.resolve(false);
     const sanitized = this._filterToSchemaColumns(table, this._sanitizer.sanitizeRow(data));
-    const entries = Object.entries(sanitized).filter(([k, v]) => v !== null && v !== void 0 && k !== "id");
+    const entries = Object.entries(sanitized).filter(
+      ([k, v]) => v !== null && v !== void 0 && k !== "id"
+    );
     if (entries.length === 0) return Promise.resolve(true);
     const cols = this._ensureColumnCache(table);
     const withTs = [...entries];
     if (cols.has("updated_at")) withTs.push(["updated_at", (/* @__PURE__ */ new Date()).toISOString()]);
     const setCols = withTs.map(([k]) => `"${k}" = ?`).join(", ");
-    this._adapter.run(`UPDATE "${table}" SET ${setCols} WHERE id = ?`, [...withTs.map(([, v]) => v), existing.id]);
-    this._fireWriteHooks(table, "update", Object.fromEntries(entries), existing.id, entries.map(([k]) => k));
+    this._adapter.run(`UPDATE "${table}" SET ${setCols} WHERE id = ?`, [
+      ...withTs.map(([, v]) => v),
+      existing.id
+    ]);
+    this._fireWriteHooks(
+      table,
+      "update",
+      Object.fromEntries(entries),
+      existing.id,
+      entries.map(([k]) => k)
+    );
     return Promise.resolve(true);
   }
   /**
@@ -1888,7 +1921,10 @@ var Lattice = class {
     const colNames = Object.keys(filtered).map((c) => `"${c}"`).join(", ");
     const placeholders = Object.keys(filtered).map(() => "?").join(", ");
     const verb = opts?.upsert ? "INSERT OR REPLACE" : "INSERT OR IGNORE";
-    this._adapter.run(`${verb} INTO "${junctionTable}" (${colNames}) VALUES (${placeholders})`, Object.values(filtered));
+    this._adapter.run(
+      `${verb} INTO "${junctionTable}" (${colNames}) VALUES (${placeholders})`,
+      Object.values(filtered)
+    );
     return Promise.resolve();
   }
   /**
@@ -1900,7 +1936,10 @@ var Lattice = class {
     const entries = Object.entries(conditions);
     if (entries.length === 0) return Promise.resolve();
     const where = entries.map(([k]) => `"${k}" = ?`).join(" AND ");
-    this._adapter.run(`DELETE FROM "${junctionTable}" WHERE ${where}`, entries.map(([, v]) => v));
+    this._adapter.run(
+      `DELETE FROM "${junctionTable}" WHERE ${where}`,
+      entries.map(([, v]) => v)
+    );
     return Promise.resolve();
   }
   // -------------------------------------------------------------------------
@@ -1927,7 +1966,13 @@ var Lattice = class {
       if (config.sourceFile) upsertOpts.sourceFile = config.sourceFile;
       if (config.sourceHash) upsertOpts.sourceHash = config.sourceHash;
       if (config.orgId) upsertOpts.orgId = config.orgId;
-      await this.upsertByNaturalKey(config.table, config.naturalKey, naturalKeyVal, record, upsertOpts);
+      await this.upsertByNaturalKey(
+        config.table,
+        config.naturalKey,
+        naturalKeyVal,
+        record,
+        upsertOpts
+      );
       upserted++;
       if (config.linkTo) {
         const recordId = await this.getByNaturalKey(config.table, config.naturalKey, naturalKeyVal);
@@ -1952,7 +1997,12 @@ var Lattice = class {
       }
     }
     if (config.softDeleteMissing && config.sourceFile && keys.length > 0) {
-      softDeleted = await this.softDeleteMissing(config.table, config.naturalKey, config.sourceFile, keys);
+      softDeleted = await this.softDeleteMissing(
+        config.table,
+        config.naturalKey,
+        config.sourceFile,
+        keys
+      );
     }
     return { upserted, linked, softDeleted };
   }
@@ -2036,7 +2086,10 @@ var Lattice = class {
       const where = conditions.length > 0 ? ` WHERE ${conditions.join(" AND ")}` : "";
       const orderBy = section.query.orderBy ? ` ORDER BY "${section.query.orderBy}" ${section.query.orderDir === "desc" ? "DESC" : "ASC"}` : "";
       const limit = section.query.limit ? ` LIMIT ${String(section.query.limit)}` : "";
-      const rows = this._adapter.all(`SELECT * FROM "${section.query.table}"${where}${orderBy}${limit}`, params);
+      const rows = this._adapter.all(
+        `SELECT * FROM "${section.query.table}"${where}${orderBy}${limit}`,
+        params
+      );
       if (rows.length > 0) allEmpty = false;
       let formatted = "";
       if (section.format === "custom" && section.customFormat) {
@@ -2359,9 +2412,7 @@ var Lattice = class {
     if (!known) return null;
     for (const col of cols) {
       if (!known.has(col)) {
-        return Promise.reject(
-          new Error(`Lattice: unknown column "${col}" in table "${table}"`)
-        );
+        return Promise.reject(new Error(`Lattice: unknown column "${col}" in table "${table}"`));
       }
     }
     return null;

package/dist/index.cjs

@@ -276,7 +276,9 @@ var SchemaManager = class {
     if (this._entityContexts.has(name)) {
       const cols = adapter.all(`PRAGMA table_info("${name}")`);
       const hasDeletedAt = cols.some((c) => c.name === "deleted_at");
-      return adapter.all(`SELECT * FROM "${name}"${hasDeletedAt ? " WHERE deleted_at IS NULL" : ""}`);
+      return adapter.all(
+        `SELECT * FROM "${name}"${hasDeletedAt ? " WHERE deleted_at IS NULL" : ""}`
+      );
     }
     throw new Error(`Unknown table: "${name}"`);
   }
@@ -855,7 +857,14 @@ var RenderEngine = class {
       const slugs = new Set(rows.map((row) => def.slug(row)));
       currentSlugsByTable.set(table, slugs);
     }
-    return cleanupEntityContexts(outputDir, entityContexts, currentSlugsByTable, prevManifest, options, newManifest);
+    return cleanupEntityContexts(
+      outputDir,
+      entityContexts,
+      currentSlugsByTable,
+      prevManifest,
+      options,
+      newManifest
+    );
   }
   /**
    * Render all entity context definitions.
