@neottia/cli 0.2.0 → 0.4.0

package/README.md

@@ -1,6 +1,6 @@
 # @neottia/cli
 
-`@neottia/cli` publishes the `neottia` command for reviewing and applying asset installation plans.
+`@neottia/cli` publishes the `neottia` command for initializing project configuration, compiling the SDLC lifecycle from that configuration, and installing it into the selected harnesses.
 
 ## Install
 
@@ -8,7 +8,21 @@
 pnpm add --global @neottia/cli
 ```
 
-## Commands
+## Workflow commands
+
+```sh
+neottia init [--harness pi|opencode]... [--project DIR]
+neottia apply [--harness ID]... [--scope project|global] [--project DIR]
+neottia doctor [--project DIR]
+```
+
+`init` writes the minimal `.neottia/config.yml` for the selected harnesses. `--harness` is repeatable and accepts `pi` and `opencode`. When the file already exists and no `--harness` is given, `init` validates it and leaves every value untouched. See the [configuration guide](../../docs/configuration.md) for the generated values.
+
+`apply` validates the project configuration, compiles the six lifecycle commands plus the shared operating-protocol skill for every configured harness (or the ones selected with repeatable `--harness`), resolves exact runtime package versions from the built-in compatibility catalog for the enabled modules, and installs everything in one run. No plan file is produced. Conflicting files (present but unowned, or modified after a previous install) are not overwritten: each one is reported as a `WARN` line with its path and reason, skipped, and everything else still installs. The command exits non-zero when files were skipped, prints a remediation summary, and never resolves package versions from a registry.
+
+`doctor` validates the configuration and statically reports, per enabled module, whether the catalog has a compatible runtime package, and per harness whether the lifecycle is installed. It changes nothing and requires no manifest.
+
+## Advanced manifest commands
 
 ```sh
 neottia plan --manifest manifest.json --output install.plan.json
@@ -19,7 +33,9 @@ neottia doctor --manifest manifest.json
 neottia recover --receipt .neottia/install/default.receipt.json
 ```
 
-`plan` prints the complete plan and can save the same JSON. `apply` accepts only a saved plan whose digest and checksums still match. If planning reports conflicts, approve each exact ID with a repeated `--approve <id>` option and generate the plan again. The CLI has no force option.
+These commands drive the release pipeline, where a compiler-produced `AssetManifest` already exists. `plan` prints the complete plan and can save the same JSON. `apply --plan` accepts only a saved plan whose digest and checksums still match. If planning reports conflicts, approve each exact ID with a repeated `--approve <id>` option and generate the plan again. The CLI has no force option.
+
+## Paths
 
 The CLI accepts `--project`, `--home`, `--xdg-config`, and `--xdg-state` on commands that inspect an installation. Defaults are resolved in the CLI before it calls the distribution library. Harness adapters receive no machine paths.
 

package/dist/catalog.d.ts

@@ -0,0 +1,8 @@
+import type { NeottiaRuntimePackageId } from '@neottia/harness-adapter';
+export interface CatalogEntry {
+    readonly logicalId: NeottiaRuntimePackageId;
+    readonly version: string;
+}
+export declare const RUNTIME_PACKAGE_CATALOG: Readonly<Record<string, readonly CatalogEntry[]>>;
+export declare function catalogEntry(harnessId: string, logicalId: NeottiaRuntimePackageId): CatalogEntry | undefined;
+//# sourceMappingURL=catalog.d.ts.map

package/dist/catalog.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"catalog.d.ts","sourceRoot":"","sources":["../src/catalog.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,uBAAuB,EAAE,MAAM,0BAA0B,CAAC;AAGxE,MAAM,WAAW,YAAY;IAC3B,QAAQ,CAAC,SAAS,EAAE,uBAAuB,CAAC;IAC5C,QAAQ,CAAC,OAAO,EAAE,MAAM,CAAC;CAC1B;AAMD,eAAO,MAAM,uBAAuB,EAAE,QAAQ,CAAC,MAAM,CAAC,MAAM,EAAE,SAAS,YAAY,EAAE,CAAC,CAapF,CAAC;AAGH,wBAAgB,YAAY,CAAC,SAAS,EAAE,MAAM,EAAE,SAAS,EAAE,uBAAuB,GAAG,YAAY,GAAG,SAAS,CAE5G"}

package/dist/catalog.js

@@ -0,0 +1,18 @@
+export const RUNTIME_PACKAGE_CATALOG = Object.freeze({
+    pi: Object.freeze([
+        { logicalId: 'memory', version: '0.1.1' },
+        { logicalId: 'issues', version: '0.2.0' },
+        { logicalId: 'design-docs', version: '0.2.0' },
+        { logicalId: 'searchable', version: '0.2.0' },
+    ]),
+    opencode: Object.freeze([
+        { logicalId: 'memory', version: '0.1.1' },
+        { logicalId: 'issues', version: '0.2.0' },
+        { logicalId: 'design-docs', version: '0.2.0' },
+        { logicalId: 'searchable', version: '0.2.0' },
+    ]),
+});
+export function catalogEntry(harnessId, logicalId) {
+    return RUNTIME_PACKAGE_CATALOG[harnessId]?.find((entry) => entry.logicalId === logicalId);
+}
+//# sourceMappingURL=catalog.js.map

