@cogitator-ai/cli 0.5.18 → 0.5.20

package/README.md

@@ -78,20 +78,23 @@ my-assistant/
 ├── tsconfig.json
 ├── .env                 # API keys, channel tokens, DATABASE_URL (mode 0600, only when needed)
 ├── .gitignore
+├── cogitator.yml        # provider, model, memory and deploy settings for `cogitator run` / `cogitator deploy`
 ├── pnpm-workspace.yaml  # pnpm only: allows the better-sqlite3 / esbuild / sharp builds
 └── src/
     ├── gateway.ts       # exports `gateway` — agent, channels, memory adapter
     └── agent.ts         # starts the gateway (pnpm dev / pnpm start)
 ```
 
-| Memory choice | Generated adapter | Extra dependency | Notes                               |
-| ------------- | ----------------- | ---------------- | ----------------------------------- |
-| SQLite        | `SQLiteAdapter`   | `better-sqlite3` | Stored in `./data/memory.db`        |
-| In-memory     | `InMemoryAdapter` | —                | Lost on restart                     |
-| PostgreSQL    | `PostgresAdapter` | `pg`             | Connection string in `DATABASE_URL` |
+| Memory choice | Generated adapter | Extra dependency | Notes                                                            |
+| ------------- | ----------------- | ---------------- | ---------------------------------------------------------------- |
+| SQLite        | `SQLiteAdapter`   | `better-sqlite3` | Stored in `./data/memory.db` (the directory is created at start) |
+| In-memory     | `InMemoryAdapter` | -                | Lost on restart                                                  |
+| PostgreSQL    | `PostgresAdapter` | `pg`             | Connection string in `DATABASE_URL`                              |
 
 `src/gateway.ts` loads `.env` itself (`process.loadEnvFile`, Node ≥ 20.12), so it works with `pnpm dev`, `cogitator assistant`, `cogitator build` and the daemon alike.
 
+`package.json` pins the package manager that ran `init` in its `packageManager` field (pnpm, Yarn or Bun), so corepack and the deploy image install with the same version. `cogitator.yml` makes the project deployable as it is: `cogitator deploy` runs the gateway as a worker (no HTTP health check, the WebChat port published when WebChat is on), keeps the SQLite database on a volume and passes the API key and channel tokens as secrets. The code in `src/` configures the gateway itself, so change the provider, model or memory in both places.
+
 ---
 
 ### cogitator wizard
@@ -173,9 +176,9 @@ cogitator run            # interactive
 | `-s, --stream`        | `true`      | Stream response tokens              |
 | `--no-stream`         | -           | Disable streaming                   |
 
-**Config resolution:** `-c` → `COGITATOR_CONFIG` → `cogitator.yml`, `cogitator.yaml`, `cogitator.json`, `.cogitator.yml`, `.cogitator.yaml`. The file is loaded with [`@cogitator-ai/config`](https://www.npmjs.com/package/@cogitator-ai/config), so `${ENV}` references and `COGITATOR_*` / provider environment variables apply even without a file.
+**Config resolution:** `-c` → `COGITATOR_CONFIG` → `cogitator.yml`, `cogitator.yaml`, `.cogitator.yml`, `.cogitator.yaml`, `cogitator.json`. The `.env` next to the file (or in the working directory without one) is loaded first, without overriding variables already set. The file is loaded with [`@cogitator-ai/config`](https://www.npmjs.com/package/@cogitator-ai/config), so `${ENV}` references and `COGITATOR_*` / provider environment variables apply even without a file. An assistant config from `cogitator wizard` is not a runtime config: `run` takes its `llm.provider` and `llm.model` as the model and everything else from the environment (`cogitator up` runs the assistant itself).
 
-**Model resolution:** `-m` → `COGITATOR_MODEL` → `llm.defaultModel` from the config → first installed Ollama model (preferring qwen3:8b, qwen3.5:9b, llama3.1:8b, llama3:8b, gemma3:4b, gemma2:9b, mistral:7b). Ollama is reached at `llm.providers.ollama.baseUrl`, `OLLAMA_URL` or `OLLAMA_HOST`.
+**Model resolution:** `-m` → `COGITATOR_MODEL` → `llm.defaultModel` from the config → the model of an assistant config → first installed Ollama model (preferring qwen3:8b, qwen3.5:9b, llama3.1:8b, llama3:8b, gemma3:4b, gemma2:9b, mistral:7b). Ollama is reached at `llm.providers.ollama.baseUrl`, `OLLAMA_URL` or `OLLAMA_HOST`.
 
 Interactive commands: `/model [name]`, `/clear`, `/help`, `exit` / `quit` (Ctrl+D also exits).
 
@@ -201,7 +204,7 @@ node dist/cogitator.mjs
 | `--minify`             | `false`              |
 | `-q, --quiet`          | `false`              |
 
-Native and optional channel dependencies (`better-sqlite3`, `pg`, `grammy`, `discord.js`, `@slack/bolt`, `playwright`, …) stay external.
+Only the project's own code is bundled: every package stays an import resolved from `node_modules` at runtime, since packages ship native addons (`better-sqlite3`, the `ssh2` behind the Docker sandbox) and optional drivers loaded on demand. Run the bundle where the project's dependencies are installed.
 
 ---
 
@@ -246,7 +249,7 @@ cogitator models --pull qwen2.5:0.5b   # pull with progress
 cogitator models --url http://gpu-box:11434
 ```
 
-The Ollama URL defaults to `OLLAMA_URL`, then `OLLAMA_HOST`, then `http://localhost:11434`; `OLLAMA_API_KEY` is sent as a bearer token. Pull errors reported by Ollama (e.g. unknown model) fail the command.
+The Ollama URL defaults to `OLLAMA_BASE_URL`, then `OLLAMA_URL`, then `OLLAMA_HOST` (read like Ollama reads it: port 11434 when none is given, `0.0.0.0` as `localhost`), then `http://localhost:11434`, `OLLAMA_API_KEY` is sent as a bearer token. Pull errors reported by Ollama (e.g. unknown model) fail the command.
 
 ---
 
@@ -283,13 +286,13 @@ cogitator deploy destroy
 | Option                  | Description                              |
 | ----------------------- | ---------------------------------------- |
 | `-t, --target <target>` | `docker` (default) or `fly`              |
-| `-c, --config <path>`   | Config file with a `deploy:` section     |
+| `-c, --config <path>`   | Config file to deploy from               |
 | `--registry <url>`      | Container registry to push to            |
 | `--no-push`             | Skip pushing even when a registry is set |
 | `--dry-run`             | Show the plan without executing          |
 | `--region <region>`     | Deploy region (Fly.io)                   |
 
-The plan lists detected services, required secrets (read from the environment or the project's `.env`), warnings and preflight checks. See [`@cogitator-ai/deploy`](https://www.npmjs.com/package/@cogitator-ai/deploy) and the [deploy guide](https://cogitator.app/docs/deployment/deploy-package) for details.
+The model, memory and `deploy:` section all come from one config file: the `-c` file, else the first of `cogitator.yml`, `cogitator.yaml`, `.cogitator.yml`, `.cogitator.yaml`. The plan lists the kind (server or worker), detected services (marked as not provisioned on Fly, where `REDIS_URL` / `DATABASE_URL` are required instead), volumes, required secrets (read from the environment or the project's `.env`), warnings and preflight checks. On Docker the deploy only succeeds when the app container keeps running after it starts, otherwise its last log lines are shown. See [`@cogitator-ai/deploy`](https://www.npmjs.com/package/@cogitator-ai/deploy) and the [deploy guide](https://cogitator.app/docs/deployment/deploy-package) for details.
 