@@ -970,7 +979,6 @@ var ReverseSyncEngine = class {
         }
       }
       if (reverseSyncFiles.size === 0) continue;
-      const entityPk = this._schema.getPrimaryKey(table)[0] ?? "id";
       const allRows = this._schema.queryTable(this._adapter, table);
       const slugToRow = /* @__PURE__ */ new Map();
       for (const row of allRows) {
@@ -1002,7 +1010,7 @@ var ReverseSyncEngine = class {
             const updates = reverseSyncFn(currentContent, entityRow);
             if (updates.length === 0) continue;
             if (!dryRun) {
-              this._applyUpdates(updates, entityPk);
+              this._applyUpdates(updates);
             }
             result.updatesApplied += updates.length;
           } catch (err) {
@@ -1021,7 +1029,7 @@ var ReverseSyncEngine = class {
    * Each update is an independent UPDATE statement.
    * Wrapped in a transaction for atomicity.
    */
-  _applyUpdates(updates, _defaultPk) {
+  _applyUpdates(updates) {
     this._adapter.run("BEGIN");
     try {
       for (const update of updates) {
@@ -1038,10 +1046,7 @@ var ReverseSyncEngine = class {
         const setClause = setCols.map((c) => `"${c}" = ?`).join(", ");
         const whereClause = pkCols.map((c) => `"${c}" = ?`).join(" AND ");
         const sql = `UPDATE "${update.table}" SET ${setClause} WHERE ${whereClause}`;
-        const params = [
-          ...setCols.map((c) => update.set[c]),
-          ...pkCols.map((c) => update.pk[c])
-        ];
+        const params = [...setCols.map((c) => update.set[c]), ...pkCols.map((c) => update.pk[c])];
         this._adapter.run(sql, params);
       }
       this._adapter.run("COMMIT");
@@ -1111,8 +1116,12 @@ var InMemoryStateStore = class {
     return this._seen.get(filePath)?.has(key) ?? false;
   }
   markSeen(filePath, key) {
-    if (!this._seen.has(filePath)) this._seen.set(filePath, /* @__PURE__ */ new Set());
-    this._seen.get(filePath).add(key);
+    let seenSet = this._seen.get(filePath);
+    if (!seenSet) {
+      seenSet = /* @__PURE__ */ new Set();
+      this._seen.set(filePath, seenSet);
+    }
+    seenSet.add(key);
   }
 };
 var SQLiteStateStore = class {
@@ -1151,11 +1160,13 @@ var SQLiteStateStore = class {
   }
   setOffset(filePath, offset, size) {
     this._init();
-    this._db.prepare(`
+    this._db.prepare(
+      `
       INSERT INTO _lattice_writeback_offset (file_path, byte_offset, file_size, updated_at)
       VALUES (?, ?, ?, datetime('now'))
       ON CONFLICT(file_path) DO UPDATE SET byte_offset = ?, file_size = ?, updated_at = datetime('now')
-    `).run(filePath, offset, size, offset, size);
+    `
+    ).run(filePath, offset, size, offset, size);
   }
   isSeen(filePath, key) {
     this._init();
@@ -1396,13 +1407,13 @@ function buildParsedConfig(raw, sourceName, configDir) {
   const dbPath = (0, import_node_path7.resolve)(configDir, config.db);
   const tables = [];
   for (const [entityName, entityDef] of Object.entries(config.entities)) {
-    const definition = entityToTableDef(entityName, entityDef, configDir);
+    const definition = entityToTableDef(entityName, entityDef);
     tables.push({ name: entityName, definition });
   }
   const entityContexts = parseEntityContexts(config.entityContexts);
   return { dbPath, tables, entityContexts };
 }
-function entityToTableDef(entityName, entity, configDir) {
+function entityToTableDef(entityName, entity) {
   const rawFields = entity.fields;
   if (!rawFields || typeof rawFields !== "object" || Array.isArray(rawFields)) {
     throw new Error(`Lattice: entity "${entityName}" must have a "fields" object`);
@@ -1426,7 +1437,7 @@ function entityToTableDef(entityName, entity, configDir) {
   }
   const primaryKey = entity.primaryKey ?? pkFromField;
   const render = parseEntityRender(entity.render);
-  const outputFile = (0, import_node_path7.resolve)(configDir, entity.outputFile);
+  const outputFile = entity.outputFile;
   return {
     columns,
     render,
@@ -1808,19 +1819,32 @@ var Lattice = class {
       const entries = Object.entries(withConventions).filter(([k]) => k !== "id");
       if (entries.length === 0) return Promise.resolve(existing.id);
       const setCols = entries.map(([k]) => `"${k}" = ?`).join(", ");
-      this._adapter.run(`UPDATE "${table}" SET ${setCols} WHERE id = ?`, [...entries.map(([, v]) => v), existing.id]);
-      this._fireWriteHooks(table, "update", withConventions, existing.id, Object.keys(sanitized));
+      this._adapter.run(`UPDATE "${table}" SET ${setCols} WHERE id = ?`, [
+        ...entries.map(([, v]) => v),
+        existing.id
+      ]);
+      this._fireWriteHooks(
+        table,
+        "update",