package/dist/catalog.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"catalog.js","sourceRoot":"","sources":["../src/catalog.ts"],"names":[],"mappings":"AAYA,MAAM,CAAC,MAAM,uBAAuB,GAAsD,MAAM,CAAC,MAAM,CAAC;IACtG,EAAE,EAAE,MAAM,CAAC,MAAM,CAAC;QAChB,EAAE,SAAS,EAAE,QAAQ,EAAE,OAAO,EAAE,OAAO,EAAE;QACzC,EAAE,SAAS,EAAE,QAAQ,EAAE,OAAO,EAAE,OAAO,EAAE;QACzC,EAAE,SAAS,EAAE,aAAa,EAAE,OAAO,EAAE,OAAO,EAAE;QAC9C,EAAE,SAAS,EAAE,YAAY,EAAE,OAAO,EAAE,OAAO,EAAE;KACrC,CAAC;IACX,QAAQ,EAAE,MAAM,CAAC,MAAM,CAAC;QACtB,EAAE,SAAS,EAAE,QAAQ,EAAE,OAAO,EAAE,OAAO,EAAE;QACzC,EAAE,SAAS,EAAE,QAAQ,EAAE,OAAO,EAAE,OAAO,EAAE;QACzC,EAAE,SAAS,EAAE,aAAa,EAAE,OAAO,EAAE,OAAO,EAAE;QAC9C,EAAE,SAAS,EAAE,YAAY,EAAE,OAAO,EAAE,OAAO,EAAE;KACrC,CAAC;CACZ,CAAC,CAAC;AAGH,MAAM,UAAU,YAAY,CAAC,SAAiB,EAAE,SAAkC;IAChF,OAAO,uBAAuB,CAAC,SAAS,CAAC,EAAE,IAAI,CAAC,CAAC,KAAK,EAAE,EAAE,CAAC,KAAK,CAAC,SAAS,KAAK,SAAS,CAAC,CAAC;AAC5F,CAAC"}

package/dist/cli.spec.js

@@ -1,5 +1,15 @@
-import { describe, expect, it } from 'vitest';
+import { access, mkdir, mkdtemp, readFile, readdir, rm, stat, writeFile } from 'node:fs/promises';
+import { tmpdir } from 'node:os';
+import { dirname, join } from 'node:path';
+import { resolveConfig, ConfigResolutionError } from '@neottia/config';
+import { officialConfigRegistry } from '@neottia/config-registry';
+import { afterEach, describe, expect, it, vi } from 'vitest';
 import { main } from './index.js';
+vi.mock('@neottia/config', async (importOriginal) => {
+    const actual = await importOriginal();
+    return { ...actual, resolveConfig: vi.fn(actual.resolveConfig) };
+});
+const roots = [];
 function capture() {
     const logs = [];
     const errors = [];
@@ -16,13 +26,254 @@ function capture() {
         },
     };
 }
+async function fixture() {
+    const root = await mkdtemp(join(tmpdir(), 'neottia-cli-init-'));
+    roots.push(root);
+    return root;
+}
+function resolveGeneratedConfig(root) {
+    return resolveConfig(officialConfigRegistry, {
+        cwd: root,
+        env: {},
+        globalFile: false,
+    });
+}
+function requiredRoleAssignments() {
+    return {
+        planner: { agent: 'current' },
+        implementer: { agent: 'current' },
+        verifier: { agent: 'current' },
+        'release-coordinator': { agent: 'current' },
+    };
+}
+async function exists(path) {
+    try {
+        await access(path);
+        return true;
+    }
+    catch {
+        return false;
+    }
+}
+afterEach(async () => {
+    await Promise.all(roots.splice(0).map((root) => rm(root, { recursive: true, force: true })));
+});
 describe('Neottia CLI', () => {
-    it('documents the explicit plan and apply workflow', async () => {
+    it('documents initialization and the explicit plan and apply workflow', async () => {
         const result = capture();
         expect(await main(['help'], result.output)).toBe(0);
+        expect(result.logs.join('\n')).toContain('neottia init');
         expect(result.logs.join('\n')).toContain('neottia plan');
         expect(result.logs.join('\n')).toContain('neottia apply');
     });
+    it('initializes one project-local Pi configuration and creates the missing config directory', async () => {
+        const root = await fixture();
+        const result = capture();
+        expect(await main(['init', '--harness', 'pi', '--project', root], result.output)).toBe(0);
+        const configPath = join(root, '.neottia', 'config.yml');
+        expect(result.errors).toEqual([]);
+        expect(result.logs).toEqual([`Created ${configPath}`, 'Harnesses: pi', 'Next: neottia apply']);
+        expect(resolveGeneratedConfig(root).toJSON()).toMatchObject({
+            version: 1,
+            modules: {
+                issues: { enabled: true },
+                design_docs: { enabled: true },
+            },
+            capabilities: {
+                issues: { provider: 'filesystem' },
+                documents: { provider: 'filesystem' },
+                source_control: { local: 'git', remote: false, workspaces: false },
+            },
+            harnesses: { install: { targets: [{ id: 'pi', scope: 'project' }] } },
+            agents: {
+                sdlc: {
+                    pi: requiredRoleAssignments(),
+                },
+            },
+        });
+    });
+    it.skipIf(process.platform === 'win32')('writes the configuration with owner-only permissions', async () => {
+        const root = await fixture();
+        expect(await main(['init', '--harness', 'pi', '--project', root], capture().output)).toBe(0);
+        expect((await stat(join(root, '.neottia', 'config.yml'))).mode & 0o777).toBe(0o600);
+    });
+    it('writes canonical multi-harness output independent of argument order', async () => {
+        const first = await fixture();
+        const second = await fixture();
+        expect(await main(['init', '--harness', 'pi', '--harness', 'opencode', '--project', first], capture().output)).toBe(0);
+        expect(await main(['init', '--harness', 'opencode', '--harness', 'pi', '--project', second], capture().output)).toBe(0);
+        const firstContent = await readFile(join(first, '.neottia', 'config.yml'), 'utf8');
+        const secondContent = await readFile(join(second, '.neottia', 'config.yml'), 'utf8');
+        expect(firstContent).toBe(secondContent);
+        expect(resolveGeneratedConfig(first).toJSON()).toMatchObject({
+            harnesses: {
+                install: {
+                    targets: [
+                        { id: 'opencode', scope: 'project' },
+                        { id: 'pi', scope: 'project' },
+                    ],
+                },
+            },
+            agents: {
+                sdlc: {
