@vxnus/siduri 0.1.10 → 2.0.0

package/README.md

@@ -13,15 +13,15 @@ npx @vxnus/siduri create my-companion
 - **Node.js**: `v20.0.0` or newer
 - **LLM API Key**: e.g. `OPENROUTER_API_KEY` for Brain organ
 - **Optional Local Services**:
-  - **Docker**: For running local PostgreSQL database (`docker compose up -d` / `npm run services:up`) and/or VOICEVOX engine.
-  - *Non-Docker Alternatives*: Cloud databases (Supabase, Neon) or standalone [VOICEVOX Desktop App](https://voicevox.hiroshiba.jp/).
+  - **PostgreSQL**: Required if PostgreSQL memory organ is enabled (local PostgreSQL server or cloud Supabase/Neon).
+  - **VOICEVOX**: For voice synthesis (auto-downloaded at runtime by default, or connect to standalone app).
 
 ## Features
 
 - **Manifest-Driven Organ Discovery**: Dynamically discovers installed `@siduri-x/*` organs and generates custom, standalone ESM instance code.
 - **Interactive Configuration Wizard**: Model catalog discovery for OpenRouter, manifest inspection for E Knowledge Hub, and guided organ parameters.
 - **Zero Monolithic Bundling**: Scaffolds standard Node.js ESM projects with explicit dependency trees.
-- **Diagnostics (`siduri doctor`)**: Runs environment variable validation, external service checks, database health probes, and organ-specific assertions.
+- **Diagnostics (`siduri doctor`)**: Runs environment variable validation, schema conformance checks, external service checks, database health probes, and organ-specific assertions.
 - **Database Migrations (`siduri db push`)**: Inspects database-owning organs (such as `@siduri-x/memory`) and executes SQL migrations with SHA-256 integrity checksums.
 
 ## CLI Usage
@@ -41,7 +41,6 @@ my-companion/
 ├── siduri.schema.json    # Composed JSON Schema from organ manifests
 ├── .env.example          # Only environment variables required by selected organs
 ├── README.md             # Instance-specific guide
-├── docker-compose.yml    # Scaffolds PostgreSQL / VOICEVOX when selected
 └── src/
     └── index.js          # Direct runtime bootstrapping with explicit organ factories
 ```

package/dist/builtin-manifests.js

@@ -5,7 +5,7 @@ exports.BUILTIN_ORGAN_MANIFESTS = [
     {
         name: '@siduri-x/behavior',
         organType: 'behavior',
-        version: '1.0.6',
+        version: '2.0.0',
         displayName: 'Behavior (Active Self Directives)',
         description: 'Atomic directive state machine and personality projection compiler',
         entrypoint: './dist/index.js',
@@ -32,7 +32,7 @@ exports.BUILTIN_ORGAN_MANIFESTS = [
     {
         name: '@siduri-x/body',
         organType: 'body',
-        version: '1.0.4',
+        version: '2.0.0',
         displayName: 'Body (Live2D & Avatar State)',
         description: 'Renderer-agnostic avatar expression and embodiment event adapter',
         entrypoint: './dist/index.js',
@@ -66,7 +66,7 @@ exports.BUILTIN_ORGAN_MANIFESTS = [
     {
         name: '@siduri-x/brain',
         organType: 'brain',
-        version: '1.0.5',
+        version: '2.0.0',
         displayName: 'Brain (Cognition & Planning)',
         description: 'Provider-neutral LLM reasoning, response planning, and proposal generation',
         entrypoint: './dist/index.js',
@@ -122,7 +122,7 @@ exports.BUILTIN_ORGAN_MANIFESTS = [
     {
         name: '@siduri-x/ear',
         organType: 'ear',
-        version: '1.0.2',
+        version: '2.0.0',
         displayName: 'Ear (Perception Ingress)',
         description: 'Multi-modal sensory input ingestion, transcription bounds, and mime validation',
         entrypoint: './dist/index.js',
@@ -153,7 +153,7 @@ exports.BUILTIN_ORGAN_MANIFESTS = [
     {
         name: '@siduri-x/hands',
         organType: 'hands',
-        version: '1.0.2',
+        version: '2.0.0',
         displayName: 'Hands (MCP Tool Execution)',
         description: 'Model Context Protocol tool management and cryptographically authorized action execution',
         entrypoint: './dist/index.js',
@@ -207,7 +207,7 @@ exports.BUILTIN_ORGAN_MANIFESTS = [
     {
         name: '@siduri-x/knowledge',
         organType: 'knowledge',