+        withConventions,
+        existing.id,
+        Object.keys(sanitized)
+      );
       return Promise.resolve(existing.id);
     }
     const id = sanitized.id ?? (0, import_uuid.v4)();
     const insertData = { ...withConventions, id, [naturalKeyCol]: naturalKeyVal };
     if (opts?.orgId && cols.has("org_id") && !insertData.org_id) insertData.org_id = opts.orgId;
     if (cols.has("deleted_at")) insertData.deleted_at = null;
-    if (cols.has("created_at") && !insertData.created_at) insertData.created_at = (/* @__PURE__ */ new Date()).toISOString();
+    if (cols.has("created_at") && !insertData.created_at)
+      insertData.created_at = (/* @__PURE__ */ new Date()).toISOString();
     const filtered = this._filterToSchemaColumns(table, insertData);
     const colNames = Object.keys(filtered).map((c) => `"${c}"`).join(", ");
     const placeholders = Object.keys(filtered).map(() => "?").join(", ");
-    this._adapter.run(`INSERT INTO "${table}" (${colNames}) VALUES (${placeholders})`, Object.values(filtered));
+    this._adapter.run(
+      `INSERT INTO "${table}" (${colNames}) VALUES (${placeholders})`,
+      Object.values(filtered)
+    );
     this._fireWriteHooks(table, "insert", filtered, id);
     return Promise.resolve(id);
   }
@@ -1837,14 +1861,25 @@ var Lattice = class {
     );
     if (!existing) return Promise.resolve(false);
     const sanitized = this._filterToSchemaColumns(table, this._sanitizer.sanitizeRow(data));
-    const entries = Object.entries(sanitized).filter(([k, v]) => v !== null && v !== void 0 && k !== "id");
+    const entries = Object.entries(sanitized).filter(
+      ([k, v]) => v !== null && v !== void 0 && k !== "id"
+    );
     if (entries.length === 0) return Promise.resolve(true);
     const cols = this._ensureColumnCache(table);
     const withTs = [...entries];
     if (cols.has("updated_at")) withTs.push(["updated_at", (/* @__PURE__ */ new Date()).toISOString()]);
     const setCols = withTs.map(([k]) => `"${k}" = ?`).join(", ");
-    this._adapter.run(`UPDATE "${table}" SET ${setCols} WHERE id = ?`, [...withTs.map(([, v]) => v), existing.id]);
-    this._fireWriteHooks(table, "update", Object.fromEntries(entries), existing.id, entries.map(([k]) => k));
+    this._adapter.run(`UPDATE "${table}" SET ${setCols} WHERE id = ?`, [
+      ...withTs.map(([, v]) => v),
+      existing.id
+    ]);
+    this._fireWriteHooks(
+      table,
+      "update",
+      Object.fromEntries(entries),
+      existing.id,
+      entries.map(([k]) => k)
+    );
     return Promise.resolve(true);
   }
   /**
@@ -1922,7 +1957,10 @@ var Lattice = class {
     const colNames = Object.keys(filtered).map((c) => `"${c}"`).join(", ");
     const placeholders = Object.keys(filtered).map(() => "?").join(", ");
     const verb = opts?.upsert ? "INSERT OR REPLACE" : "INSERT OR IGNORE";
-    this._adapter.run(`${verb} INTO "${junctionTable}" (${colNames}) VALUES (${placeholders})`, Object.values(filtered));
+    this._adapter.run(
+      `${verb} INTO "${junctionTable}" (${colNames}) VALUES (${placeholders})`,
+      Object.values(filtered)
+    );
     return Promise.resolve();
   }
   /**
@@ -1934,7 +1972,10 @@ var Lattice = class {
     const entries = Object.entries(conditions);
     if (entries.length === 0) return Promise.resolve();
     const where = entries.map(([k]) => `"${k}" = ?`).join(" AND ");
-    this._adapter.run(`DELETE FROM "${junctionTable}" WHERE ${where}`, entries.map(([, v]) => v));
+    this._adapter.run(
+      `DELETE FROM "${junctionTable}" WHERE ${where}`,
+      entries.map(([, v]) => v)
+    );
     return Promise.resolve();
   }
   // -------------------------------------------------------------------------
@@ -1961,7 +2002,13 @@ var Lattice = class {
       if (config.sourceFile) upsertOpts.sourceFile = config.sourceFile;
       if (config.sourceHash) upsertOpts.sourceHash = config.sourceHash;
       if (config.orgId) upsertOpts.orgId = config.orgId;
-      await this.upsertByNaturalKey(config.table, config.naturalKey, naturalKeyVal, record, upsertOpts);
+      await this.upsertByNaturalKey(
+        config.table,
+        config.naturalKey,
+        naturalKeyVal,
+        record,
+        upsertOpts
+      );
       upserted++;
       if (config.linkTo) {
         const recordId = await this.getByNaturalKey(config.table, config.naturalKey, naturalKeyVal);
@@ -1986,7 +2033,12 @@ var Lattice = class {
       }
     }
     if (config.softDeleteMissing && config.sourceFile && keys.length > 0) {
-      softDeleted = await this.softDeleteMissing(config.table, config.naturalKey, config.sourceFile, keys);
+      softDeleted = await this.softDeleteMissing(
