test(skills): cover install and execute option parsing

docs/plans/state.json

@@ -1478,6 +1478,14 @@
               "src/cli/skills.test.ts"
             ],
             "test_status": "pnpm typecheck + pnpm test:run src/cli/skills.test.ts + pnpm test:run + pnpm lint (warnings only, 0 errors) + pnpm build passing"
+          },
+          "skills_cli_option_parsing_integration_tests": {
+            "status": "completed",
+            "description": "Added CLI-level integration tests for `skills install`/`skills execute` option parsing and failure modes around `--execute`, `--runner`, and `--confirm`, validating command wiring through commander actions",
+            "files_modified": [
+              "src/cli/skills.test.ts"
+            ],
+            "test_status": "pnpm typecheck + pnpm test:run src/cli/skills.test.ts + pnpm test:run + pnpm lint (warnings only, 0 errors) + pnpm build passing"
           }
         }
       }
@@ -1506,7 +1514,7 @@
   },
 
   "overall_progress": {
-    "total_test_count": 1550,
+    "total_test_count": 1553,
     "all_tests_passing": true,
     "p0_completion": "3/3 (100%)",
     "p1_completion": "4/4 (100%)",
@@ -1526,7 +1534,7 @@
     "gmail_auth_cli": "flynn gmail-auth command implemented with OAuth2 flow, doctor check, config routed to Telegram",
     "native_audio_support": "completed — smart routing for native audio (Gemini/OpenAI/GitHub) vs Whisper transcription fallback",
     "remaining_phases_completion": "Phase 1: 3/3 (100%) — context levels, command registry, memory structure. Phase 2: 2/2 (100%) — component registry, confidence routing. Phase 3: 2/2 (100%) — adaptive memory/compaction, truthfulness/autonomy hardening",
-    "next_up": "Skills infrastructure Phase 3: add CLI-level integration tests for `skills install/execute` option parsing (`--execute`, `--runner`, `--confirm`) to lock behavior and failure modes"
+    "next_up": "Skills infrastructure Phase 3: add explicit user-facing error messaging/tests for invalid `--execute` usage patterns (for example, `--execute` without `--confirm`) and runner/result edge-case receipts"
   },
   "soul_md_and_cron_create": {
     "date": "2026-02-11",

src/cli/skills.test.ts

@@ -2,6 +2,7 @@ import { describe, it, expect, vi } from 'vitest';
 import { mkdtempSync, mkdirSync, writeFileSync, existsSync, rmSync } from 'fs';
 import { join } from 'path';
 import { tmpdir } from 'os';
+import { Command } from 'commander';
 import { SkillInstaller } from '../skills/index.js';
 import {
   toSkillListRows,
@@ -27,6 +28,7 @@ import {
   resolveSkillInstallerCommandRunner,
   runSkillExecuteAction,
   runSkillInstallAction,
+  registerSkillsCommand,
 } from './skills.js';
 import type { Skill } from '../skills/index.js';
 
@@ -46,6 +48,23 @@ function buildSkill(overrides: Partial<Skill>): Skill {
   };
 }
 
+function writeSkillsCliConfig(configPath: string, opts: { managedDir: string; bundledDir: string; workspaceDir: string }): void {
+  writeFileSync(
+    configPath,
+    [
+      'models:',
+      '  default:',
+      '    provider: ollama',
+      '    model: test-model',
+      'skills:',
+      `  managed_dir: ${opts.managedDir}`,
+      `  bundled_dir: ${opts.bundledDir}`,
+      `  workspace_dir: ${opts.workspaceDir}`,
+    ].join('\n'),
+    'utf-8',
+  );
+}
+
 describe('skills CLI helpers', () => {
   it('maps and sorts skill rows', () => {
     const rows = toSkillListRows([
@@ -870,4 +889,118 @@ describe('skills CLI helpers', () => {
 