 ---
 

package/dist/commands/build.d.ts

@@ -1,5 +1,20 @@
 import { Command } from 'commander';
-export declare const BUNDLE_EXTERNALS: string[];
 export declare function createGatewayEntry(configPath: string): string;
+export interface GatewayBuildOptions {
+    configPath: string;
+    outfile: string;
+    target: string;
+    sourcemap: boolean;
+    minify?: boolean;
+    quiet?: boolean;
+}
+/**
+ * esbuild options for a gateway bundle. The project's own code is bundled,
+ * while every package stays an import resolved from node_modules at runtime:
+ * packages ship native addons (better-sqlite3, the ssh2 behind the Docker
+ * sandbox) and optional drivers loaded on demand, which a bundle cannot
+ * carry, so the bundle runs next to the project's node_modules.
+ */
+export declare function gatewayBuildOptions(options: GatewayBuildOptions): Record<string, unknown>;
 export declare const buildCommand: Command;
 //# sourceMappingURL=build.d.ts.map

package/dist/commands/build.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"build.d.ts","sourceRoot":"","sources":["../../src/commands/build.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAgCpC,wBAAgB,kBAAkB,CAAC,UAAU,EAAE,MAAM,GAAG,MAAM,CA4B7D;AAED,MAAM,WAAW,mBAAmB;IAClC,UAAU,EAAE,MAAM,CAAC;IACnB,OAAO,EAAE,MAAM,CAAC;IAChB,MAAM,EAAE,MAAM,CAAC;IACf,SAAS,EAAE,OAAO,CAAC;IACnB,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,KAAK,CAAC,EAAE,OAAO,CAAC;CACjB;AAED;;;;;;GAMG;AACH,wBAAgB,mBAAmB,CAAC,OAAO,EAAE,mBAAmB,GAAG,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CA2BzF;AAQD,eAAO,MAAM,YAAY,SAgFtB,CAAC"}

package/dist/commands/build.js

@@ -5,20 +5,6 @@ import { dirname, resolve, relative } from 'node:path';
 import { log, printBanner } from '../utils/logger.js';
 import { importOptionalPackage } from '../utils/module-loader.js';
 import { BUNDLE_MARKER } from '../utils/daemon.js';
-export const BUNDLE_EXTERNALS = [
-    'grammy',
-    'discord.js',
-    '@slack/bolt',
-    '@whiskeysockets/baileys',
-    'ws',
-    'better-sqlite3',
-    'pg',
-    'ioredis',
-    'mongodb',
-    '@qdrant/js-client-rest',
-    'playwright',
-    'playwright-core',
-];
 function isEsbuildApi(value) {
     return (typeof value === 'object' &&
         value !== null &&
@@ -62,6 +48,41 @@ if (gateway && typeof gateway.start === 'function' && typeof gateway.stop === 'f
 }
 `;
 }
+/**
+ * esbuild options for a gateway bundle. The project's own code is bundled,
+ * while every package stays an import resolved from node_modules at runtime:
+ * packages ship native addons (better-sqlite3, the ssh2 behind the Docker
+ * sandbox) and optional drivers loaded on demand, which a bundle cannot
+ * carry, so the bundle runs next to the project's node_modules.
+ */
+export function gatewayBuildOptions(options) {
+    return {
+        stdin: {
+            contents: createGatewayEntry(options.configPath),
+            resolveDir: dirname(options.configPath),
+            sourcefile: 'cogitator-entry.mjs',
+            loader: 'js',
+        },
+        bundle: true,
+        packages: 'external',
+        platform: 'node',
+        target: options.target,
+        format: 'esm',
+        outfile: options.outfile,
+        sourcemap: options.sourcemap,
+        minify: options.minify ?? false,
+        treeShaking: true,
+        metafile: true,
+        logLevel: options.quiet ? 'error' : 'warning',
+        banner: {
+            js: [
+                '#!/usr/bin/env node',
+                `import { createRequire as ${BUNDLE_MARKER} } from "module";`,
+                `const require = ${BUNDLE_MARKER}(import.meta.url);`,
+            ].join('\n'),
+        },
+    };
+}
 function formatSize(bytes) {
     if (bytes < 1024)
         return `${bytes} B`;
@@ -100,32 +121,14 @@ export const buildCommand = new Command('build')
     const startTime = performance.now();
     let result;
     try {
-        result = await esbuild.build({
-            stdin: {
-                contents: createGatewayEntry(configPath),
-                resolveDir: dirname(configPath),
-                sourcefile: 'cogitator-entry.mjs',
-                loader: 'js',
-            },
-            bundle: true,
-            platform: 'node',
-            target: options.target,
-            format: 'esm',
+        result = await esbuild.build(gatewayBuildOptions({
+            configPath,
             outfile,
+            target: options.target,
             sourcemap: options.sourcemap,
-            minify: options.minify ?? false,
-            treeShaking: true,
-            metafile: true,
-            logLevel: options.quiet ? 'error' : 'warning',
-            external: BUNDLE_EXTERNALS,
-            banner: {
-                js: [
-                    '#!/usr/bin/env node',
-                    `import { createRequire as ${BUNDLE_MARKER} } from "module";`,
-                    `const require = ${BUNDLE_MARKER}(import.meta.url);`,
-                ].join('\n'),
-            },
-        });
+            minify: options.minify,
+            quiet: options.quiet,
+        }));
     }
     catch (error) {
         log.error('Build failed');