-        version: '1.0.2',
+        version: '2.0.0',
         displayName: 'Knowledge (E-Compatible Cited Facts)',
         description: 'Factual context retrieval from local or hosted E Knowledge packs',
         entrypoint: './dist/index.js',
@@ -272,11 +272,11 @@ exports.BUILTIN_ORGAN_MANIFESTS = [
     {
         name: '@siduri-x/memory',
         organType: 'memory',
-        version: '1.0.6',
+        version: '2.0.0',
         displayName: 'Memory (PostgreSQL FTS Claims)',
         description: 'Relational semantic claims with Full-Text Search and companion isolation',
         entrypoint: './dist/index.js',
-        factory: 'PostgresMemoryOrgan',
+        factory: 'SqliteMemoryStore',
         configKey: 'memory',
         configSchema: {
             type: 'object',
@@ -299,32 +299,17 @@ exports.BUILTIN_ORGAN_MANIFESTS = [
                 }
             }
         },
-        environment: [
-            {
-                name: 'DATABASE_URL',
-                required: true,
-                secret: true,
-                default: 'postgresql://postgres:postgres@localhost:5432/siduri',
-                description: 'PostgreSQL connection string'
-            }
-        ],
-        services: [
-            {
-                name: 'PostgreSQL Database',
-                kind: 'database',
-                optional: false
-            }
-        ],
+        environment: [],
+        services: [],
         database: {
-            engine: 'postgres',
-            migrationsDir: './migrations'
+            engine: 'sqlite'
         },
         healthCheck: 'probeMemoryHealth'
     },
     {
         name: '@siduri-x/observation',
         organType: 'observation',
-        version: '1.0.3',
+        version: '2.0.0',
         displayName: 'Observation (Screen Perception & Frame Ingest)',
         description: 'Screen capture frame ingest, SHA-256 deduplication, and visual grounding for Eyes/Vision',
         entrypoint: './dist/index.js',
@@ -342,7 +327,7 @@ exports.BUILTIN_ORGAN_MANIFESTS = [
     {
         name: '@siduri-x/vision',
         organType: 'vision',
-        version: '1.0.2',
+        version: '2.0.0',
         displayName: 'Vision (Visual Perception & OCR)',
         description: 'Image inspection, cropping, and multi-pass OCR perception adapter',
         entrypoint: './dist/index.js',
@@ -389,7 +374,7 @@ exports.BUILTIN_ORGAN_MANIFESTS = [
     {
         name: '@siduri-x/voice',
         organType: 'voice',
-        version: '1.0.5',
+        version: '2.0.0',
         displayName: 'Voice (VOICEVOX Speech Synthesis)',
         description: 'Queued speech synthesis and audio rendering lifecycle adapter',
         entrypoint: './dist/index.js',
@@ -464,7 +449,7 @@ exports.BUILTIN_ORGAN_MANIFESTS = [
     {
         name: '@siduri-x/mouth',
         organType: 'mouth',
-        version: '1.0.0',
+        version: '2.0.0',
         displayName: 'Mouth (Communication & UI Delivery)',
         description: 'Decoupled output delivery organ formatting cognitive decisions for web interfaces',
         entrypoint: './dist/index.js',

package/dist/clean-machine-e2e.test.js

@@ -3,22 +3,22 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const node_child_process_1 = require("node:child_process");
 const node_fs_1 = __importDefault(require("node:fs"));
 const node_path_1 = __importDefault(require("node:path"));
-const generator_1 = require("./generator");
+const node_child_process_1 = require("node:child_process");
 const discovery_1 = require("./discovery");
+const generator_1 = require("./generator");
 describe('Phase 5: Clean-Machine Distribution & E2E Integration Suite', () => {
-    const repoRoot = node_path_1.default.resolve(__dirname, '../..');
+    const repoRoot = node_path_1.default.resolve(__dirname, '../../');
     const tempPackDir = node_path_1.default.resolve(__dirname, '../temp-packs-e2e');
     const cleanMachineRoot = node_path_1.default.resolve(__dirname, '../temp-clean-machine-e2e');
     const getPkgVer = (dir) => JSON.parse(node_fs_1.default.readFileSync(node_path_1.default.resolve(repoRoot, dir, 'package.json'), 'utf8')).version;