+                    opencode: requiredRoleAssignments(),
+                    pi: requiredRoleAssignments(),
+                },
+            },
+        });
+    });
+    it('deduplicates repeated harness values', async () => {
+        const root = await fixture();
+        expect(await main(['init', '--harness', 'pi', '--harness', 'pi', '--project', root], capture().output)).toBe(0);
+        expect(resolveGeneratedConfig(root).toJSON()).toMatchObject({
+            harnesses: { install: { targets: [{ id: 'pi', scope: 'project' }] } },
+        });
+    });
+    it('validates an existing configuration when init runs without harness arguments', async () => {
+        const root = await fixture();
+        await main(['init', '--harness', 'pi', '--project', root], capture().output);
+        const result = capture();
+        expect(await main(['init', '--project', root], result.output)).toBe(0);
+        expect(result.logs).toEqual([`Validated ${join(root, '.neottia', 'config.yml')}`, 'Next: neottia apply']);
+        expect(result.errors).toEqual([]);
+    });
+    it('fails validation of a corrupt existing configuration without rewriting it', async () => {
+        const root = await fixture();
+        const configPath = join(root, '.neottia', 'config.yml');
+        await mkdir(join(root, '.neottia'), { recursive: true });
+        const invalid = 'version: 1\nbogus_root_key: true\n';
+        await writeFile(configPath, invalid, 'utf8');
+        const result = capture();
+        expect(await main(['init', '--project', root], result.output)).toBe(1);
+        expect(result.errors.join('\n')).toContain('Configuration resolution failed');
+        expect(await readFile(configPath, 'utf8')).toBe(invalid);
+    });
+    it('installs the configured lifecycle for every configured harness', async () => {
+        const root = await fixture();
+        await main(['init', '--harness', 'pi', '--harness', 'opencode', '--project', root], capture().output);
+        const result = capture();
+        expect(await main(['apply', '--project', root], result.output)).toBe(0);
+        expect(result.errors).toEqual([]);
+        expect(result.logs.some((line) => line.includes('Installed pi project lifecycle'))).toBe(true);
+        expect(result.logs.some((line) => line.includes('Installed opencode project lifecycle'))).toBe(true);
+        expect(result.logs.some((line) => line.includes('Reload'))).toBe(true);
+        for (const harness of ['pi', 'opencode']) {
+            expect(await exists(join(root, '.neottia', 'install', `sdlc-${harness}.receipt.json`))).toBe(true);
+        }
+        expect(await exists(join(root, '.pi', 'prompts', 'plan.md'))).toBe(true);
+        expect(await exists(join(root, '.opencode', 'commands', 'plan.md'))).toBe(true);
+        expect(await exists(join(root, '.pi', 'skills', 'neottia-sdlc', 'SKILL.md'))).toBe(true);
+        expect(await readFile(join(root, '.pi', 'prompts', 'plan.md'), 'utf8')).toContain('They do not grant host permissions.');
+    }, 30000);
+    it('produces deterministic compiler output and a no-op second install', async () => {
+        const root = await fixture();
+        await main(['init', '--harness', 'pi', '--project', root], capture().output);
+        const first = capture();
+        await main(['apply', '--project', root], first.output);
+        const planPath = await readFile(join(root, '.neottia', 'install', 'sdlc-pi.receipt.json'), 'utf8');
+        const second = capture();
+        expect(await main(['apply', '--project', root], second.output)).toBe(0);
+        expect(second.logs.some((line) => line.includes('0 mutation(s)'))).toBe(true);
+        expect(await readFile(join(root, '.neottia', 'install', 'sdlc-pi.receipt.json'), 'utf8')).toBe(planPath);
+    }, 30000);
+    it('installs a globally scoped target under the caller home and reports it from doctor', async () => {
+        if (process.platform === 'win32')
+            return;
+        const root = await fixture();
+        await main(['init', '--harness', 'pi', '--project', root], capture().output);
+        const configPath = join(root, '.neottia', 'config.yml');
+        await writeFile(configPath, (await readFile(configPath, 'utf8')).replace('scope: project', 'scope: global'), 'utf8');
+        const home = join(root, 'home');
+        const xdgState = join(root, 'xdg-state');
+        await mkdir(home, { recursive: true });
+        await mkdir(xdgState, { recursive: true });
+        process.env.HOME = home;
+        process.env.XDG_STATE_HOME = xdgState;
+        try {
+            const result = capture();
+            expect(await main(['apply', '--project', root], result.output)).toBe(0);
+            expect(await exists(join(xdgState, 'neottia', 'install', 'sdlc-pi.receipt.json'))).toBe(true);
+            expect(await exists(join(home, '.pi', 'agent', 'skills', 'neottia-sdlc', 'SKILL.md'))).toBe(true);
+            expect(await exists(join(root, '.neottia', 'install', 'sdlc-pi.receipt.json'))).toBe(false);
+            const doctor = capture();
+            expect(await main(['doctor', '--project', root], doctor.output)).toBe(0);
+            expect(doctor.logs.join('\n')).toContain('No missing modules or installs detected.');
+        }
+        finally {