package/dist/commands/build.js.map

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+{"version":3,"file":"build.js","sourceRoot":"","sources":["../../src/commands/build.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AACpC,OAAO,KAAK,MAAM,OAAO,CAAC;AAC1B,OAAO,EAAE,UAAU,EAAE,SAAS,EAAE,QAAQ,EAAE,MAAM,SAAS,CAAC;AAC1D,OAAO,EAAE,OAAO,EAAE,OAAO,EAAE,QAAQ,EAAE,MAAM,WAAW,CAAC;AACvD,OAAO,EAAE,GAAG,EAAE,WAAW,EAAE,MAAM,oBAAoB,CAAC;AACtD,OAAO,EAAE,qBAAqB,EAAE,MAAM,2BAA2B,CAAC;AAClE,OAAO,EAAE,aAAa,EAAE,MAAM,oBAAoB,CAAC;AAUnD,SAAS,YAAY,CAAC,KAAc;IAClC,OAAO,CACL,OAAO,KAAK,KAAK,QAAQ;QACzB,KAAK,KAAK,IAAI;QACd,OAAO,IAAI,KAAK;QAChB,OAAO,KAAK,CAAC,KAAK,KAAK,UAAU,CAClC,CAAC;AACJ,CAAC;AAED,KAAK,UAAU,WAAW,CAAC,UAAkB;IAC3C,MAAM,GAAG,GAAG,MAAM,qBAAqB,CAAC,SAAS,EAAE,UAAU,CAAC,CAAC;IAC/D,IAAI,CAAC,GAAG;QAAE,OAAO,IAAI,CAAC;IACtB,IAAI,YAAY,CAAC,GAAG,CAAC;QAAE,OAAO,GAAG,CAAC;IAClC,OAAO,YAAY,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,IAAI,CAAC;AACxD,CAAC;AAED,MAAM,UAAU,kBAAkB,CAAC,UAAkB;IACnD,OAAO,0BAA0B,IAAI,CAAC,SAAS,CAAC,UAAU,CAAC;;;;;;;;;;;;;;;;;;;;;;;;;;CA0B5D,CAAC;AACF,CAAC;AAWD;;;;;;GAMG;AACH,MAAM,UAAU,mBAAmB,CAAC,OAA4B;IAC9D,OAAO;QACL,KAAK,EAAE;YACL,QAAQ,EAAE,kBAAkB,CAAC,OAAO,CAAC,UAAU,CAAC;YAChD,UAAU,EAAE,OAAO,CAAC,OAAO,CAAC,UAAU,CAAC;YACvC,UAAU,EAAE,qBAAqB;YACjC,MAAM,EAAE,IAAI;SACb;QACD,MAAM,EAAE,IAAI;QACZ,QAAQ,EAAE,UAAU;QACpB,QAAQ,EAAE,MAAM;QAChB,MAAM,EAAE,OAAO,CAAC,MAAM;QACtB,MAAM,EAAE,KAAK;QACb,OAAO,EAAE,OAAO,CAAC,OAAO;QACxB,SAAS,EAAE,OAAO,CAAC,SAAS;QAC5B,MAAM,EAAE,OAAO,CAAC,MAAM,IAAI,KAAK;QAC/B,WAAW,EAAE,IAAI;QACjB,QAAQ,EAAE,IAAI;QACd,QAAQ,EAAE,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,SAAS;QAC7C,MAAM,EAAE;YACN,EAAE,EAAE;gBACF,qBAAqB;gBACrB,6BAA6B,aAAa,mBAAmB;gBAC7D,mBAAmB,aAAa,oBAAoB;aACrD,CAAC,IAAI,CAAC,IAAI,CAAC;SACb;KACF,CAAC;AACJ,CAAC;AAED,SAAS,UAAU,CAAC,KAAa;IAC/B,IAAI,KAAK,GAAG,IAAI;QAAE,OAAO,GAAG,KAAK,IAAI,CAAC;IACtC,IAAI,KAAK,GAAG,IAAI,GAAG,IAAI;QAAE,OAAO,GAAG,CAAC,KAAK,GAAG,IAAI,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,KAAK,CAAC;IAClE,OAAO,GAAG,CAAC,KAAK,GAAG,CAAC,IAAI,GAAG,IAAI,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,KAAK,CAAC;AACpD,CAAC;AAED,MAAM,CAAC,MAAM,YAAY,GAAG,IAAI,OAAO,CAAC,OAAO,CAAC;KAC7C,WAAW,CAAC,2EAA2E,CAAC;KACxF,MAAM,CAAC,qBAAqB,EAAE,6BAA6B,EAAE,gBAAgB,CAAC;KAC9E,MAAM,CAAC,sBAAsB,EAAE,kBAAkB,EAAE,oBAAoB,CAAC;KACxE,MAAM,CAAC,oBAAoB,EAAE,wBAAwB,EAAE,QAAQ,CAAC;KAChE,MAAM,CAAC,aAAa,EAAE,oBAAoB,EAAE,IAAI,CAAC;KACjD,MAAM,CAAC,gBAAgB,EAAE,mBAAmB,CAAC;KAC7C,MAAM,CAAC,UAAU,EAAE,eAAe,CAAC;KACnC,MAAM,CAAC,aAAa,EAAE,gBAAgB,CAAC;KACvC,MAAM,CACL,KAAK,EAAE,OAON,EAAE,EAAE;IACH,IAAI,CAAC,OAAO,CAAC,KAAK;QAAE,WAAW,EAAE,CAAC;IAElC,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,EAAE,CAAC;IAC1B,MAAM,UAAU,GAAG,OAAO,CAAC,GAAG,EAAE,OAAO,CAAC,MAAM,CAAC,CAAC;IAChD,MAAM,OAAO,GAAG,OAAO,CAAC,GAAG,EAAE,OAAO,CAAC,OAAO,CAAC,CAAC;IAE9C,IAAI,CAAC,UAAU,CAAC,UAAU,CAAC,EAAE,CAAC;QAC5B,GAAG,CAAC,KAAK,CAAC,qBAAqB,UAAU,EAAE,CAAC,CAAC;QAC7C,GAAG,CAAC,GAAG,CAAC,gDAAgD,CAAC,CAAC;QAC1D,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;IAClB,CAAC;IAED,MAAM,OAAO,GAAG,MAAM,WAAW,CAAC,GAAG,CAAC,CAAC;IACvC,IAAI,CAAC,OAAO,EAAE,CAAC;QACb,GAAG,CAAC,KAAK,CAAC,+CAA+C,CAAC,CAAC;QAC3D,GAAG,CAAC,GAAG,CAAC,uBAAuB,CAAC,CAAC;QACjC,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;IAClB,CAAC;IAED,SAAS,CAAC,OAAO,CAAC,OAAO,CAAC,EAAE,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC;IAEjD,GAAG,CAAC,IAAI,CAAC,YAAY,KAAK,CAAC,GAAG,CAAC,QAAQ,CAAC,GAAG,EAAE,UAAU,CAAC,CAAC,EAAE,CAAC,CAAC;IAC7D,MAAM,SAAS,GAAG,WAAW,CAAC,GAAG,EAAE,CAAC;IAEpC,IAAI,MAA0B,CAAC;IAC/B,IAAI,CAAC;QACH,MAAM,GAAG,MAAM,OAAO,CAAC,KAAK,CAC1B,mBAAmB,CAAC;YAClB,UAAU;YACV,OAAO;YACP,MAAM,EAAE,OAAO,CAAC,MAAM;YACtB,SAAS,EAAE,OAAO,CAAC,SAAS;YAC5B,MAAM,EAAE,OAAO,CAAC,MAAM;YACtB,KAAK,EAAE,OAAO,CAAC,KAAK;SACrB,CAAC,CACH,CAAC;IACJ,CAAC;IAAC,OAAO,KAAK,EAAE,CAAC;QACf,GAAG,CAAC,KAAK,CAAC,cAAc,CAAC,CAAC;QAC1B,IAAI,KAAK,YAAY,KAAK;YAAE,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC;QACnD,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;IAClB,CAAC;IAED,MAAM,OAAO,GAAG,CAAC,CAAC,WAAW,CAAC,GAAG,EAAE,GAAG,SAAS,CAAC,GAAG,IAAI,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC;IACpE,MAAM,OAAO,GAAG,UAAU,CAAC,QAAQ,CAAC,OAAO,CAAC,CAAC,IAAI,CAAC,CAAC;IAEnD,OAAO,CAAC,GAAG,EAAE,CAAC;IACd,GAAG,CAAC,OAAO,CAAC,YAAY,OAAO,GAAG,CAAC,CAAC;IACpC,OAAO,CAAC,GAAG,EAAE,CAAC;IACd,OAAO,CAAC,GAAG,CAAC,KAAK,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,MAAM,QAAQ,CAAC,GAAG,EAAE,OAAO,CAAC,EAAE,CAAC,CAAC;IACrE,OAAO,CAAC,GAAG,CAAC,KAAK,KAAK,CAAC,IAAI,CAAC,MAAM,CAAC,QAAQ,OAAO,EAAE,CAAC,CAAC;IACtD,OAAO,CAAC,GAAG,CAAC,KAAK,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,MAAM,OAAO,CAAC,MAAM,EAAE,CAAC,CAAC;IAE7D,IAAI,MAAM,CAAC,QAAQ,EAAE,CAAC;QACpB,MAAM,MAAM,GAAG,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC,MAAM,CAAC;QAC1D,OAAO,CAAC,GAAG,CAAC,KAAK,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,KAAK,MAAM,gBAAgB,CAAC,CAAC;IACrE,CAAC;IAED,OAAO,CAAC,GAAG,EAAE,CAAC;IACd,GAAG,CAAC,GAAG,CAAC,aAAa,QAAQ,CAAC,GAAG,EAAE,OAAO,CAAC,EAAE,CAAC,CAAC;IAC/C,GAAG,CAAC,GAAG,CAAC,0CAA0C,CAAC,CAAC;IACpD,OAAO,CAAC,GAAG,EAAE,CAAC;AAChB,CAAC,CACF,CAAC"}

package/dist/commands/deploy.d.ts

@@ -1,3 +1,28 @@
 import { Command } from 'commander';
+import type { DeployConfig } from '@cogitator-ai/types';
+export interface DeployFlags {
+    target?: string;
+    config?: string;
+    registry?: string;
+    push: boolean;
+    dryRun?: boolean;
+    region?: string;
+}
+/** What `cogitator deploy` hands the deployer: the config file, the target's name and the settings over the file. */
+export interface DeployInputs {
+    /** The `-c` file, else the project's own config file (`findConfigFile`) */
+    configPath?: string;
+    /** `--target`, else `deploy.target` from the environment or the config file */
+    target?: string;
+    /** `COGITATOR_DEPLOY_*` variables and flags, applied over the config file's deploy section */
+    overrides: Partial<DeployConfig>;
+}
+/**
+ * Resolves the config file and the settings of a deploy. The config file is
+ * the one passed with `-c` (an error when it does not exist), else the
+ * project's own, found like `loadConfig` finds it. The analyzer reads the
+ * model, memory and deploy section from that same file.
+ */
+export declare function resolveDeployInputs(projectDir: string, flags: Pick<DeployFlags, 'config' | 'target' | 'registry' | 'region'>): DeployInputs;
 export declare const deployCommand: Command;
 //# sourceMappingURL=deploy.d.ts.map