+        config.table,
+        config.naturalKey,
+        config.sourceFile,
+        keys
+      );
     }
     return { upserted, linked, softDeleted };
   }
@@ -2070,7 +2122,10 @@ var Lattice = class {
       const where = conditions.length > 0 ? ` WHERE ${conditions.join(" AND ")}` : "";
       const orderBy = section.query.orderBy ? ` ORDER BY "${section.query.orderBy}" ${section.query.orderDir === "desc" ? "DESC" : "ASC"}` : "";
       const limit = section.query.limit ? ` LIMIT ${String(section.query.limit)}` : "";
-      const rows = this._adapter.all(`SELECT * FROM "${section.query.table}"${where}${orderBy}${limit}`, params);
+      const rows = this._adapter.all(
+        `SELECT * FROM "${section.query.table}"${where}${orderBy}${limit}`,
+        params
+      );
       if (rows.length > 0) allEmpty = false;
       let formatted = "";
       if (section.format === "custom" && section.customFormat) {
@@ -2393,9 +2448,7 @@ var Lattice = class {
     if (!known) return null;
     for (const col of cols) {
       if (!known.has(col)) {
-        return Promise.reject(
-          new Error(`Lattice: unknown column "${col}" in table "${table}"`)
-        );
+        return Promise.reject(new Error(`Lattice: unknown column "${col}" in table "${table}"`));
       }
     }
     return null;
@@ -2479,7 +2532,9 @@ function parseBlock(block) {
     return { error: { line, message: "Missing required field: op" } };
   }
   if (rawOp !== "create" && rawOp !== "update" && rawOp !== "delete") {
-    return { error: { line, message: `Invalid op: "${rawOp}". Must be create, update, or delete` } };
+    return {
+      error: { line, message: `Invalid op: "${rawOp}". Must be create, update, or delete` }
+    };
   }
   const op = rawOp;
   const table = header.table;
@@ -2487,7 +2542,9 @@ function parseBlock(block) {
     return { error: { line, message: "Missing required field: table" } };
   }
   if (!TABLE_NAME_RE.test(table)) {
-    return { error: { line, message: `Invalid table name: "${table}". Only [a-zA-Z0-9_] allowed` } };
+    return {
+      error: { line, message: `Invalid table name: "${table}". Only [a-zA-Z0-9_] allowed` }
+    };
   }
   const target = header.target || void 0;
   if ((op === "update" || op === "delete") && !target) {
@@ -2629,7 +2686,12 @@ function parseSessionMD(content, startOffset = 0, options) {
         writeFields[key] = (m[2] ?? "").trim();
       }
     }
-    const newEntry = { id: entryId, type: resolvedType, timestamp: headers.timestamp, body };
+    const newEntry = {
+      id: entryId,
+      type: resolvedType,
+      timestamp: headers.timestamp,
+      body
+    };
     if (headers.project) newEntry.project = headers.project;
     if (headers.task) newEntry.task = headers.task;
     if (tags) newEntry.tags = tags;
@@ -2765,7 +2827,9 @@ function applyWriteEntry(db, entry) {
       const allFields = { ...fields, id };
       const cols = Object.keys(allFields).map((c) => `"${c}"`).join(", ");
       const placeholders = Object.keys(allFields).map(() => "?").join(", ");
-      db.prepare(`INSERT INTO "${table}" (${cols}) VALUES (${placeholders})`).run(...Object.values(allFields));
+      db.prepare(`INSERT INTO "${table}" (${cols}) VALUES (${placeholders})`).run(
+        ...Object.values(allFields)
+      );
       recordId = id;
     } else if (op === "update") {
       if (!target) {
@@ -2773,7 +2837,10 @@ function applyWriteEntry(db, entry) {
       }
       const pkCol = columnRows.find((r) => r.name === "id") ? "id" : columnRows[0]?.name ?? "id";
       const setCols = Object.keys(fields).map((c) => `"${c}" = ?`).join(", ");
-      db.prepare(`UPDATE "${table}" SET ${setCols} WHERE "${pkCol}" = ?`).run(...Object.values(fields), target);
+      db.prepare(`UPDATE "${table}" SET ${setCols} WHERE "${pkCol}" = ?`).run(
+        ...Object.values(fields),
+        target
+      );
       recordId = target;
     } else {
       if (!target) {
@@ -2781,7 +2848,9 @@ function applyWriteEntry(db, entry) {
       }
       const pkCol = columnRows.find((r) => r.name === "id") ? "id" : columnRows[0]?.name ?? "id";
       if (knownColumns.has("deleted_at")) {
-        db.prepare(`UPDATE "${table}" SET deleted_at = datetime('now') WHERE "${pkCol}" = ?`).run(target);
+        db.prepare(`UPDATE "${table}" SET deleted_at = datetime('now') WHERE "${pkCol}" = ?`).run(
+          target
+        );
       } else {
         db.prepare(`DELETE FROM "${table}" WHERE "${pkCol}" = ?`).run(target);
       }

package/dist/index.d.cts

@@ -1403,8 +1403,9 @@ interface ParsedConfig {
 /**
  * Read, parse, and validate a `lattice.config.yml` file.