+            delete process.env.HOME;
+            delete process.env.XDG_STATE_HOME;
+        }
+    }, 30000);
+    it('skips conflicting files with warnings, installs the rest, and exits non-zero', async () => {
+        const root = await fixture();
+        await main(['init', '--harness', 'pi', '--project', root], capture().output);
+        const contested = join(root, '.pi', 'prompts', 'plan.md');
+        await mkdir(dirname(contested), { recursive: true });
+        await writeFile(contested, 'user-owned\n', 'utf8');
+        const result = capture();
+        const code = await main(['apply', '--project', root], result.output);
+        expect(code).toBe(2);
+        expect(result.errors.some((line) => line.includes('WARN:') && line.includes(contested))).toBe(true);
+        expect(result.errors.some((line) => line.includes('1 file(s) skipped'))).toBe(true);
+        expect(await readFile(contested, 'utf8')).toBe('user-owned\n');
+        expect(await exists(join(root, '.pi', 'prompts', 'build.md'))).toBe(true);
+    }, 30000);
+    it('fails closed when apply runs without a configuration', async () => {
+        const root = await fixture();
+        const result = capture();
+        expect(await main(['apply', '--project', root], result.output)).toBe(1);
+        expect(result.errors).toEqual(['Run neottia init first. Missing project configuration.']);
+    });
+    it('reports missing installs and unknown modules through doctor', async () => {
+        const root = await fixture();
+        await main(['init', '--harness', 'pi', '--project', root], capture().output);
+        const result = capture();
+        expect(await main(['doctor', '--project', root], result.output)).toBe(2);
+        expect(result.logs[0]).toContain('Configuration valid. Harnesses: pi');
+        expect(result.errors.some((line) => line.includes('pi lifecycle is not installed. Run neottia apply.'))).toBe(true);
+    });
+    it('reports healthy state through doctor after a successful apply', async () => {
+        const root = await fixture();
+        await main(['init', '--harness', 'pi', '--project', root], capture().output);
+        await main(['apply', '--project', root], capture().output);
+        const result = capture();
+        expect(await main(['doctor', '--project', root], result.output)).toBe(0);
+        expect(result.logs.join('\n')).toContain('No missing modules or installs detected.');
+    }, 30000);
+    it('refuses to replace an existing configuration', async () => {
+        const root = await fixture();
+        const directory = join(root, '.neottia');
+        const configPath = join(directory, 'config.yml');
+        await mkdir(directory);
+        await writeFile(configPath, 'version: 1\n# user-owned\n', 'utf8');
+        const result = capture();
+        expect(await main(['init', '--harness', 'pi', '--project', root], result.output)).toBe(1);
+        expect(await readFile(configPath, 'utf8')).toBe('version: 1\n# user-owned\n');
+        expect(result.errors).toEqual([`Configuration already exists: ${configPath}`]);
+        expect(await readdir(directory)).toEqual(['config.yml']);
+    });
+    it('reports registry validation failure without writing the configuration', async () => {
+        const root = await fixture();
+        const result = capture();
+        vi.mocked(resolveConfig).mockImplementationOnce(() => {
+            throw new ConfigResolutionError([
+                { code: 'VERSION', message: 'configuration version must be the supported integer version 1' },
+            ]);
+        });
+        expect(await main(['init', '--harness', 'pi', '--project', root], result.output)).toBe(1);
+        expect(result.errors.join('\n')).toContain('Configuration resolution failed');
+        expect(await exists(join(root, '.neottia'))).toBe(false);
+    });
+    it.each([
+        [['init'], 'At least one --harness is required.'],
+        [['init', '--harness', 'claude-code'], 'Unsupported harness: claude-code. Expected one of: opencode, pi.'],
+    ])('rejects invalid harness selection before mutation', async (arguments_, message) => {
+        const root = await fixture();
+        const result = capture();
+        expect(await main([...arguments_, '--project', root], result.output)).toBe(1);
+        expect(result.errors).toEqual([message]);
+        expect(await exists(join(root, '.neottia'))).toBe(false);
+    });
     it('returns a failure for an unknown command', async () => {
         const result = capture();
         expect(await main(['unknown'], result.output)).toBe(1);

package/dist/cli.spec.js.map

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package/dist/index.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAgDA,MAAM,WAAW,SAAS;IACxB,GAAG,CAAC,OAAO,EAAE,MAAM,GAAG,IAAI,CAAC;IAC3B,KAAK,CAAC,OAAO,EAAE,MAAM,GAAG,IAAI,CAAC;CAC9B;AAGD,wBAAsB,IAAI,CACxB,IAAI,GAAE,SAAS,MAAM,EAA0B,EAC/C,MAAM,GAAE,SAAmB,EAC3B,GAAG,GAAE,MAAM,CAAC,UAAwB,GACnC,OAAO,CAAC,MAAM,CAAC,CAkBjB"}

package/dist/index.js

@@ -1,8 +1,23 @@
-import { readFile, writeFile } from 'node:fs/promises';
+import { randomUUID } from 'node:crypto';
+import { link, lstat, mkdir, open, readFile, unlink, writeFile } from 'node:fs/promises';
+import { createRequire } from 'node:module';