package/dist/commands/deploy.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"deploy.d.ts","sourceRoot":"","sources":["../../src/commands/deploy.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAyQpC,eAAO,MAAM,aAAa,SAyBtB,CAAC"}
+{"version":3,"file":"deploy.d.ts","sourceRoot":"","sources":["../../src/commands/deploy.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAQpC,OAAO,KAAK,EAAE,YAAY,EAA4C,MAAM,qBAAqB,CAAC;AAElG,MAAM,WAAW,WAAW;IAC1B,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,IAAI,EAAE,OAAO,CAAC;IACd,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB;AAgBD,qHAAqH;AACrH,MAAM,WAAW,YAAY;IAC3B,2EAA2E;IAC3E,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,+EAA+E;IAC/E,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,8FAA8F;IAC9F,SAAS,EAAE,OAAO,CAAC,YAAY,CAAC,CAAC;CAClC;AAED;;;;;GAKG;AACH,wBAAgB,mBAAmB,CACjC,UAAU,EAAE,MAAM,EAClB,KAAK,EAAE,IAAI,CAAC,WAAW,EAAE,QAAQ,GAAG,QAAQ,GAAG,UAAU,GAAG,QAAQ,CAAC,GACpE,YAAY,CAqBd;AA4ND,eAAO,MAAM,aAAa,SAyBtB,CAAC"}

package/dist/commands/deploy.js

@@ -3,14 +3,14 @@ import chalk from 'chalk';
 import ora from 'ora';
 import { existsSync } from 'node:fs';
 import { resolve } from 'node:path';
-import { loadConfig } from '@cogitator-ai/config';
+import { findConfigFile, loadConfig, loadEnvConfig } from '@cogitator-ai/config';
 import { Deployer } from '@cogitator-ai/deploy';
 import { log } from '../utils/logger.js';
 function isDeployTarget(value, available) {
     return available.includes(value);
 }
-function resolveTarget(flag, configTarget, available) {
-    const raw = flag ?? configTarget ?? 'docker';
+function resolveTarget(requested, available) {
+    const raw = requested ?? 'docker';
     if (!isDeployTarget(raw, available)) {
         log.error(`Unsupported deploy target: "${raw}"`);
         log.dim(`Available targets: ${available.join(', ')}`);
@@ -18,39 +18,47 @@ function resolveTarget(flag, configTarget, available) {
     }
     return raw;
 }
-function loadDeployConfig(projectDir, configPath) {
-    if (configPath && !existsSync(resolve(projectDir, configPath))) {
-        log.error(`Config file not found: ${resolve(projectDir, configPath)}`);
-        process.exit(1);
+/**
+ * Resolves the config file and the settings of a deploy. The config file is
+ * the one passed with `-c` (an error when it does not exist), else the
+ * project's own, found like `loadConfig` finds it. The analyzer reads the
+ * model, memory and deploy section from that same file.
+ */
+export function resolveDeployInputs(projectDir, flags) {
+    const configPath = flags.config ? resolve(projectDir, flags.config) : findConfigFile(projectDir);
+    if (flags.config && configPath && !existsSync(configPath)) {
+        throw new Error(`Config file not found: ${configPath}`);
     }
+    const fileDeploy = configPath ? loadConfig({ configPath, skipEnv: true }).deploy : undefined;
+    const envDeploy = loadEnvConfig().deploy ?? {};
+    const overrides = {
+        ...(envDeploy.target ? { target: envDeploy.target } : {}),
+        ...(envDeploy.port ? { port: envDeploy.port } : {}),
+        ...(envDeploy.registry ? { registry: envDeploy.registry } : {}),
+        ...(flags.registry ? { registry: flags.registry } : {}),
+        ...(flags.region ? { region: flags.region } : {}),
+    };
+    return {
+        configPath,
+        target: flags.target ?? overrides.target ?? fileDeploy?.target,
+        overrides,
+    };
+}
+function loadDeployInputs(projectDir, flags) {
     try {
-        const config = loadConfig(configPath ? { configPath: resolve(projectDir, configPath) } : {});
-        return config.deploy;
+        return resolveDeployInputs(projectDir, flags);
     }
     catch (error) {
         log.error(`Failed to load config: ${error instanceof Error ? error.message : String(error)}`);
         process.exit(1);
     }
 }
-function buildConfigOverrides(flags, fileConfig) {
-    const overrides = {};
-    if (fileConfig) {
-        Object.assign(overrides, fileConfig);
-    }
-    if (flags.registry) {
-        overrides.registry = flags.registry;
-    }
-    if (flags.region) {
-        overrides.region = flags.region;
-    }
-    return overrides;
-}
 async function runDeploy(flags) {
     const projectDir = resolve(process.cwd());
     const deployer = new Deployer();
-    const fileConfig = loadDeployConfig(projectDir, flags.config);
-    const target = resolveTarget(flags.target, fileConfig?.target, deployer.availableTargets());
-    const configOverrides = buildConfigOverrides(flags, fileConfig);
+    const inputs = loadDeployInputs(projectDir, flags);
+    const target = resolveTarget(inputs.target, deployer.availableTargets());
+    const configOverrides = inputs.overrides;
     const spinner = ora('Analyzing project...').start();
     let plan;
     try {
@@ -60,6 +68,7 @@ async function runDeploy(flags) {
             dryRun: flags.dryRun,
             noPush: !flags.push,
             configOverrides,
+            configPath: inputs.configPath,
         });
     }
     catch (error) {
@@ -73,7 +82,11 @@ async function runDeploy(flags) {
     console.log();
     const { config, preflight } = plan;
     console.log(chalk.dim('  Configuration:'));
+    if (inputs.configPath)
+        console.log(`    Config:   ${chalk.cyan(inputs.configPath)}`);
     console.log(`    Target:   ${chalk.cyan(target)}`);
+    if (config.kind)
+        console.log(`    Kind:     ${chalk.cyan(config.kind)}`);
     if (config.server)
         console.log(`    Server:   ${chalk.cyan(config.server)}`);
     if (config.port)
@@ -95,11 +108,21 @@ async function runDeploy(flags) {
         console.log();
     }
     if (config.services?.redis || config.services?.postgres) {
+        const provisioned = target === 'docker';
+        const icon = provisioned ? chalk.green('●') : chalk.yellow('○');
+        const note = (variable) => provisioned ? '' : chalk.dim(` (not provisioned on ${target}, set ${variable})`);
         console.log(chalk.dim('  Services:'));
         if (config.services.redis)
-            console.log(`    ${chalk.green('●')} Redis`);
+            console.log(`    ${icon} Redis${note('REDIS_URL')}`);
         if (config.services.postgres)
-            console.log(`    ${chalk.green('●')} PostgreSQL`);
+            console.log(`    ${icon} PostgreSQL${note('DATABASE_URL')}`);
+        console.log();
+    }
+    if (config.volumes && config.volumes.length > 0) {
+        console.log(chalk.dim('  Volumes:'));
+        for (const volume of config.volumes) {
+            console.log(`    ${chalk.green('●')} ${volume.path}`);
+        }
         console.log();
     }
     if (config.secrets && config.secrets.length > 0) {
@@ -139,6 +162,7 @@ async function runDeploy(flags) {
             dryRun: false,
             noPush: !flags.push,
             configOverrides,
+            configPath: inputs.configPath,
         });
     }
     catch (error) {
@@ -176,14 +200,15 @@ async function runDeploy(flags) {
 async function runDeployStatus(flags) {
     const projectDir = resolve(process.cwd());
     const deployer = new Deployer();
-    const fileConfig = loadDeployConfig(projectDir, flags.config);
-    const target = resolveTarget(flags.target, fileConfig?.target, deployer.availableTargets());
-    const configOverrides = buildConfigOverrides(flags, fileConfig);
+    const inputs = loadDeployInputs(projectDir, flags);
+    const target = resolveTarget(inputs.target, deployer.availableTargets());
     const spinner = ora('Checking deployment status...').start();
-    const deployConfig = { ...configOverrides, target };
+    const deployConfig = { ...inputs.overrides, target };
     let status;
     try {
-        status = await deployer.status(target, deployConfig, projectDir);
+        status = await deployer.status(target, deployConfig, projectDir, {
+            configPath: inputs.configPath,
+        });
     }
     catch (error) {
         spinner.fail('Failed to check status');
@@ -210,13 +235,12 @@ async function runDeployStatus(flags) {
 async function runDeployDestroy(flags) {
     const projectDir = resolve(process.cwd());
     const deployer = new Deployer();
-    const fileConfig = loadDeployConfig(projectDir, flags.config);
-    const target = resolveTarget(flags.target, fileConfig?.target, deployer.availableTargets());
-    const configOverrides = buildConfigOverrides(flags, fileConfig);
+    const inputs = loadDeployInputs(projectDir, flags);
+    const target = resolveTarget(inputs.target, deployer.availableTargets());
     const spinner = ora(`Destroying ${target} deployment...`).start();
-    const deployConfig = { ...configOverrides, target };
+    const deployConfig = { ...inputs.overrides, target };
     try {
-        await deployer.destroy(target, deployConfig, projectDir);
+        await deployer.destroy(target, deployConfig, projectDir, { configPath: inputs.configPath });
         spinner.succeed('Deployment destroyed');
     }
     catch (err) {

