fix: refresh server plugin skills after enable toggles

The previous hot-reload fix covered the running CLI process, but empty desktop sessions build their slash skill list through the server-side /api/skills path. If the server had already cached disabled plugin settings, /api/plugins/reload could still reload plugin state from stale settings and /api/skills stayed empty until a real chat spawned a fresh CLI.

Reset the server settings cache at the plugin reload boundary before clearing plugin caches. This keeps the desktop server, active CLI reload, and empty-session skills API aligned on enable-after-disable transitions.

Constraint: EmptySession uses /api/skills, not the active CLI slash-command cache

Rejected: Rely on starting a real CLI session to repopulate skills | delays visibility and makes empty-session slash commands stale

Confidence: high

Scope-risk: narrow

Directive: Plugin reload paths must invalidate settings before resolving enabledPlugins

Tested: bun test src/server/__tests__/skills.test.ts src/server/__tests__/plugins.test.ts

Tested: bun run check:server

Tested: cd desktop && bun run test --run src/pages/EmptySession.test.tsx src/stores/pluginStore.test.ts

src/server/__tests__/skills.test.ts

@@ -3,6 +3,10 @@ import * as fs from 'node:fs/promises'
 import * as os from 'node:os'
 import * as path from 'node:path'
 import { getCwdState, setCwdState } from '../../bootstrap/state.js'
+import { clearInstalledPluginsCache } from '../../utils/plugins/installedPluginsManager.js'
+import { clearPluginCache } from '../../utils/plugins/pluginLoader.js'
+import { resetSettingsCache } from '../../utils/settings/settingsCache.js'
+import { handlePluginsApi } from '../api/plugins.js'
 import { handleSkillsApi } from '../api/skills.js'
 
 let tmpHome: string
@@ -21,6 +25,16 @@ function makeRequest(urlStr: string): { req: Request; url: URL; segments: string
   }
 }
 
+function makePluginReloadRequest(): { req: Request; url: URL; segments: string[] } {
+  const url = new URL('/api/plugins/reload', 'http://localhost:3456')
+  const req = new Request(url.toString(), { method: 'POST' })
+  return {
+    req,
+    url,
+    segments: url.pathname.split('/').filter(Boolean),
+  }
+}
+
 async function writeSkill(root: string, skillName: string, content: string): Promise<void> {
   const skillDir = path.join(root, skillName)
   await fs.mkdir(skillDir, { recursive: true })
@@ -39,9 +53,15 @@ describe('Skills API', () => {
     process.env.USERPROFILE = tmpHome
     process.env.CLAUDE_CONFIG_DIR = path.join(tmpHome, '.claude')
     setCwdState(tmpHome)
+    clearInstalledPluginsCache()
+    clearPluginCache('skills-api-test-setup')
+    resetSettingsCache()
   })
 
   afterEach(async () => {
+    clearInstalledPluginsCache()
+    clearPluginCache('skills-api-test-teardown')
+    resetSettingsCache()
     if (originalHome === undefined) {
       delete process.env.HOME
     } else {
@@ -148,4 +168,115 @@ describe('Skills API', () => {
       expect.objectContaining({ path: 'SKILL.md', body: 'child body' }),
     )
   })
+
+  it('lists plugin skills after reload rereads an external enable toggle', async () => {
+    const marketplaceRoot = path.join(tmpHome, 'marketplace-root')
+    const pluginRoot = path.join(marketplaceRoot, 'plugins', 'draw')
+    const pluginsDir = path.join(tmpHome, '.claude', 'plugins')
+    const marketplaceFile = path.join(
+      marketplaceRoot,
+      '.claude-plugin',
+      'marketplace.json',
+    )
+
+    await fs.mkdir(path.join(pluginRoot, '.claude-plugin'), { recursive: true })
+    await fs.mkdir(path.join(pluginRoot, 'skills', 'render'), { recursive: true })
+    await fs.mkdir(path.dirname(marketplaceFile), { recursive: true })
+    await fs.mkdir(pluginsDir, { recursive: true })
+
+    await fs.writeFile(
+      path.join(pluginRoot, '.claude-plugin', 'plugin.json'),
+      JSON.stringify({
+        name: 'draw',
+        version: '1.0.0',
+        description: 'Drawing plugin',
+      }),
+      'utf-8',
+    )
+    await fs.writeFile(
+      path.join(pluginRoot, 'skills', 'render', 'SKILL.md'),
+      [
+        '---',
+        'description: Render with the drawing plugin.',
+        '---',
+        '',
+        '# Render',
+      ].join('\n'),
+      'utf-8',
+    )
+    await fs.writeFile(
+      marketplaceFile,
+      JSON.stringify({
+        name: 'test-market',
+        owner: { name: 'Test' },
+        plugins: [
+          {
+            name: 'draw',
+            source: './plugins/draw',
+            version: '1.0.0',
+          },
+        ],
+      }),
+      'utf-8',
+    )
+    await fs.writeFile(
+      path.join(pluginsDir, 'known_marketplaces.json'),
+      JSON.stringify({
+        'test-market': {
+          source: { source: 'directory', path: marketplaceRoot },
+          installLocation: marketplaceRoot,
+          lastUpdated: new Date(0).toISOString(),
+        },
+      }),
+      'utf-8',
+    )
+
+    const settingsPath = path.join(tmpHome, '.claude', 'settings.json')
+    await fs.writeFile(
+      settingsPath,
+      JSON.stringify({
+        enabledPlugins: {
+          'draw@test-market': false,
+        },
+      }),
+      'utf-8',
+    )
+
+    const initial = makeRequest('/api/skills')
+    const initialRes = await handleSkillsApi(initial.req, initial.url, initial.segments)
+    const initialBody = await initialRes.json() as {
+      skills: Array<{ name: string; source: string }>
+    }
+    expect(initialBody.skills).not.toContainEqual(
+      expect.objectContaining({ name: 'draw:render', source: 'plugin' }),
+    )
+
+    await fs.writeFile(
+      settingsPath,
+      JSON.stringify({
+        enabledPlugins: {
+          'draw@test-market': true,
+        },
+      }),
+      'utf-8',
+    )
+
+    const reload = makePluginReloadRequest()
+    const reloadRes = await handlePluginsApi(reload.req, reload.url, reload.segments)
+    expect(reloadRes.status).toBe(200)
+
+    const after = makeRequest('/api/skills')
+    const afterRes = await handleSkillsApi(after.req, after.url, after.segments)
+    const afterBody = await afterRes.json() as {
+      skills: Array<{ name: string; source: string; description: string }>
+    }
+
+    expect(afterBody.skills).toContainEqual(
+      expect.objectContaining({
+        name: 'draw:render',
+        source: 'plugin',
+        description: 'Render with the drawing plugin.',
+      }),
+    )
+  })
 })

src/server/services/pluginService.ts

@@ -28,6 +28,7 @@ import { getPluginCommands } from '../../utils/plugins/loadPluginCommands.js'
 import { clearPluginCacheExclusions } from '../../utils/plugins/orphanedPluginFilter.js'
 import { parseFrontmatter } from '../../utils/frontmatterParser.js'
 import { extractDescriptionFromMarkdown } from '../../utils/markdownConfigLoader.js'
+import { resetSettingsCache } from '../../utils/settings/settingsCache.js'
 import type {
   PluginInstallationEntry,
   PluginScope,
@@ -230,6 +231,7 @@ export class PluginService {
   }
 
   async reloadPlugins(cwd?: string): Promise<ApiPluginReloadResponse> {
+    resetSettingsCache()
     clearAllCaches()
     clearPluginCacheExclusions()