 import { homedir } from 'node:os';
-import { resolve } from 'node:path';
+import { dirname, join, resolve } from 'node:path';
 import { parseArgs } from 'node:util';
-import { applyInstallationPlan, authorizePlan, canonicalJson, createInstallationPlan, decodeInstallationPlan, diagnoseSnapshot, inspectInstallation, inspectUninstall, recoverInstallation, runDoctor, validateManifest, } from '@neottia/distribution';
+import { resolveConfig } from '@neottia/config';
+import { harnessInstallConfigContribution, officialConfigRegistry } from '@neottia/config-registry';
+import { designDocsConfigContribution } from '@neottia/design-docs';
+import { applyInstallationPlan, authorizePlan, canonicalJson, createInstallationPlan, decodeInstallationPlan, diagnoseSnapshot, inspectInstallation, inspectUninstall, receiptPath as distributionReceiptPath, recoverInstallation, runDoctor, validateManifest, } from '@neottia/distribution';
+import { issueConfigContribution } from '@neottia/issues';
+import { memoryConfigContribution } from '@neottia/memory-core';
+import { opencodeHarnessAdapter } from '@neottia/opencode-adapter';
+import { piHarnessAdapter } from '@neottia/pi-adapter';
+import { compileSdlc, createSdlcCompilerInput, loadSdlcTemplateLayers } from '@neottia/sdlc';
+import { searchableConfigContribution } from '@neottia/searchable-core';
+import { catalogEntry } from './catalog.js';
+const SUPPORTED_HARNESSES = Object.freeze(['opencode', 'pi']);
+const HARNESS_ADAPTERS = Object.freeze({ pi: piHarnessAdapter, opencode: opencodeHarnessAdapter });
+const WARN_PREFIX = 'WARN: ';
 export async function main(argv = process.argv.slice(2), output = console, env = process.env) {
     try {
         const [command, ...arguments_] = argv;
@@ -11,15 +26,17 @@ export async function main(argv = process.argv.slice(2), output = console, env =
             return 0;
         }
         if (command === 'apply')
-            return applyCommand(arguments_, output);
+            return await applyCommand(arguments_, output, env);
+        if (command === 'init')
+            return await initCommand(arguments_, output, env);
         if (command === 'recover')
-            return recoverCommand(arguments_, output);
+            return await recoverCommand(arguments_, output);
         if (command === 'doctor')
-            return doctorCommand(arguments_, output, env);
+            return await doctorCommand(arguments_, output, env);
         if (command === 'uninstall')
-            return uninstallCommand(arguments_, output, env);
+            return await uninstallCommand(arguments_, output, env);
         if (command === 'plan')
-            return planCommand(arguments_, output, env);
+            return await planCommand(arguments_, output, env);
         throw new TypeError(`Unknown command: ${command}`);
     }
     catch (error) {
@@ -27,6 +44,39 @@ export async function main(argv = process.argv.slice(2), output = console, env =
         return 1;
     }
 }
+async function initCommand(arguments_, output, env) {
+    const { values } = parseArgs({
+        args: [...arguments_],
+        strict: true,
+        allowPositionals: false,
+        options: {
+            harness: { type: 'string', multiple: true, default: [] },
+            project: { type: 'string' },
+        },
+    });
+    const project = resolve(values.project ?? process.cwd());
+    const configPath = join(project, '.neottia', 'config.yml');
+    if (values.harness.length === 0 && (await isRegularFile(configPath))) {
+        resolveConfig(officialConfigRegistry, { cwd: project, env });
+        output.log(`Validated ${configPath}`);
+        output.log('Next: neottia apply');
+        return 0;
+    }
+    const harnesses = normalizeInitHarnesses(values.harness);
+    const document = createInitDocument(harnesses);
+    resolveConfig(officialConfigRegistry, {
+        cwd: project,
+        env: {},
+        globalFile: false,
+        projectFile: false,
+        overrides: document,
+    });
+    await publishNewConfig(configPath, renderInitConfig(harnesses));
+    output.log(`Created ${configPath}`);
+    output.log(`Harnesses: ${harnesses.join(', ')}`);
+    output.log('Next: neottia apply');
+    return 0;
+}
 async function planCommand(arguments_, output, env) {
     const values = parseCommon(arguments_);
     if (values.manifest === undefined)
@@ -48,30 +98,196 @@ async function uninstallCommand(arguments_, output, env) {
     await emitPlan(plan, values.output, output);
     return plan.conflicts.some((conflict) => !conflict.approved) ? 2 : 0;
 }
-async function applyCommand(arguments_, output) {
+async function applyCommand(arguments_, output, env) {
     const { values } = parseArgs({
         args: [...arguments_],
         strict: true,
         allowPositionals: false,
-        options: { plan: { type: 'string' } },
+        options: {
+            plan: { type: 'string' },
+            harness: { type: 'string', multiple: true, default: [] },
+            scope: { type: 'string' },
+            project: { type: 'string' },
+        },
     });
-    if (values.plan === undefined)
-        throw new TypeError('apply requires --plan.');
-    const plan = decodeInstallationPlan(JSON.parse(await readFile(values.plan, 'utf8')));