package/dist/commands/deploy.js.map

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package/dist/commands/init.d.ts

@@ -21,7 +21,11 @@ export interface ScaffoldOptions {
     dependencyVersions: Record<string, string>;
     /** When `pnpm`, a pnpm-workspace.yaml allowing the native dependency builds is generated */
     packageManager?: PackageManager;
+    /** `name@version` written to the `packageManager` field, e.g. `pnpm@10.26.0` */
+    packageManagerSpec?: string;
 }
+/** Port the WebChat channel listens on. */
+export declare const WEBCHAT_PORT = 18789;
 /**
  * pnpm 10.26+ skips dependency build scripts unless they are allowed, and pnpm 11 fails the
  * install instead. These are the native/binary packages a Cogitator project pulls in.
@@ -31,11 +35,26 @@ export declare const DEFAULT_POSTGRES_URL = "postgresql://cogitator:cogitator@lo
 export declare function validateProjectName(name: string): string | undefined;
 export declare function resolveDependencyVersions(cliPackageJson?: string): Record<string, string>;
 export declare function detectPackageManager(userAgent?: string | undefined): PackageManager;
+/**
+ * The `packageManager` field for the pnpm, Yarn or Bun that runs the
+ * scaffolder, e.g. `pnpm@10.26.0`, so corepack and the deploy image install
+ * with the same version instead of the latest one. Undefined for npm, which
+ * corepack leaves alone, and when the version is unknown.
+ */
+export declare function detectPackageManagerSpec(userAgent?: string | undefined): string | undefined;
 export declare function buildPackageJson(answers: InitAnswers, options: ScaffoldOptions): string;
 export declare function buildEnvFile(answers: InitAnswers): string | null;
 export declare function buildGatewayFile(answers: InitAnswers): string;
 export declare function buildAgentFile(answers: InitAnswers): string;
 export declare function buildGitignore(answers: InitAnswers): string;
+/**
+ * `cogitator.yml` in the shape `@cogitator-ai/config` loads, read by
+ * `cogitator run` and `cogitator deploy`: the provider and model, the memory
+ * the gateway uses, and how the project deploys. It runs as a worker (the
+ * gateway serves no HTTP health check), publishes the WebChat port, keeps
+ * the SQLite database on a volume and needs the API key and channel tokens.
+ */
+export declare function buildCogitatorYml(answers: InitAnswers): string;
 export declare const TSCONFIG: {
     compilerOptions: {
         target: string;

package/dist/commands/init.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"init.d.ts","sourceRoot":"","sources":["../../src/commands/init.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAUpC,OAAO,EAKL,KAAK,aAAa,EACnB,MAAM,6BAA6B,CAAC;AAErC,MAAM,MAAM,WAAW,GAAG,UAAU,GAAG,SAAS,GAAG,OAAO,GAAG,SAAS,CAAC;AACvE,MAAM,MAAM,UAAU,GAAG,QAAQ,GAAG,QAAQ,GAAG,UAAU,CAAC;AAC1D,MAAM,MAAM,cAAc,GAAG,MAAM,GAAG,KAAK,GAAG,MAAM,GAAG,KAAK,CAAC;AAE7D,MAAM,WAAW,WAAW;IAC1B,WAAW,EAAE,MAAM,CAAC;IACpB,QAAQ,EAAE,aAAa,CAAC;IACxB,MAAM,EAAE,MAAM,CAAC;IACf,KAAK,EAAE,MAAM,CAAC;IACd,QAAQ,EAAE,WAAW,EAAE,CAAC;IACxB,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,kBAAkB,CAAC,EAAE,MAAM,CAAC;IAC5B,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,MAAM,EAAE,UAAU,CAAC;IACnB,WAAW,CAAC,EAAE,MAAM,CAAC;CACtB;AAED,MAAM,WAAW,eAAe;IAC9B,kBAAkB,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IAC3C,4FAA4F;IAC5F,cAAc,CAAC,EAAE,cAAc,CAAC;IAChC,gFAAgF;IAChF,kBAAkB,CAAC,EAAE,MAAM,CAAC;CAC7B;AAED,2CAA2C;AAC3C,eAAO,MAAM,YAAY,QAAQ,CAAC;AAElC;;;GAGG;AACH,eAAO,MAAM,mBAAmB,iDAAkD,CAAC;AAEnF,eAAO,MAAM,oBAAoB,8DAA8D,CAAC;AAIhG,wBAAgB,mBAAmB,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,GAAG,SAAS,CAQpE;AAED,wBAAgB,yBAAyB,CACvC,cAAc,GAAE,MAA4E,GAC3F,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAsBxB;AAED,wBAAgB,oBAAoB,CAClC,SAAS,qBAAoC,GAC5C,cAAc,CAIhB;AAED;;;;;GAKG;AACH,wBAAgB,wBAAwB,CACtC,SAAS,qBAAoC,GAC5C,MAAM,GAAG,SAAS,CAGpB;AAMD,wBAAgB,gBAAgB,CAAC,OAAO,EAAE,WAAW,EAAE,OAAO,EAAE,eAAe,GAAG,MAAM,CA0CvF;AAED,wBAAgB,YAAY,CAAC,OAAO,EAAE,WAAW,GAAG,MAAM,GAAG,IAAI,CAkBhE;AA0BD,wBAAgB,gBAAgB,CAAC,OAAO,EAAE,WAAW,GAAG,MAAM,CA4F7D;AAED,wBAAgB,cAAc,CAAC,OAAO,EAAE,WAAW,GAAG,MAAM,CAyB3D;AAED,wBAAgB,cAAc,CAAC,OAAO,EAAE,WAAW,GAAG,MAAM,CAI3D;AA8BD;;;;;;GAMG;AACH,wBAAgB,iBAAiB,CAAC,OAAO,EAAE,WAAW,GAAG,MAAM,CA2B9D;AAED,eAAO,MAAM,QAAQ;;;;;;;;;;;;CAYpB,CAAC;AAEF,wBAAgB,iBAAiB,CAC/B,OAAO,EAAE,WAAW,EACpB,OAAO,EAAE,eAAe,GACvB,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAmBxB;AAED,wBAAgB,iBAAiB,CAAC,WAAW,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,GAAG,IAAI,CAM1F;AAuID,eAAO,MAAM,WAAW,SAuEpB,CAAC"}