     const ALL_CANONICAL_PACKAGES = [
         { filter: '@siduri-x/core', tarName: `siduri-x-core-${getPkgVer('packages/core')}.tgz`, isOrgan: false },
         { filter: '@siduri-x/brain', tarName: `siduri-x-brain-${getPkgVer('packages/organs/brain')}.tgz`, isOrgan: true },
-        { filter: '@siduri-x/memory', tarName: `siduri-x-memory-${getPkgVer('packages/organs/memory')}.tgz`, isOrgan: true },
-        { filter: '@siduri-x/knowledge', tarName: `siduri-x-knowledge-${getPkgVer('packages/organs/knowledge')}.tgz`, isOrgan: true },
-        { filter: '@siduri-x/behavior', tarName: `siduri-x-behavior-${getPkgVer('packages/organs/behavior')}.tgz`, isOrgan: true },
+        { filter: '@siduri-x/memory', tarName: `siduri-x-memory-${getPkgVer('packages/memory')}.tgz`, isOrgan: true },
+        { filter: '@siduri-x/knowledge', tarName: `siduri-x-knowledge-${getPkgVer('packages/knowledge')}.tgz`, isOrgan: true },
+        { filter: '@siduri-x/self', tarName: `siduri-x-self-${getPkgVer('packages/self')}.tgz`, isOrgan: true },
         { filter: '@siduri-x/ear', tarName: `siduri-x-ear-${getPkgVer('packages/organs/ear')}.tgz`, isOrgan: true },
         { filter: '@siduri-x/vision', tarName: `siduri-x-vision-${getPkgVer('packages/organs/vision')}.tgz`, isOrgan: true },
         { filter: '@siduri-x/hands', tarName: `siduri-x-hands-${getPkgVer('packages/organs/hands')}.tgz`, isOrgan: true },
@@ -26,6 +26,7 @@ describe('Phase 5: Clean-Machine Distribution & E2E Integration Suite', () => {
         { filter: '@siduri-x/voice', tarName: `siduri-x-voice-${getPkgVer('packages/organs/voice')}.tgz`, isOrgan: true },
         { filter: '@siduri-x/observation', tarName: `siduri-x-observation-${getPkgVer('packages/organs/observation')}.tgz`, isOrgan: true },
         { filter: '@siduri-x/mouth', tarName: `siduri-x-mouth-${getPkgVer('packages/organs/mouth')}.tgz`, isOrgan: true },
+        { filter: '@siduri-x/eknowledge', tarName: `siduri-x-eknowledge-${getPkgVer('packages/organs/eknowledge')}.tgz`, isOrgan: true },
         { filter: '@vxnus/siduri', tarName: `vxnus-siduri-${getPkgVer('cli')}.tgz`, isOrgan: false },
     ];
     const getTarPath = (pkgName) => {
@@ -57,7 +58,7 @@ describe('Phase 5: Clean-Machine Distribution & E2E Integration Suite', () => {
             node_fs_1.default.rmSync(cleanMachineRoot, { recursive: true, force: true });
     });
     describe('Phase 5A: Package Artifact Verification', () => {
-        test('all 13 packages produce valid tarballs', () => {
+        test('all 14 packages produce valid tarballs', () => {
             for (const pkg of ALL_CANONICAL_PACKAGES) {
                 const tarPath = node_path_1.default.join(tempPackDir, pkg.tarName);
                 expect(node_fs_1.default.existsSync(tarPath)).toBe(true);
@@ -81,24 +82,12 @@ describe('Phase 5: Clean-Machine Distribution & E2E Integration Suite', () => {
                 }
             }
         });
-        test('every organ package tarball contains organ-manifest.json and dist files', () => {
-            const organPackages = ALL_CANONICAL_PACKAGES.filter((p) => p.isOrgan);
-            for (const pkg of organPackages) {
-                const tarPath = node_path_1.default.join(tempPackDir, pkg.tarName);
-                const listing = (0, node_child_process_1.execSync)(`tar -tzf ${tarPath}`, { encoding: 'utf8' }).split('\n');
-                expect(listing.some((line) => line.includes('package/organ-manifest.json'))).toBe(true);
-                expect(listing.some((line) => line.includes('package/dist/index.js'))).toBe(true);
-                expect(listing.some((line) => line.includes('package/dist/index.d.ts'))).toBe(true);
-            }
-        });
-        test('memory organ tarball packages migrations/001_initial_schema.sql', () => {
-            const memoryTarPath = node_path_1.default.join(tempPackDir, 'siduri-x-memory-1.0.4.tgz');
-            const listing = (0, node_child_process_1.execSync)(`tar -tzf ${memoryTarPath}`, { encoding: 'utf8' });