-    const result = await applyInstallationPlan(plan);
-    output.log(canonicalJson(result));
+    if (values.plan !== undefined) {
+        const plan = decodeInstallationPlan(JSON.parse(await readFile(values.plan, 'utf8')));
+        const result = await applyInstallationPlan(plan);
+        output.log(canonicalJson(result));
+        return 0;
+    }
+    const project = resolve(values.project ?? process.cwd());
+    if (!(await isRegularFile(join(project, '.neottia', 'config.yml')))) {
+        throw new TypeError('Run neottia init first. Missing project configuration.');
+    }
+    const harnesses = selectHarnesses(values.harness, project, env);
+    const override = values.scope === undefined ? undefined : parseScope(values.scope);
+    const configuredScopes = new Map(resolveConfig(officialConfigRegistry, { cwd: project, env })
+        .get(harnessInstallConfigContribution)
+        .targets.map((target) => [target.id, target.scope]));
+    let skipped = 0;
+    for (const harnessId of harnesses) {
+        const scope = override ?? configuredScopes.get(harnessId) ?? 'project';
+        skipped += await installHarness(harnessId, { project, env, scope }, output);
+    }
+    if (skipped > 0) {
+        output.error(`${skipped} file(s) skipped. Resolve the warnings above, then run neottia apply again.`);
+        return 2;
+    }
+    output.log('Done. Reload the harness so generated assets are picked up.');
     return 0;
 }
+async function installHarness(harnessId, context, output) {
+    const adapter = HARNESS_ADAPTERS[harnessId];
+    const snapshot = resolveConfig(officialConfigRegistry, { cwd: context.project, env: context.env });
+    const templateLayers = await loadSdlcTemplateLayers({ projectRoot: context.project });
+    const runtimePackages = selectedRuntimePackages(harnessId, snapshot);
+    const input = createSdlcCompilerInput(snapshot, {
+        compilerVersion: CLI_VERSION,
+        harnessId,
+        harnessDeclaration: adapter.declaration,
+        scope: context.scope,
+        templateLayers,
+        runtimePackages,
+    });
+    const compiled = compileSdlc(input, adapter);
+    const installRoots = installRootsFor(context.project, context.env);
+    const inspected = await inspectInstallation(compiled.assets, installRoots);
+    const action = inspected.receipt === undefined ? 'install' : 'update';
+    const plan = createInstallationPlan(inspected, action);
+    const conflicts = plan.conflicts.filter((conflict) => !conflict.approved);
+    for (const conflict of conflicts) {
+        output.error(`${WARN_PREFIX}skipped ${conflict.path} (${conflict.reason}). Resolve or remove the file, then rerun neottia apply.`);
+    }
+    const conflictedAssets = new Set(conflicts.map((conflict) => conflict.assetId));
+    const filtered = {
+        ...inspected,
+        units: inspected.units.filter((unit) => !conflictedAssets.has(unit.assetId)),
+    };
+    const partial = createInstallationPlan(filtered, action);
+    const result = await applyInstallationPlan(authorizePlan(partial, []));
+    output.log(`Installed ${harnessId} ${context.scope} lifecycle (${result.appliedMutations.length} mutation(s), ${conflicts.length} skipped).`);
+    if (result.reloadNotice !== undefined)
+        output.log(result.reloadNotice.message);
+    return conflicts.length;
+}
+const CLI_VERSION = createRequire(import.meta.url)('../package.json').version;
+void CLI_VERSION;
+function selectHarnesses(requested, project, env) {
+    if (requested.length > 0)
+        return normalizeInitHarnesses(requested);
+    const configured = resolveConfig(officialConfigRegistry, { cwd: project, env })
+        .get(harnessInstallConfigContribution)
+        .targets.map((target) => target.id);
+    const unsupported = configured.find((id) => !SUPPORTED_HARNESSES.includes(id));
+    if (unsupported !== undefined)
+        throw new TypeError(`Unsupported configured harness: ${unsupported}.`);
+    if (configured.length === 0)
+        throw new TypeError('No configured harnesses. Add harnesses.install.targets first.');
+    return Object.freeze([...new Set(configured)].sort((left, right) => left.localeCompare(right)));
+}
+function selectedRuntimePackages(harnessId, snapshot) {
+    const packages = [];
+    const candidates = [
+        ['memory', snapshot.get(memoryConfigContribution).enabled],
+        ['issues', snapshot.get(issueConfigContribution).enabled],
+        ['design-docs', snapshot.get(designDocsConfigContribution).enabled],
+        ['searchable', snapshot.get(searchableConfigContribution).enabled],
+    ];
+    for (const [logicalId, enabled] of candidates) {
+        if (!enabled)
+            continue;
+        const entry = catalogEntry(harnessId, logicalId);
+        if (entry === undefined) {
+            throw new TypeError(`No compatible runtime package for ${harnessId} ${logicalId}.`);
+        }
+        packages.push({ logicalId, version: entry.version });
+    }
+    return Object.freeze(packages);
+}
+function parseScope(value) {
+    if (value === undefined)
+        return 'project';
+    if (value === 'project' || value === 'global')
+        return value;
+    throw new TypeError('apply --scope must be project or global.');
+}
+function installRootsFor(project, env) {