package/dist/commands/init.js

@@ -9,6 +9,8 @@ import { printBanner } from '../utils/logger.js';
 import { formatEnvLine } from '../utils/env.js';
 import { DEFAULT_OLLAMA_URL, resolveOllamaUrl } from '../utils/ollama.js';
 import { API_KEY_ENV, fetchOllamaModelOptions, fetchProviderModels, isSetupProvider, } from '../utils/provider-models.js';
+/** Port the WebChat channel listens on. */
+export const WEBCHAT_PORT = 18789;
 /**
  * pnpm 10.26+ skips dependency build scripts unless they are allowed, and pnpm 11 fails the
  * install instead. These are the native/binary packages a Cogitator project pulls in.
@@ -57,6 +59,16 @@ export function detectPackageManager(userAgent = process.env.npm_config_user_age
         return name;
     return 'pnpm';
 }
+/**
+ * The `packageManager` field for the pnpm, Yarn or Bun that runs the
+ * scaffolder, e.g. `pnpm@10.26.0`, so corepack and the deploy image install
+ * with the same version instead of the latest one. Undefined for npm, which
+ * corepack leaves alone, and when the version is unknown.
+ */
+export function detectPackageManagerSpec(userAgent = process.env.npm_config_user_agent) {
+    const match = /^(pnpm|yarn|bun)\/(\d+\.\d+\.\d+[^\s]*)/.exec(userAgent?.trim() ?? '');
+    return match ? `${match[1]}@${match[2]}` : undefined;
+}
 function runScript(pm, script) {
     return pm === 'npm' ? `npm run ${script}` : `${pm} ${script}`;
 }
@@ -83,6 +95,7 @@ export function buildPackageJson(answers, options) {
         version: '0.1.0',
         private: true,
         type: 'module',
+        ...(options.packageManagerSpec ? { packageManager: options.packageManagerSpec } : {}),
         engines: { node: '>=22.12.0' },
         scripts: {
             dev: 'tsx watch src/agent.ts',
@@ -123,7 +136,8 @@ function memorySetup(memory) {
         case 'sqlite':
             return {
                 importName: 'SQLiteAdapter',
-                code: `const memory = new SQLiteAdapter({ provider: 'sqlite', path: './data/memory.db' });`,
+                code: `mkdirSync('./data', { recursive: true });
+const memory = new SQLiteAdapter({ provider: 'sqlite', path: './data/memory.db' });`,
             };
         case 'postgres':
             return {
@@ -159,7 +173,7 @@ export function buildGatewayFile(answers) {
                 break;
             case 'webchat':
                 channelImports.push('webchatChannel');
-                channelSetup.push(`    webchatChannel({ port: 18789 }),`);
+                channelSetup.push(`    webchatChannel({ port: ${WEBCHAT_PORT} }),`);
                 break;
         }
     }
@@ -167,7 +181,8 @@ export function buildGatewayFile(answers) {
         ? `      ollama: { baseUrl: process.env.OLLAMA_URL ?? '${DEFAULT_OLLAMA_URL}' },`
         : `      ${answers.provider}: { apiKey: requireEnv('${API_KEY_ENV[answers.provider]}') },`;
     const memory = memorySetup(answers.memory);
-    return `import { existsSync } from 'node:fs';
+    const fsImports = answers.memory === 'sqlite' ? 'existsSync, mkdirSync' : 'existsSync';
+    return `import { ${fsImports} } from 'node:fs';
 import { fileURLToPath } from 'node:url';
 import { Cogitator, Agent } from '@cogitator-ai/core';
 import { Gateway, ${channelImports.join(', ')} } from '@cogitator-ai/channels';
@@ -213,7 +228,7 @@ ${channelSetup.join('\n')}
   ],
   memory,
   session: {
-    compaction: { strategy: 'hybrid', threshold: 50, keepRecent: 10 },
+    compaction: { strategy: 'hybrid', messageThreshold: 50, keepRecent: 10 },
   },
   stream: { flushInterval: 500, minChunkSize: 20 },
   onError: (err, msg) => {
@@ -224,7 +239,7 @@ ${channelSetup.join('\n')}
 }
 export function buildAgentFile(answers) {
     const webchatLine = answers.channels.includes('webchat')
-        ? `  console.log('WebChat: ws://localhost:18789/ws');\n`
+        ? `  console.log('WebChat: ws://localhost:${WEBCHAT_PORT}/ws');\n`
         : '';
     return `import { gateway } from './gateway.js';
 
@@ -253,6 +268,70 @@ export function buildGitignore(answers) {
         lines.push('data/');
     return lines.join('\n') + '\n';
 }
+/** Variables the generated gateway reads, in the order it reads them. */
+function channelSecrets(answers) {
+    const secrets = [];
+    if (answers.channels.includes('telegram'))
+        secrets.push('TELEGRAM_BOT_TOKEN');
+    if (answers.channels.includes('discord'))
+        secrets.push('DISCORD_BOT_TOKEN');
+    if (answers.channels.includes('slack')) {
+        secrets.push('SLACK_BOT_TOKEN', 'SLACK_SIGNING_SECRET');
+        if (answers.slackAppToken)
+            secrets.push('SLACK_APP_TOKEN');
+    }
+    return secrets;
+}
+function memoryYml(memory) {
+    switch (memory) {
+        case 'sqlite':
+            return ['memory:', '  adapter: sqlite', '  sqlite:', '    path: ./data/memory.db'];
+        case 'postgres':
+            return [
+                'memory:',
+                '  adapter: postgres',
+                '  postgres:',
+                '    connectionString: ${DATABASE_URL}',
+            ];
+        case 'memory':
+            return ['memory:', '  adapter: memory'];
+    }
+}
+/**
+ * `cogitator.yml` in the shape `@cogitator-ai/config` loads, read by
+ * `cogitator run` and `cogitator deploy`: the provider and model, the memory
+ * the gateway uses, and how the project deploys. It runs as a worker (the
+ * gateway serves no HTTP health check), publishes the WebChat port, keeps
+ * the SQLite database on a volume and needs the API key and channel tokens.
+ */
+export function buildCogitatorYml(answers) {
+    const secrets = [
+        ...(answers.provider === 'ollama' ? [] : [API_KEY_ENV[answers.provider]]),
+        ...channelSecrets(answers),
+    ];
+    const lines = [
+        '# Read by `cogitator run` and `cogitator deploy`. src/gateway.ts configures the',
+        '# assistant itself, so change the provider, model or memory in both places.',
+        '',
+        'llm:',
+        `  defaultProvider: ${answers.provider}`,
+        `  defaultModel: ${JSON.stringify(answers.model)}`,
+        ...(answers.provider === 'ollama'
+            ? ['  providers:', '    ollama:', `      baseUrl: \${OLLAMA_URL:-${DEFAULT_OLLAMA_URL}}`]
+            : []),
+        '',
+        ...memoryYml(answers.memory),
+        '',
+        'deploy:',
+        '  kind: worker',
+        ...(answers.channels.includes('webchat') ? [`  port: ${WEBCHAT_PORT}`] : []),
+        ...(secrets.length > 0
+            ? ['  secrets:', ...secrets.map((name) => `    - ${name}`)]
+            : ['  secrets: []']),
+        '',
+    ];
+    return lines.join('\n');
+}
 export const TSCONFIG = {
     compilerOptions: {
         target: 'ES2022',
@@ -272,6 +351,7 @@ export function buildProjectFiles(answers, options) {
         'tsconfig.json': JSON.stringify(TSCONFIG, null, 2) + '\n',
         'src/gateway.ts': buildGatewayFile(answers),
         'src/agent.ts': buildAgentFile(answers),
+        'cogitator.yml': buildCogitatorYml(answers),
         '.gitignore': buildGitignore(answers),
     };
     const env = buildEnvFile(answers);
@@ -417,6 +497,7 @@ export const initCommand = new Command('init')
     const files = buildProjectFiles(answers, {
         dependencyVersions: resolveDependencyVersions(),
         packageManager: pm,
+        packageManagerSpec: detectPackageManagerSpec(),
     });
     let installed = false;
     await p.tasks([

package/dist/commands/init.js.map

@@ -1 +1 @@
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package/dist/commands/run.d.ts