  *
- * Paths inside the config (e.g. `db`, `outputFile`) are resolved relative to
- * the config file's directory.
+ * The `db` path is resolved relative to the config file's directory.
+ * `outputFile` values are kept as-is (they are relative to the `outputDir`
+ * passed to `render()`, not to the config file location).
  *
  * @throws If the file cannot be read, the YAML is malformed, or required
  *         keys are missing.
@@ -1413,7 +1414,8 @@ declare function parseConfigFile(configPath: string): ParsedConfig;
 /**
  * Parse and validate a raw YAML string as a Lattice config.
  *
- * `configDir` is used to resolve relative `db` and `outputFile` paths.
+ * `configDir` is used to resolve the `db` path. `outputFile` values are kept
+ * as-is (relative to the `outputDir` passed to `render()`).
  * Typically this should be the directory that contains `lattice.config.yml`.
  *
  * Useful for testing without touching the filesystem.
@@ -1588,7 +1590,7 @@ declare const DEFAULT_TYPE_ALIASES: Readonly<Record<string, string>>;
  * Each entry looks like:
  * ```
  * ---
- * id: 2026-03-12T15:30:42Z-cortex-a1b2c3
+ * id: 2026-03-12T15:30:42Z-agent1-a1b2c3
  * type: event
  * timestamp: 2026-03-12T15:30:42Z
  * ---

package/dist/index.d.ts

@@ -1403,8 +1403,9 @@ interface ParsedConfig {
 /**
  * Read, parse, and validate a `lattice.config.yml` file.
  *
- * Paths inside the config (e.g. `db`, `outputFile`) are resolved relative to
- * the config file's directory.
+ * The `db` path is resolved relative to the config file's directory.
+ * `outputFile` values are kept as-is (they are relative to the `outputDir`
+ * passed to `render()`, not to the config file location).
  *
  * @throws If the file cannot be read, the YAML is malformed, or required
  *         keys are missing.
@@ -1413,7 +1414,8 @@ declare function parseConfigFile(configPath: string): ParsedConfig;
 /**
  * Parse and validate a raw YAML string as a Lattice config.
  *
- * `configDir` is used to resolve relative `db` and `outputFile` paths.
+ * `configDir` is used to resolve the `db` path. `outputFile` values are kept
+ * as-is (relative to the `outputDir` passed to `render()`).
  * Typically this should be the directory that contains `lattice.config.yml`.
  *
  * Useful for testing without touching the filesystem.
@@ -1588,7 +1590,7 @@ declare const DEFAULT_TYPE_ALIASES: Readonly<Record<string, string>>;
  * Each entry looks like:
  * ```
  * ---
- * id: 2026-03-12T15:30:42Z-cortex-a1b2c3
+ * id: 2026-03-12T15:30:42Z-agent1-a1b2c3
  * type: event
  * timestamp: 2026-03-12T15:30:42Z
  * ---

package/dist/index.js

@@ -214,7 +214,9 @@ var SchemaManager = class {
     if (this._entityContexts.has(name)) {
       const cols = adapter.all(`PRAGMA table_info("${name}")`);
       const hasDeletedAt = cols.some((c) => c.name === "deleted_at");
-      return adapter.all(`SELECT * FROM "${name}"${hasDeletedAt ? " WHERE deleted_at IS NULL" : ""}`);
+      return adapter.all(
+        `SELECT * FROM "${name}"${hasDeletedAt ? " WHERE deleted_at IS NULL" : ""}`
+      );
     }
     throw new Error(`Unknown table: "${name}"`);
   }
@@ -793,7 +795,14 @@ var RenderEngine = class {
       const slugs = new Set(rows.map((row) => def.slug(row)));
       currentSlugsByTable.set(table, slugs);
     }
-    return cleanupEntityContexts(outputDir, entityContexts, currentSlugsByTable, prevManifest, options, newManifest);
+    return cleanupEntityContexts(
+      outputDir,
+      entityContexts,
+      currentSlugsByTable,
+      prevManifest,
+      options,
+      newManifest
+    );
   }
   /**
    * Render all entity context definitions.