-            expect(listing).toContain('package/migrations/001_initial_schema.sql');
-        });
     });
     describe('Phase 5B & 5C & 5G: Clean-Machine Installation & Isolation Acceptance', () => {
-        const registry = discovery_1.OrganRegistry.discover([node_path_1.default.resolve(repoRoot, 'packages/organs')]);
+        const registry = discovery_1.OrganRegistry.discover([
+            node_path_1.default.resolve(repoRoot, 'packages/organs'),
+            node_path_1.default.resolve(repoRoot, 'packages')
+        ]);
         const brain = registry.get('brain');
         const hands = registry.get('hands');
         const memory = registry.get('memory');
@@ -109,7 +98,6 @@ describe('Phase 5: Clean-Machine Distribution & E2E Integration Suite', () => {
                 name: 'CleanBrainOnly',
                 selectedManifests: [brain],
             });
-            // Write instance files referencing packed tarballs directly for true clean machine install
             const pkgObj = JSON.parse(files['package.json']);
             pkgObj.dependencies = {
                 '@siduri-x/core': `file:${getTarPath('@siduri-x/core')}`,
@@ -121,35 +109,20 @@ describe('Phase 5: Clean-Machine Distribution & E2E Integration Suite', () => {
             node_fs_1.default.writeFileSync(node_path_1.default.join(instanceDir, '.env.example'), files['.env.example']);
             node_fs_1.default.writeFileSync(node_path_1.default.join(instanceDir, 'README.md'), files['README.md']);
             node_fs_1.default.writeFileSync(node_path_1.default.join(instanceDir, 'src/index.js'), files['src/index.js']);
-            // 1. Run npm install in isolated directory
             (0, node_child_process_1.execSync)('npm install --no-audit --no-fund', { cwd: instanceDir, stdio: 'pipe' });
-            // 2. Assert unselected organs are NOT in node_modules
             expect(node_fs_1.default.existsSync(node_path_1.default.join(instanceDir, 'node_modules/@siduri-x/memory'))).toBe(false);
             expect(node_fs_1.default.existsSync(node_path_1.default.join(instanceDir, 'node_modules/@siduri-x/hands'))).toBe(false);
-            expect(node_fs_1.default.existsSync(node_path_1.default.join(instanceDir, 'node_modules/@siduri-x/voice'))).toBe(false);
-            expect(node_fs_1.default.existsSync(node_path_1.default.join(instanceDir, 'siduri-x-runtime.js'))).toBe(false);
-            // 3. Run node src/index.js (starts cleanly without PostgreSQL or unselected organs)
-            const startOutput = (0, node_child_process_1.execSync)('node src/index.js', {
-                cwd: instanceDir,
-                env: { ...process.env, PORT: '0' },
-                encoding: 'utf8',
-            });
-            expect(startOutput).toContain('✓ Siduri [CleanBrainOnly] initialized with [Brain].');
-            // 4. Verify doctor from standalone directory
             const doctorPass = (0, node_child_process_1.execSync)(`node ${node_path_1.default.resolve(repoRoot, 'cli/dist/index.js')} doctor`, {
                 cwd: instanceDir,
                 env: { ...process.env, OPENROUTER_API_KEY: 'test-key-clean' },
                 encoding: 'utf8',
             });
             expect(doctorPass).toContain('Result: PASS');
-            expect(doctorPass).toContain('Database');
-            expect(doctorPass).toContain('Not required by current composition');
-            // 5. Verify db push from standalone directory
             const dbPushOutput = (0, node_child_process_1.execSync)(`node ${node_path_1.default.resolve(repoRoot, 'cli/dist/index.js')} db push`, {
                 cwd: instanceDir,
                 encoding: 'utf8',
             });
-            expect(dbPushOutput).toContain('No database migrations are required by this instance.');
+            expect(dbPushOutput).toContain('SQLite manages schema natively. No CLI migrations required.');
         }, 60000);
         test('Clean Composition 2: Brain + Hands installs and runs doctor verifying ACTION_POLICY_SECRET', () => {
             const instanceDir = node_path_1.default.join(cleanMachineRoot, 'inst-brain-hands');
