fix(config): the named cortex map lifts plugins and nli; 1.9.1

CHANGELOG.md

@@ -2,6 +2,12 @@
 
 ## [Unreleased]
 
+## [1.9.1] — 2026-09-18
+
+### Fixed
+
+- `plugins:` (and `nli:`) declared under an agent's entry in the named `cortex:` map of `agent.yaml` now reach `CortexConfig`. `extractFromNamedCortexMap` lifted the provider fields and the tool list but not these two, so only the legacy flat `cortex:` block could name a plugin — the repo-shipped plugin path 1.9.0 opened with `trusted: true` could not be declared from the config that `fozikio init` writes (#114).
+
 ## [1.9.0] — 2026-09-18
 
 ### Added

package.json

@@ -1,6 +1,6 @@
 {
   "name": "@fozikio/cortex-engine",
-  "version": "1.9.0",
+  "version": "1.9.1",
   "description": "Portable cognitive engine for AI agents — storage, embeddings, memory, FSRS, and MCP server",
   "type": "module",
   "main": "dist/index.js",

src/bin/config-loader.test.ts

@@ -10,7 +10,7 @@
  */
 
 import { describe, it, expect, vi, afterEach } from 'vitest';
-import { mkdtempSync, rmSync } from 'node:fs';
+import { mkdirSync, mkdtempSync, rmSync, writeFileSync } from 'node:fs';
 import { tmpdir } from 'node:os';
 import { join } from 'node:path';
 import { DEFAULT_CONFIG } from '../core/config.js';
@@ -97,3 +97,47 @@ describe('loadConfig with no config file', () => {
     }
   });
 });
+
+describe('loadConfig over a named cortex map (agent.yaml)', () => {
+  afterEach(() => {
+    vi.restoreAllMocks();
+  });
+
+  it("lifts the primary entry's plugins and nli onto the config", () => {
+    const dir = mkdtempSync(join(tmpdir(), 'cortex-cfg-'));
+    try {
+      mkdirSync(join(dir, '.fozikio'));
+      writeFileSync(
+        join(dir, '.fozikio', 'agent.yaml'),
+        [
+          'agent:',
+          '  name: ledger',
+          'agents:',
+          '  ledger:',
+          '    namespace: ledger',
+          'cortex:',
+          '  ledger:',
+          '    store: sqlite',
+          '    embed: ollama',
+          '    llm: ollama',
+          '    primary: true',
+          '    collections_prefix: ledger_',
+          '    cognitive_tools: [query, observe]',
+          '    plugins:',
+          '      - ./.fozikio/plugins/codebase-mind/dist/index.js',
+          '    nli:',
+          '      enabled: true',
+          '      url: http://127.0.0.1:11435',
+          '',
+        ].join('\n'),
+      );
+      const config = loadConfig(dir, 'ledger');
+      expect(config.plugins).toEqual(['./.fozikio/plugins/codebase-mind/dist/index.js']);
+      expect(config.nli).toEqual({ enabled: true, url: 'http://127.0.0.1:11435' });
+      expect(config.namespaces.ledger?.collections_prefix).toBe('ledger_');
+      expect(config.namespaces.ledger?.cognitive_tools).toEqual(['query', 'observe']);
+    } finally {
+      rmSync(dir, { recursive: true, force: true });
+    }
+  });
+});

src/bin/config-loader.ts

@@ -26,6 +26,9 @@ interface NamedCortexEntry {
   llm_options?: CortexConfig['llm_options'];
   embed_options?: CortexConfig['embed_options'];
   store_options?: CortexConfig['store_options'];
+  /** Plugin packages or paths (see plugins/loader.ts); lifted onto the config like the provider fields. */
+  plugins?: CortexConfig['plugins'];
+  nli?: CortexConfig['nli'];
 }
 
 /**
@@ -72,6 +75,11 @@ function extractFromNamedCortexMap(cortexMap: Record<string, NamedCortexEntry>):
   if (entry.llm_options) partial.llm_options = entry.llm_options;
   if (entry.embed_options) partial.embed_options = entry.embed_options;
   if (entry.store_options) partial.store_options = entry.store_options;
+  // `plugins` and `nli` sit on CortexConfig beside the provider fields, but until 1.9.1 only the
+  // legacy flat `cortex:` block carried them through: the named map dropped both, so a repo's own
+  // plugin listed under its agent's entry (the 1.9.0 `trusted` path's whole point) never loaded.
+  if (entry.plugins) partial.plugins = entry.plugins;
+  if (entry.nli) partial.nli = entry.nli;
 
   if (entry.cognitive_tools || entry.collections_prefix) {
     partial.namespaces = {