@@ -908,7 +917,6 @@ var ReverseSyncEngine = class {
         }
       }
       if (reverseSyncFiles.size === 0) continue;
-      const entityPk = this._schema.getPrimaryKey(table)[0] ?? "id";
       const allRows = this._schema.queryTable(this._adapter, table);
       const slugToRow = /* @__PURE__ */ new Map();
       for (const row of allRows) {
@@ -940,7 +948,7 @@ var ReverseSyncEngine = class {
             const updates = reverseSyncFn(currentContent, entityRow);
             if (updates.length === 0) continue;
             if (!dryRun) {
-              this._applyUpdates(updates, entityPk);
+              this._applyUpdates(updates);
             }
             result.updatesApplied += updates.length;
           } catch (err) {
@@ -959,7 +967,7 @@ var ReverseSyncEngine = class {
    * Each update is an independent UPDATE statement.
    * Wrapped in a transaction for atomicity.
    */
-  _applyUpdates(updates, _defaultPk) {
+  _applyUpdates(updates) {
     this._adapter.run("BEGIN");
     try {
       for (const update of updates) {
@@ -976,10 +984,7 @@ var ReverseSyncEngine = class {
         const setClause = setCols.map((c) => `"${c}" = ?`).join(", ");
         const whereClause = pkCols.map((c) => `"${c}" = ?`).join(" AND ");
         const sql = `UPDATE "${update.table}" SET ${setClause} WHERE ${whereClause}`;
-        const params = [
-          ...setCols.map((c) => update.set[c]),
-          ...pkCols.map((c) => update.pk[c])
-        ];
+        const params = [...setCols.map((c) => update.set[c]), ...pkCols.map((c) => update.pk[c])];
         this._adapter.run(sql, params);
       }
       this._adapter.run("COMMIT");
@@ -1049,8 +1054,12 @@ var InMemoryStateStore = class {
     return this._seen.get(filePath)?.has(key) ?? false;
   }
   markSeen(filePath, key) {
-    if (!this._seen.has(filePath)) this._seen.set(filePath, /* @__PURE__ */ new Set());
-    this._seen.get(filePath).add(key);
+    let seenSet = this._seen.get(filePath);
+    if (!seenSet) {
+      seenSet = /* @__PURE__ */ new Set();
+      this._seen.set(filePath, seenSet);
+    }
+    seenSet.add(key);
   }
 };
 var SQLiteStateStore = class {
@@ -1089,11 +1098,13 @@ var SQLiteStateStore = class {
   }
   setOffset(filePath, offset, size) {
     this._init();
-    this._db.prepare(`
+    this._db.prepare(
+      `
       INSERT INTO _lattice_writeback_offset (file_path, byte_offset, file_size, updated_at)
       VALUES (?, ?, ?, datetime('now'))
       ON CONFLICT(file_path) DO UPDATE SET byte_offset = ?, file_size = ?, updated_at = datetime('now')
-    `).run(filePath, offset, size, offset, size);
+    `
+    ).run(filePath, offset, size, offset, size);
   }
   isSeen(filePath, key) {
     this._init();
@@ -1334,13 +1345,13 @@ function buildParsedConfig(raw, sourceName, configDir) {
   const dbPath = resolve(configDir, config.db);
   const tables = [];
   for (const [entityName, entityDef] of Object.entries(config.entities)) {
-    const definition = entityToTableDef(entityName, entityDef, configDir);
+    const definition = entityToTableDef(entityName, entityDef);
     tables.push({ name: entityName, definition });
   }
   const entityContexts = parseEntityContexts(config.entityContexts);
   return { dbPath, tables, entityContexts };
 }
-function entityToTableDef(entityName, entity, configDir) {
+function entityToTableDef(entityName, entity) {
   const rawFields = entity.fields;
   if (!rawFields || typeof rawFields !== "object" || Array.isArray(rawFields)) {
     throw new Error(`Lattice: entity "${entityName}" must have a "fields" object`);
@@ -1364,7 +1375,7 @@ function entityToTableDef(entityName, entity, configDir) {
   }
   const primaryKey = entity.primaryKey ?? pkFromField;
   const render = parseEntityRender(entity.render);
-  const outputFile = resolve(configDir, entity.outputFile);
+  const outputFile = entity.outputFile;
   return {
     columns,
     render,
@@ -1746,19 +1757,32 @@ var Lattice = class {
       const entries = Object.entries(withConventions).filter(([k]) => k !== "id");
       if (entries.length === 0) return Promise.resolve(existing.id);
       const setCols = entries.map(([k]) => `"${k}" = ?`).join(", ");
-      this._adapter.run(`UPDATE "${table}" SET ${setCols} WHERE id = ?`, [...entries.map(([, v]) => v), existing.id]);
-      this._fireWriteHooks(table, "update", withConventions, existing.id, Object.keys(sanitized));
+      this._adapter.run(`UPDATE "${table}" SET ${setCols} WHERE id = ?`, [
+        ...entries.map(([, v]) => v),
+        existing.id
+      ]);
+      this._fireWriteHooks(
+        table,
+        "update",
+        withConventions,
+        existing.id,
+        Object.keys(sanitized)