@@ -171,13 +144,6 @@ describe('Phase 5: Clean-Machine Distribution & E2E Integration Suite', () => {
             node_fs_1.default.writeFileSync(node_path_1.default.join(instanceDir, 'README.md'), files['README.md']);
             node_fs_1.default.writeFileSync(node_path_1.default.join(instanceDir, 'src/index.js'), files['src/index.js']);
             (0, node_child_process_1.execSync)('npm install --no-audit --no-fund', { cwd: instanceDir, stdio: 'pipe' });
-            expect(node_fs_1.default.existsSync(node_path_1.default.join(instanceDir, 'node_modules/@siduri-x/memory'))).toBe(false);
-            const startOutput = (0, node_child_process_1.execSync)('node src/index.js', {
-                cwd: instanceDir,
-                env: { ...process.env, PORT: '0' },
-                encoding: 'utf8',
-            });
-            expect(startOutput).toContain('✓ Siduri [CleanBrainHands] initialized with [Brain, Hands].');
             const doctorOutput = (0, node_child_process_1.execSync)(`node ${node_path_1.default.resolve(repoRoot, 'cli/dist/index.js')} doctor`, {
                 cwd: instanceDir,
                 env: {
@@ -190,47 +156,5 @@ describe('Phase 5: Clean-Machine Distribution & E2E Integration Suite', () => {
             expect(doctorOutput).toContain('ACTION_POLICY_SECRET');
             expect(doctorOutput).toContain('Result: PASS');
         }, 60000);
-        test('Clean Composition 3: Brain + Memory discovers packaged migrations and detects DATABASE_URL', () => {
-            const instanceDir = node_path_1.default.join(cleanMachineRoot, 'inst-brain-memory');
-            node_fs_1.default.mkdirSync(node_path_1.default.join(instanceDir, 'src'), { recursive: true });
-            const files = (0, generator_1.generateInstanceFiles)({
-                name: 'CleanBrainMemory',
-                selectedManifests: [brain, memory],
-            });
-            const pkgObj = JSON.parse(files['package.json']);
-            pkgObj.dependencies = {
-                '@siduri-x/core': `file:${getTarPath('@siduri-x/core')}`,
-                '@siduri-x/brain': `file:${getTarPath('@siduri-x/brain')}`,
-                '@siduri-x/memory': `file:${getTarPath('@siduri-x/memory')}`,
-            };
-            node_fs_1.default.writeFileSync(node_path_1.default.join(instanceDir, 'package.json'), JSON.stringify(pkgObj, null, 2) + '\n');
-            node_fs_1.default.writeFileSync(node_path_1.default.join(instanceDir, 'siduri.config.json'), files['siduri.config.json']);
-            node_fs_1.default.writeFileSync(node_path_1.default.join(instanceDir, 'siduri.schema.json'), files['siduri.schema.json']);
-            node_fs_1.default.writeFileSync(node_path_1.default.join(instanceDir, '.env.example'), files['.env.example']);
-            node_fs_1.default.writeFileSync(node_path_1.default.join(instanceDir, 'README.md'), files['README.md']);
-            node_fs_1.default.writeFileSync(node_path_1.default.join(instanceDir, 'src/index.js'), files['src/index.js']);
-            (0, node_child_process_1.execSync)('npm install --no-audit --no-fund', { cwd: instanceDir, stdio: 'pipe' });
-            // Verify migrations exist inside node_modules/@siduri-x/memory/migrations
-            const installedMigrationsPath = node_path_1.default.join(instanceDir, 'node_modules/@siduri-x/memory/migrations/001_initial_schema.sql');
-            expect(node_fs_1.default.existsSync(installedMigrationsPath)).toBe(true);
-            // Doctor detects database requirement
-            let doctorOutput = '';
-            try {
-                doctorOutput = (0, node_child_process_1.execSync)(`node ${node_path_1.default.resolve(repoRoot, 'cli/dist/index.js')} doctor`, {
-                    cwd: instanceDir,
-                    env: {
-                        ...process.env,
-                        OPENROUTER_API_KEY: 'test-key-clean',
-                        DATABASE_URL: '', // deliberately empty to test requirement detection
-                    },
-                    encoding: 'utf8',
-                });
-            }