     rmSync(root, { recursive: true, force: true });
   });
+
+  it('skills install reports invalid runner via CLI option parsing path', async () => {
+    const root = mkdtempSync(join(tmpdir(), 'flynn-skills-cli-'));
+    const configPath = join(root, 'config.yaml');
+    const managedDir = join(root, 'managed');
+    const bundledDir = join(root, 'bundled');
+    const workspaceDir = join(root, 'workspace');
+    mkdirSync(managedDir, { recursive: true });
+    mkdirSync(bundledDir, { recursive: true });
+    mkdirSync(workspaceDir, { recursive: true });
+    writeSkillsCliConfig(configPath, { managedDir, bundledDir, workspaceDir });
+
+    const program = new Command();
+    registerSkillsCommand(program);
+
+    const errorSpy = vi.spyOn(console, 'error').mockImplementation(() => undefined);
+    process.exitCode = undefined;
+
+    await program.parseAsync(['skills', 'install', '/tmp/any-skill', '--runner', 'invalid', '-c', configPath], { from: 'user' });
+
+    expect(errorSpy).toHaveBeenCalledWith("Invalid runner 'invalid'. Allowed values: noop, shell.");
+    expect(process.exitCode).toBe(1);
+
+    errorSpy.mockRestore();
+    process.exitCode = undefined;
+    rmSync(root, { recursive: true, force: true });
+  });
+
+  it('skills install parses execute flags and emits execution-enabled JSON receipt', async () => {
+    const root = mkdtempSync(join(tmpdir(), 'flynn-skills-cli-'));
+    const configPath = join(root, 'config.yaml');
+    const sourceDir = join(root, 'source-skill');
+    const managedDir = join(root, 'managed');
+    const bundledDir = join(root, 'bundled');
+    const workspaceDir = join(root, 'workspace');
+    mkdirSync(sourceDir, { recursive: true });
+    mkdirSync(managedDir, { recursive: true });
+    mkdirSync(bundledDir, { recursive: true });
+    mkdirSync(workspaceDir, { recursive: true });
+    writeSkillsCliConfig(configPath, { managedDir, bundledDir, workspaceDir });
+    writeFileSync(join(sourceDir, 'SKILL.md'), '# Install Skill\nInstructions');
+    writeFileSync(
+      join(sourceDir, 'manifest.json'),
+      JSON.stringify({
+        name: 'cli-install-skill',
+        description: 'CLI install parse',
+        version: '1.0.0',
+        installers: [{ type: 'download', url: 'https://example.com/cli-install.tgz' }],
+      }),
+      'utf-8',
+    );
+
+    const program = new Command();
+    registerSkillsCommand(program);
+
+    const logSpy = vi.spyOn(console, 'log').mockImplementation(() => undefined);
+    process.exitCode = undefined;
+
+    await program.parseAsync(
+      ['skills', 'install', sourceDir, '--json', '--execute', '--confirm', '--runner', 'noop', '-c', configPath],
+      { from: 'user' },
+    );
+
+    const payload = JSON.parse(String(logSpy.mock.calls[logSpy.mock.calls.length - 1]?.[0]));
+    expect(payload.execution.execution_enabled).toBe(true);
+    expect(payload.execution.reason).toBe('execution_enabled');
+
+    logSpy.mockRestore();
+    process.exitCode = undefined;
+    rmSync(root, { recursive: true, force: true });
+  });
+
+  it('skills execute parses execute flags and emits execution-enabled JSON receipt', async () => {
+    const root = mkdtempSync(join(tmpdir(), 'flynn-skills-cli-'));
+    const configPath = join(root, 'config.yaml');
+    const managedDir = join(root, 'managed');
+    const bundledDir = join(root, 'bundled');
+    const workspaceDir = join(root, 'workspace');
+    const skillDir = join(managedDir, 'cli-exec-skill');
+    mkdirSync(skillDir, { recursive: true });
+    mkdirSync(bundledDir, { recursive: true });
+    mkdirSync(workspaceDir, { recursive: true });
+    writeSkillsCliConfig(configPath, { managedDir, bundledDir, workspaceDir });
+    writeFileSync(join(skillDir, 'SKILL.md'), '# Execute Skill\nInstructions');
+    writeFileSync(
+      join(skillDir, 'manifest.json'),
+      JSON.stringify({
+        name: 'cli-exec-skill',
+        description: 'CLI execute parse',
+        version: '1.0.0',
+        installers: [{ type: 'download', url: 'https://example.com/cli-exec.tgz' }],
+      }),
+      'utf-8',
+    );
+
+    const program = new Command();
+    registerSkillsCommand(program);
+
+    const logSpy = vi.spyOn(console, 'log').mockImplementation(() => undefined);
+    process.exitCode = undefined;
+
+    await program.parseAsync(
+      ['skills', 'execute', 'cli-exec-skill', '--json', '--execute', '--confirm', '--runner', 'noop', '-c', configPath],
+      { from: 'user' },
+    );
+
+    const payload = JSON.parse(String(logSpy.mock.calls[0]?.[0]));
+    expect(payload.execution_enabled).toBe(true);
+    expect(payload.reason).toBe('execution_enabled');
+
+    logSpy.mockRestore();
+    process.exitCode = undefined;
+    rmSync(root, { recursive: true, force: true });
+  });
 });