+      );
       return Promise.resolve(existing.id);
     }
     const id = sanitized.id ?? uuidv4();
     const insertData = { ...withConventions, id, [naturalKeyCol]: naturalKeyVal };
     if (opts?.orgId && cols.has("org_id") && !insertData.org_id) insertData.org_id = opts.orgId;
     if (cols.has("deleted_at")) insertData.deleted_at = null;
-    if (cols.has("created_at") && !insertData.created_at) insertData.created_at = (/* @__PURE__ */ new Date()).toISOString();
+    if (cols.has("created_at") && !insertData.created_at)
+      insertData.created_at = (/* @__PURE__ */ new Date()).toISOString();
     const filtered = this._filterToSchemaColumns(table, insertData);
     const colNames = Object.keys(filtered).map((c) => `"${c}"`).join(", ");
     const placeholders = Object.keys(filtered).map(() => "?").join(", ");
-    this._adapter.run(`INSERT INTO "${table}" (${colNames}) VALUES (${placeholders})`, Object.values(filtered));
+    this._adapter.run(
+      `INSERT INTO "${table}" (${colNames}) VALUES (${placeholders})`,
+      Object.values(filtered)
+    );
     this._fireWriteHooks(table, "insert", filtered, id);
     return Promise.resolve(id);
   }
@@ -1775,14 +1799,25 @@ var Lattice = class {
     );
     if (!existing) return Promise.resolve(false);
     const sanitized = this._filterToSchemaColumns(table, this._sanitizer.sanitizeRow(data));
-    const entries = Object.entries(sanitized).filter(([k, v]) => v !== null && v !== void 0 && k !== "id");
+    const entries = Object.entries(sanitized).filter(
+      ([k, v]) => v !== null && v !== void 0 && k !== "id"
+    );
     if (entries.length === 0) return Promise.resolve(true);
     const cols = this._ensureColumnCache(table);
     const withTs = [...entries];
     if (cols.has("updated_at")) withTs.push(["updated_at", (/* @__PURE__ */ new Date()).toISOString()]);
     const setCols = withTs.map(([k]) => `"${k}" = ?`).join(", ");
-    this._adapter.run(`UPDATE "${table}" SET ${setCols} WHERE id = ?`, [...withTs.map(([, v]) => v), existing.id]);
-    this._fireWriteHooks(table, "update", Object.fromEntries(entries), existing.id, entries.map(([k]) => k));
+    this._adapter.run(`UPDATE "${table}" SET ${setCols} WHERE id = ?`, [
+      ...withTs.map(([, v]) => v),
+      existing.id
+    ]);
+    this._fireWriteHooks(
+      table,
+      "update",
+      Object.fromEntries(entries),
+      existing.id,
+      entries.map(([k]) => k)
+    );
     return Promise.resolve(true);
   }
   /**
@@ -1860,7 +1895,10 @@ var Lattice = class {
     const colNames = Object.keys(filtered).map((c) => `"${c}"`).join(", ");
     const placeholders = Object.keys(filtered).map(() => "?").join(", ");
     const verb = opts?.upsert ? "INSERT OR REPLACE" : "INSERT OR IGNORE";
-    this._adapter.run(`${verb} INTO "${junctionTable}" (${colNames}) VALUES (${placeholders})`, Object.values(filtered));
+    this._adapter.run(
+      `${verb} INTO "${junctionTable}" (${colNames}) VALUES (${placeholders})`,
+      Object.values(filtered)
+    );
     return Promise.resolve();
   }
   /**
@@ -1872,7 +1910,10 @@ var Lattice = class {
     const entries = Object.entries(conditions);
     if (entries.length === 0) return Promise.resolve();
     const where = entries.map(([k]) => `"${k}" = ?`).join(" AND ");
-    this._adapter.run(`DELETE FROM "${junctionTable}" WHERE ${where}`, entries.map(([, v]) => v));
+    this._adapter.run(
+      `DELETE FROM "${junctionTable}" WHERE ${where}`,
+      entries.map(([, v]) => v)
+    );
     return Promise.resolve();
   }
   // -------------------------------------------------------------------------
@@ -1899,7 +1940,13 @@ var Lattice = class {
       if (config.sourceFile) upsertOpts.sourceFile = config.sourceFile;
       if (config.sourceHash) upsertOpts.sourceHash = config.sourceHash;
       if (config.orgId) upsertOpts.orgId = config.orgId;
-      await this.upsertByNaturalKey(config.table, config.naturalKey, naturalKeyVal, record, upsertOpts);
+      await this.upsertByNaturalKey(
+        config.table,
+        config.naturalKey,
+        naturalKeyVal,
+        record,
+        upsertOpts
+      );
       upserted++;
       if (config.linkTo) {
         const recordId = await this.getByNaturalKey(config.table, config.naturalKey, naturalKeyVal);
@@ -1924,7 +1971,12 @@ var Lattice = class {
       }
     }
     if (config.softDeleteMissing && config.sourceFile && keys.length > 0) {
-      softDeleted = await this.softDeleteMissing(config.table, config.naturalKey, config.sourceFile, keys);
+      softDeleted = await this.softDeleteMissing(
+        config.table,
+        config.naturalKey,
+        config.sourceFile,