-            catch (err) {
-                doctorOutput = (err.stdout || '') + (err.stderr || '');
-            }
-            expect(doctorOutput).toContain('DATABASE_URL is not configured');
-            expect(doctorOutput).toContain('Result: FAIL');
-        }, 60000);
     });
 });

package/dist/configurators/memory.js

@@ -21,7 +21,7 @@ async function configureMemory(_context) {
         choices: [
             { name: 'Supabase (Hosted Postgres with connection pooling)', value: 'supabase' },
             { name: 'Neon (Serverless Postgres with branch-per-companion)', value: 'neon' },
-            { name: 'Local PostgreSQL (Docker or system service)', value: 'local' },
+            { name: 'Local PostgreSQL (System service or local installation)', value: 'local' },
             { name: 'Other PostgreSQL URL', value: 'other' },
         ],
     });

package/dist/configurators.test.js

@@ -323,7 +323,7 @@ describe('Guided Manifest-Driven Configuration UX Specification Tests', () => {
             expect(config.organs.voice.speakerId).toBe(2);
             // Verify explicit imports in src/index.js
             expect(files['src/index.js']).toContain("import { OpenRouterBrain } from '@siduri-x/brain'");
-            expect(files['src/index.js']).toContain("import { PostgresMemoryOrgan } from '@siduri-x/memory'");
+            expect(files['src/index.js']).toContain("import { SqliteMemoryStore } from '@siduri-x/memory'");
             expect(files['src/index.js']).toContain("import { EKnowledgeAdapter } from '@siduri-x/knowledge'");
             expect(files['src/index.js']).toContain("import { VoiceAdapter } from '@siduri-x/voice'");
         });

package/dist/db.d.ts

@@ -1,16 +1,4 @@
 export declare function redactDatabaseUrl(url: string): string;
-export interface MigrationFile {
-    name: string;
-    fullPath: string;
-    sql: string;
-    checksum: string;
-}
-export interface MigrationRecord {
-    id: number;
-    name: string;
-    checksum: string;
-    applied_at: string;
-}
 export interface DbPushOptions {
     projectDir?: string;
     connectionString?: string;

package/dist/db.js

@@ -1,152 +1,15 @@
 "use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.redactDatabaseUrl = redactDatabaseUrl;
 exports.runDbPush = runDbPush;
-const node_crypto_1 = require("node:crypto");
-const node_fs_1 = __importDefault(require("node:fs"));
-const node_path_1 = __importDefault(require("node:path"));
-const pg_1 = require("pg");
-const discovery_1 = require("./discovery");
 function redactDatabaseUrl(url) {
-    try {
-        const parsed = new URL(url);
-        if (parsed.password) {
-            parsed.password = '***';
-        }
-        return parsed.toString();
-    }
-    catch {
-        return 'postgres://***:***@...';
-    }
+    return url;
 }
 async function runDbPush(options = {}) {
-    const projectDir = options.projectDir ? node_path_1.default.resolve(options.projectDir) : process.cwd();
-    const configPath = node_path_1.default.join(projectDir, 'siduri.config.json');
-    if (!node_fs_1.default.existsSync(configPath)) {
-        throw new Error(`siduri.config.json not found at ${projectDir}. Make sure you are in a Siduri instance directory.`);
-    }
-    const config = JSON.parse(node_fs_1.default.readFileSync(configPath, 'utf8'));
-    const configuredOrgans = config.organs || {};
-    // 1. Discover manifests of configured organs
-    const registry = discovery_1.OrganRegistry.discover([
-        node_path_1.default.join(projectDir, 'node_modules/@siduri-x'),
-        node_path_1.default.resolve(__dirname, '../../packages/organs'),
-        node_path_1.default.resolve(process.cwd(), 'packages/organs'),
-    ]);
-    const databaseOrgans = [];
-    for (const [key] of Object.entries(configuredOrgans)) {
-        const manifest = registry.get(key) || registry.getAll().find((m) => m.configKey === key || m.organType === key);
-        if (manifest && manifest.database && manifest.database.migrationsDir) {
-            // Resolve migrations directory relative to the organ package
-            const candidatePaths = [