+    const home = resolve(env.HOME ?? homedir());
+    return {
+        project,
+        home,
+        xdgConfig: resolve(env.XDG_CONFIG_HOME ?? `${home}/.config`),
+        xdgState: resolve(env.XDG_STATE_HOME ?? `${home}/.local/state`),
+    };
+}
+async function isRegularFile(path) {
+    try {
+        return (await lstat(path)).isFile();
+    }
+    catch {
+        return false;
+    }
+}
 async function doctorCommand(arguments_, output, env) {
     const values = parseCommon(arguments_);
-    if (values.manifest === undefined)
-        throw new TypeError('doctor requires --manifest.');
-    const manifest = await readManifest(values.manifest);
-    const rootValues = roots(values, env);
-    const snapshot = await inspectInstallation(manifest, rootValues);
-    const results = [...(await runDoctor(manifest, rootValues, env)), ...diagnoseSnapshot(snapshot)];
-    output.log(canonicalJson(results));
-    return results.some((result) => result.status === 'error') ? 2 : 0;
+    const project = resolve(values.project ?? process.cwd());
+    if (values.manifest !== undefined) {
+        const manifest = await readManifest(values.manifest);
+        const rootValues = roots(values, env);
+        const snapshot = await inspectInstallation(manifest, rootValues);
+        const results = [...(await runDoctor(manifest, rootValues, env)), ...diagnoseSnapshot(snapshot)];
+        output.log(canonicalJson(results));
+        return results.some((result) => result.status === 'error') ? 2 : 0;
+    }
+    if (!(await isRegularFile(join(project, '.neottia', 'config.yml')))) {
+        output.error(`${WARN_PREFIX}Missing project configuration. Run neottia init first.`);
+        return 2;
+    }
+    const snapshot = resolveConfig(officialConfigRegistry, { cwd: project, env });
+    const modules = [
+        ['memory', 'modules.memory.enabled', snapshot.get(memoryConfigContribution).enabled],
+        ['issues', 'modules.issues.enabled', snapshot.get(issueConfigContribution).enabled],
+        ['design-docs', 'modules.design_docs.enabled', snapshot.get(designDocsConfigContribution).enabled],
+        ['searchable', 'modules.searchable.enabled', snapshot.get(searchableConfigContribution).enabled],
+    ];
+    const harnesses = selectHarnesses([], project, env);
+    let failures = 0;
+    output.log(`Configuration valid. Harnesses: ${harnesses.join(', ')}`);
+    for (const harnessId of harnesses) {
+        for (const [logicalId, configPath, enabled] of modules) {
+            if (!enabled)
+                continue;
+            void configPath;
+            const entry = catalogEntry(harnessId, logicalId);
+            if (entry === undefined) {
+                output.error(`${WARN_PREFIX}No compatible runtime package for ${harnessId} ${logicalId}. Remove the module or extend the catalog.`);
+                failures += 1;
+            }
+        }
+    }
+    const configuredScopes = new Map(snapshot.get(harnessInstallConfigContribution).targets.map((target) => [target.id, target.scope]));
+    for (const harnessId of harnesses) {
+        const scope = configuredScopes.get(harnessId) ?? 'project';
+        const installRoots = installRootsFor(project, env);
+        const receiptPath = receiptPathFor(harnessId, scope, installRoots);
+        if (await isRegularFile(receiptPath)) {
+            const inspected = await inspectUninstall(receiptPath, installRoots);
+            if (!diagnoseSnapshot(inspected).some((result) => result.status === 'error'))
+                continue;
+            output.error(`${WARN_PREFIX}${harnessId} lifecycle is installed but drifted. Rerun neottia apply.`);
+        }
+        else {
+            output.error(`${WARN_PREFIX}${harnessId} lifecycle is not installed. Run neottia apply.`);
+        }
+        failures += 1;
+    }
+    if (failures === 0)
+        output.log('No missing modules or installs detected.');
+    return failures > 0 ? 2 : 0;
+}
+function receiptPathFor(harnessId, scope, installRoots) {
+    return distributionReceiptPath(`sdlc-${harnessId}`, scope, installRoots);
 }
 async function recoverCommand(arguments_, output) {
     const { values } = parseArgs({
@@ -113,6 +329,122 @@ function roots(values, env) {
         xdgState: resolve(typeof values['xdg-state'] === 'string' ? values['xdg-state'] : (env.XDG_STATE_HOME ?? `${home}/.local/state`)),
     };
 }
+function normalizeInitHarnesses(values) {
+    if (values.length === 0)
+        throw new TypeError('At least one --harness is required.');
+    const unsupported = values.find((value) => !SUPPORTED_HARNESSES.includes(value));
+    if (unsupported !== undefined) {
+        throw new TypeError(`Unsupported harness: ${unsupported}. Expected one of: ${SUPPORTED_HARNESSES.join(', ')}.`);
+    }
+    return Object.freeze([...new Set(values)].sort((left, right) => left.localeCompare(right)));
+}
+function createInitDocument(harnesses) {
+    const assignments = Object.fromEntries(harnesses.map((harness) => [
+        harness,
+        {
+            planner: { agent: 'current' },
+            implementer: { agent: 'current' },
+            verifier: { agent: 'current' },
+            'release-coordinator': { agent: 'current' },
+        },
+    ]));
+    return Object.freeze({
+        modules: {