@@ -3,8 +3,24 @@
  */
 import { Command } from 'commander';
 import type { CogitatorConfig } from '@cogitator-ai/types';
+import { type ProjectConfigKind } from '../utils/project-config.js';
 export declare function pickOllamaModel(available: readonly string[]): string | null;
 export declare function findConfig(explicitPath?: string, env?: Record<string, string | undefined>, cwd?: string): string | null;
-export declare function resolveRunModel(flagModel: string | undefined, env: Record<string, string | undefined>, config: CogitatorConfig): string | undefined;
+export interface RunConfig {
+    config: CogitatorConfig;
+    /** What the config file configures, undefined without one */
+    kind?: ProjectConfigKind;
+    /** `provider/model` of an assistant config, which has no `llm.defaultModel` */
+    model?: string;
+}
+/**
+ * The runtime config `cogitator run` uses. The `.env` next to the config file
+ * (or in `cwd` without one) is loaded first, without overriding variables
+ * already set, so API keys reach the env loader. An assistant config from
+ * `cogitator wizard` is not a runtime config: only its model is taken, and
+ * the rest comes from the environment.
+ */
+export declare function loadRunConfig(configPath: string | null, cwd?: string): RunConfig;
+export declare function resolveRunModel(flagModel: string | undefined, env: Record<string, string | undefined>, config: CogitatorConfig, configModel?: string): string | undefined;
 export declare const runCommand: Command;
 //# sourceMappingURL=run.d.ts.map

package/dist/commands/run.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"run.d.ts","sourceRoot":"","sources":["../../src/commands/run.ts"],"names":[],"mappings":"AAAA;;GAEG;AAEH,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAQpC,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,qBAAqB,CAAC;AAuC3D,wBAAgB,eAAe,CAAC,SAAS,EAAE,SAAS,MAAM,EAAE,GAAG,MAAM,GAAG,IAAI,CAI3E;AAWD,wBAAgB,UAAU,CACxB,YAAY,CAAC,EAAE,MAAM,EACrB,GAAG,GAAE,MAAM,CAAC,MAAM,EAAE,MAAM,GAAG,SAAS,CAAe,EACrD,GAAG,GAAE,MAAsB,GAC1B,MAAM,GAAG,IAAI,CAiBf;AAED,wBAAgB,eAAe,CAC7B,SAAS,EAAE,MAAM,GAAG,SAAS,EAC7B,GAAG,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,GAAG,SAAS,CAAC,EACvC,MAAM,EAAE,eAAe,GACtB,MAAM,GAAG,SAAS,CAEpB;AAqHD,eAAO,MAAM,UAAU,SA0EnB,CAAC"}
+{"version":3,"file":"run.d.ts","sourceRoot":"","sources":["../../src/commands/run.ts"],"names":[],"mappings":"AAAA;;GAEG;AAEH,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AASpC,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,qBAAqB,CAAC;AAG3D,OAAO,EAAoB,KAAK,iBAAiB,EAAE,MAAM,4BAA4B,CAAC;AAgCtF,wBAAgB,eAAe,CAAC,SAAS,EAAE,SAAS,MAAM,EAAE,GAAG,MAAM,GAAG,IAAI,CAI3E;AAWD,wBAAgB,UAAU,CACxB,YAAY,CAAC,EAAE,MAAM,EACrB,GAAG,GAAE,MAAM,CAAC,MAAM,EAAE,MAAM,GAAG,SAAS,CAAe,EACrD,GAAG,GAAE,MAAsB,GAC1B,MAAM,GAAG,IAAI,CAiBf;AAED,MAAM,WAAW,SAAS;IACxB,MAAM,EAAE,eAAe,CAAC;IACxB,6DAA6D;IAC7D,IAAI,CAAC,EAAE,iBAAiB,CAAC;IACzB,+EAA+E;IAC/E,KAAK,CAAC,EAAE,MAAM,CAAC;CAChB;AAeD;;;;;;GAMG;AACH,wBAAgB,aAAa,CAAC,UAAU,EAAE,MAAM,GAAG,IAAI,EAAE,GAAG,GAAE,MAAsB,GAAG,SAAS,CAkB/F;AAED,wBAAgB,eAAe,CAC7B,SAAS,EAAE,MAAM,GAAG,SAAS,EAC7B,GAAG,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,GAAG,SAAS,CAAC,EACvC,MAAM,EAAE,eAAe,EACvB,WAAW,CAAC,EAAE,MAAM,GACnB,MAAM,GAAG,SAAS,CAEpB;AAqHD,eAAO,MAAM,UAAU,SAiFnB,CAAC"}

package/dist/commands/run.js

@@ -2,21 +2,18 @@
  * cogitator run [message] - run agent
  */
 import { Command } from 'commander';
-import { existsSync } from 'node:fs';
-import { resolve } from 'node:path';
+import { existsSync, readFileSync } from 'node:fs';
+import { dirname, join, resolve } from 'node:path';
 import { createInterface } from 'node:readline';
 import chalk from 'chalk';
+import { parse as parseYaml } from 'yaml';
 import { log, printBanner } from '../utils/logger.js';
 import { Cogitator, Agent } from '@cogitator-ai/core';
-import { loadConfig } from '@cogitator-ai/config';
+import { CONFIG_FILE_NAMES, loadConfig } from '@cogitator-ai/config';
 import { listOllamaModels, resolveOllamaUrl } from '../utils/ollama.js';
-const CONFIG_FILE_NAMES = [
-    'cogitator.yml',
-    'cogitator.yaml',
-    'cogitator.json',
-    '.cogitator.yml',
-    '.cogitator.yaml',
-];
+import { loadDotenvInto } from '../utils/env.js';
+import { detectConfigKind } from '../utils/project-config.js';
+const RUN_CONFIG_FILE_NAMES = [...CONFIG_FILE_NAMES, 'cogitator.json'];
 const PREFERRED_OLLAMA_MODELS = [
     'qwen3:8b',
     'qwen3.5:9b',
@@ -60,15 +57,55 @@ export function findConfig(explicitPath, env = process.env, cwd = process.cwd())
         const full = resolve(cwd, envConfig);
         return existsSync(full) ? full : null;
     }
-    for (const name of CONFIG_FILE_NAMES) {
+    for (const name of RUN_CONFIG_FILE_NAMES) {
         const full = resolve(cwd, name);
         if (existsSync(full))
             return full;
     }
     return null;
 }
-export function resolveRunModel(flagModel, env, config) {
-    return flagModel || env.COGITATOR_MODEL || config.llm?.defaultModel || undefined;
+function isRecord(value) {
+    return typeof value === 'object' && value !== null && !Array.isArray(value);
+}
+/** `llm.provider` and `llm.model` of an assistant config as one model string. */
+function assistantModel(document) {
+    const llm = isRecord(document) ? document.llm : undefined;
+    if (!isRecord(llm) || typeof llm.model !== 'string' || !llm.model.trim())
+        return undefined;
+    const model = llm.model.trim();
+    if (model.includes('/') || typeof llm.provider !== 'string')
+        return model;
+    return `${llm.provider}/${model}`;
+}
+/**
+ * The runtime config `cogitator run` uses. The `.env` next to the config file
+ * (or in `cwd` without one) is loaded first, without overriding variables
+ * already set, so API keys reach the env loader. An assistant config from
+ * `cogitator wizard` is not a runtime config: only its model is taken, and
+ * the rest comes from the environment.
+ */
+export function loadRunConfig(configPath, cwd = process.cwd()) {
+    loadDotenvInto(join(configPath ? dirname(configPath) : cwd, '.env'), process.env);
+    if (!configPath)
+        return { config: loadConfig({ skipYaml: true }) };
+    let document;
+    try {
+        document = parseYaml(readFileSync(configPath, 'utf-8'));
+    }
+    catch {
+        document = undefined;
+    }
+    if (document !== undefined && detectConfigKind(document) === 'assistant') {
+        return {
+            config: loadConfig({ skipYaml: true }),
+            kind: 'assistant',
+            model: assistantModel(document),
+        };
+    }
+    return { config: loadConfig({ configPath }), kind: 'runtime' };
+}
+export function resolveRunModel(flagModel, env, config, configModel) {
+    return flagModel || env.COGITATOR_MODEL || config.llm?.defaultModel || configModel || undefined;
 }
 async function runInteractive(cog, initialModel, stream) {
     const rl = createInterface({ input: process.stdin, output: process.stdout });
@@ -195,17 +232,22 @@ export const runCommand = new Command('run')
         log.error(`COGITATOR_CONFIG points to a missing file: ${process.env.COGITATOR_CONFIG}`);
         process.exit(1);
     }
-    let config;
+    let loaded;
     try {
-        config = loadConfig(configPath ? { configPath } : { skipYaml: true });
+        loaded = loadRunConfig(configPath);
     }
     catch (error) {
         log.error(`Failed to load config: ${error instanceof Error ? error.message : error}`);
         process.exit(1);
     }
-    if (configPath)
+    const { config } = loaded;
+    if (configPath && loaded.kind === 'assistant') {
+        log.dim(`Using the model of assistant config ${configPath} (run the assistant itself with "cogitator up")`);
+    }
+    else if (configPath) {
         log.dim(`Using config: ${configPath}`);
-    let model = resolveRunModel(options.model, process.env, config);
+    }
+    let model = resolveRunModel(options.model, process.env, config, loaded.model);
     if (!model) {
         const ollama = config.llm?.providers?.ollama;
         const baseUrl = resolveOllamaUrl(process.env, ollama?.baseUrl);