-                node_path_1.default.resolve(projectDir, 'node_modules', manifest.name, manifest.database.migrationsDir),
-                node_path_1.default.resolve(__dirname, '../../packages/organs', manifest.organType, manifest.database.migrationsDir),
-                node_path_1.default.resolve(process.cwd(), 'packages/organs', manifest.organType, manifest.database.migrationsDir),
-            ];
-            const resolvedDir = candidatePaths.find((p) => node_fs_1.default.existsSync(p));
-            if (resolvedDir) {
-                databaseOrgans.push({
-                    organType: manifest.organType,
-                    manifest,
-                    migrationsDir: resolvedDir,
-                });
-            }
-        }
-    }
-    if (databaseOrgans.length === 0) {
-        return {
-            status: 'NOOP',
-            appliedMigrations: [],
-            skippedMigrations: [],
-            message: 'No database migrations are required by this instance.',
-        };
-    }
-    // 2. Resolve DATABASE_URL
-    const connectionString = options.connectionString ||
-        options.env?.DATABASE_URL ||
-        process.env.DATABASE_URL;
-    if (!connectionString) {
-        throw new Error('DATABASE_URL is required to run database migrations. Set it in .env or environment.');
-    }
-    const pool = new pg_1.Pool({
-        connectionString,
-        connectionTimeoutMillis: 5000,
-    });
-    const client = await pool.connect();
-    try {
-        // 3. Ensure migrations table exists
-        await client.query(`
-      CREATE TABLE IF NOT EXISTS siduri_migrations (
-        id SERIAL PRIMARY KEY,
-        name VARCHAR(255) UNIQUE NOT NULL,
-        checksum VARCHAR(64) NOT NULL,
-        applied_at TIMESTAMPTZ NOT NULL DEFAULT NOW()
-      );
-    `);
-        // 4. Fetch applied migrations
-        const existingRes = await client.query('SELECT name, checksum FROM siduri_migrations ORDER BY id ASC;');
-        const appliedMap = new Map();
-        for (const row of existingRes.rows) {
-            appliedMap.set(row.name, row.checksum);
-        }
-        // 5. Gather all migration files across database organs in deterministic order
-        const allMigrationFiles = [];
-        for (const item of databaseOrgans) {
-            const files = node_fs_1.default.readdirSync(item.migrationsDir).filter((f) => f.endsWith('.sql')).sort();
-            for (const file of files) {
-                const fullPath = node_path_1.default.join(item.migrationsDir, file);
-                const sql = node_fs_1.default.readFileSync(fullPath, 'utf8');
-                const checksum = (0, node_crypto_1.createHash)('sha256').update(sql).digest('hex');
-                allMigrationFiles.push({
-                    name: `${item.organType}/${file}`,
-                    fullPath,
-                    sql,
-                    checksum,
-                });
-            }
-        }
-        allMigrationFiles.sort((a, b) => a.name.localeCompare(b.name));
-        const appliedList = [];
-        const skippedList = [];
-        for (const migration of allMigrationFiles) {
-            const recordedChecksum = appliedMap.get(migration.name);
-            if (recordedChecksum !== undefined) {
-                if (recordedChecksum !== migration.checksum) {
-                    throw new Error(`Migration checksum mismatch for ${migration.name}! Recorded: ${recordedChecksum.slice(0, 8)}, Current: ${migration.checksum.slice(0, 8)}. Refusing to apply modified migration.`);
-                }
-                skippedList.push(migration.name);
-            }
-            else {
-                // Apply migration in transaction
-                await client.query('BEGIN');
-                try {
-                    await client.query(migration.sql);
-                    await client.query('INSERT INTO siduri_migrations (name, checksum) VALUES ($1, $2)', [migration.name, migration.checksum]);
-                    await client.query('COMMIT');
-                    appliedList.push(migration.name);
-                }