+            issues: { enabled: true },
+            design_docs: { enabled: true },
+        },
+        capabilities: {
+            issues: { provider: 'filesystem' },
+            documents: { provider: 'filesystem' },
+            source_control: { local: 'git', remote: false, workspaces: false },
+        },
+        harnesses: {
+            install: { targets: harnesses.map((id) => ({ id, scope: 'project' })) },
+        },
+        agents: { sdlc: assignments },
+    });
+}
+function renderInitConfig(harnesses) {
+    const targets = harnesses.flatMap((harness) => [`      - id: ${harness}`, '        scope: project']);
+    const assignments = harnesses.flatMap((harness) => [
+        `    ${harness}:`,
+        '      planner: {agent: current}',
+        '      implementer: {agent: current}',
+        '      verifier: {agent: current}',
+        '      release-coordinator: {agent: current}',
+    ]);
+    return [
+        'version: 1',
+        'modules:',
+        '  issues:',
+        '    enabled: true',
+        '  design_docs:',
+        '    enabled: true',
+        'capabilities:',
+        '  issues:',
+        '    provider: filesystem',
+        '  documents:',
+        '    provider: filesystem',
+        '  source_control:',
+        '    local: git',
+        '    remote: false',
+        '    workspaces: false',
+        'harnesses:',
+        '  install:',
+        '    targets:',
+        ...targets,
+        'agents:',
+        '  sdlc:',
+        ...assignments,
+        '',
+    ].join('\n');
+}
+async function publishNewConfig(path, content) {
+    const directory = dirname(path);
+    await ensureConfigDirectory(directory);
+    const temporary = join(directory, `.config.yml.${process.pid}.${randomUUID()}.tmp`);
+    let handle;
+    try {
+        handle = await open(temporary, 'wx', 0o600);
+        await handle.writeFile(content, 'utf8');
+        await handle.sync();
+        await handle.close();
+        handle = undefined;
+        await link(temporary, path);
+    }
+    catch (error) {
+        if (hasErrorCode(error, 'EEXIST'))
+            throw new TypeError(`Configuration already exists: ${path}`);
+        throw error;
+    }
+    finally {
+        await handle?.close().catch(() => undefined);
+        await unlink(temporary).catch((error) => {
+            if (!hasErrorCode(error, 'ENOENT'))
+                throw error;
+        });
+    }
+}
+async function ensureConfigDirectory(path) {
+    try {
+        const metadata = await lstat(path);
+        if (!metadata.isDirectory() || metadata.isSymbolicLink()) {
+            throw new TypeError(`Configuration parent is not a regular directory: ${path}`);
+        }
+    }
+    catch (error) {
+        if (!hasErrorCode(error, 'ENOENT'))
+            throw error;
+        await mkdir(path, { recursive: true, mode: 0o700 });
+        const metadata = await lstat(path);
+        if (!metadata.isDirectory() || metadata.isSymbolicLink()) {
+            throw new TypeError(`Configuration parent is not a regular directory: ${path}`);
+        }
+    }
+}
+function hasErrorCode(error, code) {
+    return error instanceof Error && 'code' in error && error.code === code;
+}
 async function readManifest(path) {
     const manifest = JSON.parse(await readFile(path, 'utf8'));
     validateManifest(manifest);
@@ -127,6 +459,9 @@ async function emitPlan(plan, path, output) {
 function help() {
     return [
         'Usage:',
+        '  neottia init [--harness pi|opencode]... [--project DIR]   # create, or validate if present',
+        '  neottia apply [--harness ID]... [--scope project|global] [--project DIR]',
+        '  neottia doctor [--project DIR]                            # static config + install report',
         '  neottia plan --manifest FILE [--action install|update] [--output FILE] [--approve ID]...',
         '  neottia apply --plan FILE',
         '  neottia uninstall --receipt FILE [--output FILE] [--approve ID]...',

package/dist/index.js.map

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

@@ -1,6 +1,6 @@
 {
   "name": "@neottia/cli",
-  "version": "0.2.0",
+  "version": "0.4.0",
   "description": "Command-line planner, installer, updater, uninstaller, and doctor for Neottia assets",
   "author": "Dragos Cirjan",
   "license": "MIT",
@@ -38,7 +38,17 @@
     "node": ">=22.20.0"
   },
   "dependencies": {
-    "@neottia/distribution": "^0.2.0"
+    "@neottia/config": "^0.2.0",
+    "@neottia/config-registry": "^0.2.1",
+    "@neottia/design-docs": "^0.2.0",
+    "@neottia/distribution": "^0.2.0",
+    "@neottia/issues": "^0.2.0",
+    "@neottia/harness-adapter": "^0.2.0",
+    "@neottia/memory-core": "^0.2.0",
+    "@neottia/opencode-adapter": "^0.2.0",
+    "@neottia/pi-adapter": "^0.2.0",
+    "@neottia/sdlc": "^0.3.0",
+    "@neottia/searchable-core": "^0.2.0"
   },
   "devDependencies": {
     "@templ-project/tsconfig": "^0.2.2",
@@ -48,6 +58,7 @@
   },
   "scripts": {
     "build": "node -e \"require('node:fs').rmSync('dist',{recursive:true,force:true})\" && tsc -p tsconfig.build.json",
+    "pretest": "node ../../scripts/run-unless-workspace-prebuilt.mjs pnpm --filter @neottia/cli... run build",
     "test": "vitest run --root ../.. packages/cli/src",
     "typecheck": "tsc --noEmit"
   }