package/dist/commands/run.js.map

@@ -1 +1 @@
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package/dist/utils/ollama.d.ts

@@ -13,6 +13,11 @@ export interface OllamaRequestOptions {
     apiKey?: string;
     timeoutMs?: number;
 }
+/**
+ * The Ollama URL to use: `configured` (a flag or cogitator.yml), else
+ * `OLLAMA_BASE_URL`, `OLLAMA_URL` or `OLLAMA_HOST`, each read the way Ollama
+ * reads `OLLAMA_HOST`, the same way `loadConfig` reads them.
+ */
 export declare function resolveOllamaUrl(env?: Record<string, string | undefined>, configured?: string): string;
 export declare function listOllamaModels(baseUrl: string, options?: OllamaRequestOptions): Promise<OllamaModelInfo[]>;
 export declare function readNdjson(stream: ReadableStream<Uint8Array>): AsyncGenerator<unknown>;

package/dist/utils/ollama.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"ollama.d.ts","sourceRoot":"","sources":["../../src/utils/ollama.ts"],"names":[],"mappings":"AAEA,eAAO,MAAM,kBAAkB,2BAA2B,CAAC;AAE3D,MAAM,WAAW,eAAe;IAC9B,IAAI,EAAE,MAAM,CAAC;IACb,IAAI,EAAE,MAAM,CAAC;IACb,WAAW,EAAE,MAAM,CAAC;CACrB;AAED,MAAM,WAAW,kBAAkB;IACjC,MAAM,EAAE,MAAM,CAAC;IACf,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,KAAK,CAAC,EAAE,MAAM,CAAC;CAChB;AAED,MAAM,WAAW,oBAAoB;IACnC,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,SAAS,CAAC,EAAE,MAAM,CAAC;CACpB;AAED;;;;GAIG;AACH,wBAAgB,gBAAgB,CAC9B,GAAG,GAAE,MAAM,CAAC,MAAM,EAAE,MAAM,GAAG,SAAS,CAAe,EACrD,UAAU,CAAC,EAAE,MAAM,GAClB,MAAM,CAOR;AAsBD,wBAAsB,gBAAgB,CACpC,OAAO,EAAE,MAAM,EACf,OAAO,GAAE,oBAAyB,GACjC,OAAO,CAAC,eAAe,EAAE,CAAC,CAa5B;AAED,wBAAuB,UAAU,CAAC,MAAM,EAAE,cAAc,CAAC,UAAU,CAAC,GAAG,cAAc,CAAC,OAAO,CAAC,CAgC7F;AAED,wBAAsB,eAAe,CACnC,OAAO,EAAE,MAAM,EACf,KAAK,EAAE,MAAM,EACb,UAAU,EAAE,CAAC,QAAQ,EAAE,kBAAkB,KAAK,IAAI,EAClD,OAAO,GAAE,IAAI,CAAC,oBAAoB,EAAE,QAAQ,CAAM,GACjD,OAAO,CAAC,IAAI,CAAC,CAiCf"}

package/dist/utils/ollama.js

@@ -1,10 +1,18 @@
+import { resolveOllamaHost } from '@cogitator-ai/config';
 export const DEFAULT_OLLAMA_URL = 'http://localhost:11434';
+/**
+ * The Ollama URL to use: `configured` (a flag or cogitator.yml), else
+ * `OLLAMA_BASE_URL`, `OLLAMA_URL` or `OLLAMA_HOST`, each read the way Ollama
+ * reads `OLLAMA_HOST`, the same way `loadConfig` reads them.
+ */
 export function resolveOllamaUrl(env = process.env, configured) {
-    const raw = configured?.trim() || env.OLLAMA_URL?.trim() || env.OLLAMA_HOST?.trim();
-    if (!raw)
-        return DEFAULT_OLLAMA_URL;
-    const withScheme = /^https?:\/\//i.test(raw) ? raw : `http://${raw}`;
-    return withScheme.replace(/\/+$/, '');
+    const candidates = [configured, env.OLLAMA_BASE_URL, env.OLLAMA_URL, env.OLLAMA_HOST];
+    for (const candidate of candidates) {
+        const url = resolveOllamaHost(candidate);
+        if (url)
+            return url;
+    }
+    return DEFAULT_OLLAMA_URL;
 }
 function buildHeaders(apiKey, json) {
     const headers = {};

package/dist/utils/ollama.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@cogitator-ai/cli",
-  "version": "0.5.18",
+  "version": "0.5.20",
   "description": "CLI for Cogitator AI Agent Runtime",
   "keywords": [
     "cogitator",
@@ -21,7 +21,8 @@
   "exports": {
     ".": {
       "types": "./dist/index.d.ts",
-      "import": "./dist/index.js"
+      "import": "./dist/index.js",
+      "default": "./dist/index.js"
     }
   },
   "files": [
@@ -32,17 +33,18 @@
   },
   "dependencies": {
     "@clack/prompts": "^1.8.1",
-    "@cogitator-ai/channels": "0.8.5",
-    "@cogitator-ai/config": "0.11.7",
-    "@cogitator-ai/core": "0.32.0",
-    "@cogitator-ai/models": "18.2.1",
-    "@cogitator-ai/deploy": "0.4.7",
-    "@cogitator-ai/memory": "0.11.7",
-    "@cogitator-ai/types": "0.34.0",
+    "@cogitator-ai/channels": "0.9.0",
+    "@cogitator-ai/config": "0.12.0",
+    "@cogitator-ai/core": "0.34.0",
+    "@cogitator-ai/models": "18.3.0",
+    "@cogitator-ai/deploy": "0.5.0",
+    "@cogitator-ai/memory": "0.12.0",
+    "@cogitator-ai/types": "0.36.0",
     "chalk": "^6.0.1",
     "commander": "^15.0.0",
     "ora": "^9.4.1",
-    "yaml": "^2.9.1"
+    "yaml": "^2.9.1",
+    "better-sqlite3": "^13.0.3"
   },
   "devDependencies": {
     "@types/node": "^22.20.4",