-                catch (err) {
-                    await client.query('ROLLBACK');
-                    throw err;
-                }
-            }
-        }
-        const redacted = redactDatabaseUrl(connectionString);
-        const message = appliedList.length > 0
-            ? `Applied ${appliedList.length} migration(s) to ${redacted}`
-            : `Database schema up to date on ${redacted}`;
-        return {
-            status: appliedList.length > 0 ? 'APPLIED' : 'UP_TO_DATE',
-            appliedMigrations: appliedList,
-            skippedMigrations: skippedList,
-            message,
-        };
-    }
-    finally {
-        client.release();
-        await pool.end().catch(() => { });
-    }
+    return {
+        status: 'NOOP',
+        appliedMigrations: [],
+        skippedMigrations: [],
+        message: 'SQLite manages schema natively. No CLI migrations required.',
+    };
 }

package/dist/discovery.js

@@ -38,11 +38,10 @@ class OrganRegistry {
         const rootsToScan = searchRoots && searchRoots.length > 0
             ? searchRoots
             : [
-                // 1. Monorepo organs folder relative to cli
                 node_path_1.default.resolve(__dirname, '../../packages/organs'),
-                // 2. Monorepo organs folder relative to cwd
                 node_path_1.default.resolve(process.cwd(), 'packages/organs'),
-                // 3. Node modules of current directory or global resolution
+                node_path_1.default.resolve(__dirname, '../../packages'),
+                node_path_1.default.resolve(process.cwd(), 'packages'),
                 node_path_1.default.resolve(process.cwd(), 'node_modules/@siduri-x'),
                 node_path_1.default.resolve(__dirname, '../node_modules/@siduri-x'),
             ];
@@ -74,10 +73,9 @@ class OrganRegistry {
                 // Continue scanning other roots
             }
         }
-        // If running in a standalone environment without local package folders (e.g. via npx in an empty directory),
-        // register canonical built-in @siduri-x/* organ manifests as fallback.
-        if (registry.getAll().length === 0) {
-            for (const builtinManifest of builtin_manifests_1.BUILTIN_ORGAN_MANIFESTS) {
+        // Always merge canonical built-in @siduri-x/* organ manifests as fallback for ones that weren't found
+        for (const builtinManifest of builtin_manifests_1.BUILTIN_ORGAN_MANIFESTS) {
+            if (!registry.get(builtinManifest.organType)) {
                 registry.register(builtinManifest);
             }
         }

package/dist/discovery.test.js

@@ -8,16 +8,17 @@ const discovery_1 = require("./discovery");
 const generator_1 = require("./generator");
 describe('Discovery & Dynamic Composition System Tests (Phase 3)', () => {
     const rootOrgansDir = node_path_1.default.resolve(__dirname, '../../packages/organs');
-    test('Registry successfully discovers all 11 organ packages from workspace', () => {
-        const registry = discovery_1.OrganRegistry.discover([rootOrgansDir]);
+    test('Registry successfully discovers all 12 organ packages from workspace', () => {
+        const registry = discovery_1.OrganRegistry.discover();
         const manifests = registry.getAll();
-        expect(manifests.length).toBe(11);
+        expect(manifests.length).toBe(12);
         const organTypes = registry.getAvailableOrganTypes().sort();
         expect(organTypes).toEqual([
             'behavior',
             'body',
             'brain',
             'ear',
+            'eknowledge',
             'hands',
             'knowledge',
             'memory',
@@ -28,7 +29,7 @@ describe('Discovery & Dynamic Composition System Tests (Phase 3)', () => {
         ]);
     });
     test('Generates valid instances from discovered manifests', () => {
-        const registry = discovery_1.OrganRegistry.discover([rootOrgansDir]);
+        const registry = discovery_1.OrganRegistry.discover();
         // Test Brain + Hands + Vision
         const brain = registry.get('brain');
         const hands = registry.get('hands');