feat(skills): guard uninstall with explicit confirmation

docs/plans/state.json

@@ -1237,6 +1237,15 @@
               "src/cli/skills.test.ts"
             ],
             "test_status": "typecheck + targeted skills CLI tests + full test suite + lint (warnings only, 0 errors) + build passing"
+          },
+          "skills_uninstall_command": {
+            "status": "completed",
+            "description": "Added `flynn skills uninstall <name>` command dispatch with --yes confirmation guard and managed-tier uninstall protection",
+            "files_modified": [
+              "src/cli/skills.ts",
+              "src/cli/skills.test.ts"
+            ],
+            "test_status": "typecheck + targeted skills CLI tests + full test suite + lint (warnings only, 0 errors) + build passing"
           }
         }
       },
@@ -1277,7 +1286,7 @@
   },
 
   "overall_progress": {
-    "total_test_count": 1497,
+    "total_test_count": 1500,
     "all_tests_passing": true,
     "p0_completion": "3/3 (100%)",
     "p1_completion": "4/4 (100%)",
@@ -1297,7 +1306,7 @@
     "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 1: add `flynn skills uninstall <name>` command dispatch"
+    "next_up": "Skills infrastructure Phase 1: add `flynn skills refresh` command dispatch"
   },
   "soul_md_and_cron_create": {
     "date": "2026-02-11",

src/cli/skills.test.ts

@@ -3,7 +3,13 @@ import { mkdtempSync, mkdirSync, writeFileSync, existsSync, rmSync } from 'fs';
 import { join } from 'path';
 import { tmpdir } from 'os';
 import { SkillInstaller } from '../skills/index.js';
-import { toSkillListRows, renderSkillsTable, renderSkillInfo, installSkillFromDirectory } from './skills.js';
+import {
+  toSkillListRows,
+  renderSkillsTable,
+  renderSkillInfo,
+  installSkillFromDirectory,
+  uninstallSkillByName,
+} from './skills.js';
 import type { Skill } from '../skills/index.js';
 
 function buildSkill(overrides: Partial<Skill>): Skill {
@@ -129,4 +135,62 @@ describe('skills CLI helpers', () => {
 
     rmSync(root, { recursive: true, force: true });
   });
+
+  it('requires --yes confirmation for uninstall helper', () => {
+    const root = mkdtempSync(join(tmpdir(), 'flynn-skills-cli-'));
+    const installer = new SkillInstaller(join(root, 'managed'));
+
+    const result = uninstallSkillByName(installer, 'any-skill', { confirm: false });
+
+    expect(result.removed).toBeUndefined();
+    expect(result.error).toContain('--yes');
+
+    rmSync(root, { recursive: true, force: true });
+  });
+
+  it('uninstalls managed skill when confirmed', () => {
+    const root = mkdtempSync(join(tmpdir(), 'flynn-skills-cli-'));
+    const sourceDir = join(root, 'source-skill');
+    const managedDir = join(root, 'managed');
+    mkdirSync(sourceDir, { recursive: true });
+    writeFileSync(join(sourceDir, 'SKILL.md'), '# Managed\nInstructions');
+    writeFileSync(
+      join(sourceDir, 'manifest.json'),
+      JSON.stringify({ name: 'managed-skill', description: 'Managed', version: '1.0.0' }),
+      'utf-8',
+    );
+
+    const installer = new SkillInstaller(managedDir);
+    installSkillFromDirectory(installer, sourceDir);
+
+    const result = uninstallSkillByName(installer, 'managed-skill', { confirm: true });
+
+    expect(result.error).toBeUndefined();
+    expect(result.removed).toBe(true);
+    expect(existsSync(join(managedDir, 'managed-skill', 'SKILL.md'))).toBe(false);
+
+    rmSync(root, { recursive: true, force: true });
+  });
+
+  it('blocks uninstall of bundled/workspace-only skill', () => {
+    const root = mkdtempSync(join(tmpdir(), 'flynn-skills-cli-'));
+    const installer = new SkillInstaller(join(root, 'managed'));
+
+    const result = uninstallSkillByName(installer, 'bundled-only', {
+      confirm: true,
+      discoveredSkill: buildSkill({
+        manifest: {
+          name: 'bundled-only',
+          description: 'Bundled',
+          version: '1.0.0',
+          tier: 'bundled',
+        },
+      }),
+    });
+
+    expect(result.removed).toBeUndefined();
+    expect(result.error).toContain('cannot be uninstalled from managed skills');
+
+    rmSync(root, { recursive: true, force: true });
+  });
 });

src/cli/skills.ts

@@ -100,6 +100,28 @@ export function installSkillFromDirectory(installer: SkillInstaller, sourcePath:
   }
 }
 
+export function uninstallSkillByName(
+  installer: SkillInstaller,
+  name: string,
+  opts: { confirm: boolean; discoveredSkill?: Skill },
+): { removed?: true; error?: string } {
+  if (!opts.confirm) {
+    return { error: 'Refusing to uninstall without --yes. Re-run with --yes to confirm.' };
+  }
+
+  if (opts.discoveredSkill && opts.discoveredSkill.manifest.tier !== 'managed' && !installer.isInstalled(name)) {
+    return {
+      error: `Skill '${name}' is '${opts.discoveredSkill.manifest.tier}' and cannot be uninstalled from managed skills.`,
+    };
+  }
+
+  if (!installer.uninstall(name)) {
+    return { error: `Managed skill '${name}' is not installed.` };
+  }
+
+  return { removed: true };
+}
+
 export function registerSkillsCommand(program: Command): void {
   const skills = program
     .command('skills')
@@ -182,4 +204,42 @@ export function registerSkillsCommand(program: Command): void {
 
       console.log(`Installed skill '${result.skill.manifest.name}' (${result.skill.manifest.version}).`);
     });
+
+  skills
+    .command('uninstall <name>')
+    .description('Uninstall a managed skill by name')
+    .option('--yes', 'Confirm uninstall without prompt')
+    .option('-c, --config <path>', 'Config file path')
+    .action((name: string, opts: { yes?: boolean; config?: string }) => {
+      const loaded = loadConfigSafe(opts.config);
+      if (loaded.error || !loaded.config) {
+        console.error(loaded.error ?? 'Failed to load config');
+        process.exitCode = 1;
+        return;
+      }
+
+      const defaultManagedDir = resolve(homedir(), '.flynn/workspace/skills');
+      const installer = new SkillInstaller(loaded.config.skills.managed_dir ?? defaultManagedDir);
+      const discoveredSkills = loadAllSkills({
+        bundledDir: loaded.config.skills.bundled_dir,
+        managedDir: loaded.config.skills.managed_dir ?? defaultManagedDir,
+        workspaceDir: loaded.config.skills.workspace_dir,
+      });
+      const discovered = discoveredSkills.find(
+        (skill) => skill.manifest.name === name && skill.manifest.tier === 'managed',
+      ) ?? discoveredSkills.find((skill) => skill.manifest.name === name);
+
+      const result = uninstallSkillByName(installer, name, {
+        confirm: opts.yes ?? false,
+        discoveredSkill: discovered,
+      });
+
+      if (result.error || !result.removed) {
+        console.error(result.error ?? `Failed to uninstall skill '${name}'.`);
+        process.exitCode = 1;
+        return;
+      }
+
+      console.log(`Uninstalled skill '${name}'.`);
+    });
 }