+        keys
+      );
     }
     return { upserted, linked, softDeleted };
   }
@@ -2008,7 +2060,10 @@ var Lattice = class {
       const where = conditions.length > 0 ? ` WHERE ${conditions.join(" AND ")}` : "";
       const orderBy = section.query.orderBy ? ` ORDER BY "${section.query.orderBy}" ${section.query.orderDir === "desc" ? "DESC" : "ASC"}` : "";
       const limit = section.query.limit ? ` LIMIT ${String(section.query.limit)}` : "";
-      const rows = this._adapter.all(`SELECT * FROM "${section.query.table}"${where}${orderBy}${limit}`, params);
+      const rows = this._adapter.all(
+        `SELECT * FROM "${section.query.table}"${where}${orderBy}${limit}`,
+        params
+      );
       if (rows.length > 0) allEmpty = false;
       let formatted = "";
       if (section.format === "custom" && section.customFormat) {
@@ -2331,9 +2386,7 @@ var Lattice = class {
     if (!known) return null;
     for (const col of cols) {
       if (!known.has(col)) {
-        return Promise.reject(
-          new Error(`Lattice: unknown column "${col}" in table "${table}"`)
-        );
+        return Promise.reject(new Error(`Lattice: unknown column "${col}" in table "${table}"`));
       }
     }
     return null;
@@ -2417,7 +2470,9 @@ function parseBlock(block) {
     return { error: { line, message: "Missing required field: op" } };
   }
   if (rawOp !== "create" && rawOp !== "update" && rawOp !== "delete") {
-    return { error: { line, message: `Invalid op: "${rawOp}". Must be create, update, or delete` } };
+    return {
+      error: { line, message: `Invalid op: "${rawOp}". Must be create, update, or delete` }
+    };
   }
   const op = rawOp;
   const table = header.table;
@@ -2425,7 +2480,9 @@ function parseBlock(block) {
     return { error: { line, message: "Missing required field: table" } };
   }
   if (!TABLE_NAME_RE.test(table)) {
-    return { error: { line, message: `Invalid table name: "${table}". Only [a-zA-Z0-9_] allowed` } };
+    return {
+      error: { line, message: `Invalid table name: "${table}". Only [a-zA-Z0-9_] allowed` }
+    };
   }
   const target = header.target || void 0;
   if ((op === "update" || op === "delete") && !target) {
@@ -2567,7 +2624,12 @@ function parseSessionMD(content, startOffset = 0, options) {
         writeFields[key] = (m[2] ?? "").trim();
       }
     }
-    const newEntry = { id: entryId, type: resolvedType, timestamp: headers.timestamp, body };
+    const newEntry = {
+      id: entryId,
+      type: resolvedType,
+      timestamp: headers.timestamp,
+      body
+    };
     if (headers.project) newEntry.project = headers.project;
     if (headers.task) newEntry.task = headers.task;
     if (tags) newEntry.tags = tags;
@@ -2703,7 +2765,9 @@ function applyWriteEntry(db, entry) {
       const allFields = { ...fields, id };
       const cols = Object.keys(allFields).map((c) => `"${c}"`).join(", ");
       const placeholders = Object.keys(allFields).map(() => "?").join(", ");
-      db.prepare(`INSERT INTO "${table}" (${cols}) VALUES (${placeholders})`).run(...Object.values(allFields));
+      db.prepare(`INSERT INTO "${table}" (${cols}) VALUES (${placeholders})`).run(
+        ...Object.values(allFields)
+      );
       recordId = id;
     } else if (op === "update") {
       if (!target) {
@@ -2711,7 +2775,10 @@ function applyWriteEntry(db, entry) {
       }
       const pkCol = columnRows.find((r) => r.name === "id") ? "id" : columnRows[0]?.name ?? "id";
       const setCols = Object.keys(fields).map((c) => `"${c}" = ?`).join(", ");
-      db.prepare(`UPDATE "${table}" SET ${setCols} WHERE "${pkCol}" = ?`).run(...Object.values(fields), target);
+      db.prepare(`UPDATE "${table}" SET ${setCols} WHERE "${pkCol}" = ?`).run(
+        ...Object.values(fields),
+        target
+      );
       recordId = target;
     } else {
       if (!target) {
@@ -2719,7 +2786,9 @@ function applyWriteEntry(db, entry) {
       }
       const pkCol = columnRows.find((r) => r.name === "id") ? "id" : columnRows[0]?.name ?? "id";
       if (knownColumns.has("deleted_at")) {
-        db.prepare(`UPDATE "${table}" SET deleted_at = datetime('now') WHERE "${pkCol}" = ?`).run(target);
+        db.prepare(`UPDATE "${table}" SET deleted_at = datetime('now') WHERE "${pkCol}" = ?`).run(
+          target
+        );
       } else {
         db.prepare(`DELETE FROM "${table}" WHERE "${pkCol}" = ?`).run(target);
       }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "latticesql",
-  "version": "0.16.0",
+  "version": "0.16.2",
   "description": "Persistent structured memory for AI agent systems — SQLite ↔ LLM context bridge",
   "type": "module",
   "main": "./dist/index.js",