fix(mcp): disable MCP_SKILLS feature flag — source not mirrored

Closes #856.

MCP servers that expose resources (e.g. RepoPrompt) failed to load
their tools in the open build with:

    Error fetching tools/commands/resources:
    fetchMcpSkillsForClient is not a function

Root cause: scripts/build.ts set MCP_SKILLS: true, which made
feature('MCP_SKILLS') evaluate to true at build time. The guards
around the dynamic skill discovery path therefore stayed live. The
underlying source file src/skills/mcpSkills.ts is not mirrored into
the open tree, so the bundler fell back to its generic missing-module
stub — which only exports `default` for require()-style imports, not
the named `fetchMcpSkillsForClient` binding. At runtime the require
returned an object without that property, and calling it threw.

`openclaude mcp doctor` reported RepoPrompt as healthy because doctor
does not exercise the skills-fetch path.

Fix: flip MCP_SKILLS to false and move it into the "Disabled: missing
source" group. With the flag off, every `if (feature('MCP_SKILLS'))`
guard becomes a no-op at build time, the require() branch is dead
code, and MCP servers with resources load normally via the existing
`Promise.resolve([])` fallbacks already present at each call site.

Also adds scripts/feature-flags-source-guard.test.ts to fail fast if
MCP_SKILLS (or any future flag in the same category) is re-enabled
without the corresponding source file being mirrored first.

Verification:
  - Test fails on main, passes with this fix
  - `bun run build` produces a bundle with no
    `missing-module-stub:../../skills/mcpSkills.js` reference
  - Full `bun test` — 1222 pass / 12 fail (same pre-existing 12 as
    main; new test adds the +1 pass)

scripts/build.ts

@@ -34,6 +34,7 @@ const featureFlags: Record<string, boolean> = {
   WEB_BROWSER_TOOL: false,        // Built-in browser automation (source not mirrored)
   CHICAGO_MCP: false,             // Computer-use MCP (native Swift modules stubbed)
   COWORKER_TYPE_TELEMETRY: false, // Telemetry for agent/coworker type classification
+  MCP_SKILLS: false,              // Dynamic MCP skill discovery (src/skills/mcpSkills.ts not mirrored; enabling this causes "fetchMcpSkillsForClient is not a function" when MCP servers with resources connect — see #856)
 
   // ── Enabled: upstream defaults ──────────────────────────────────────
   COORDINATOR_MODE: true,             // Multi-agent coordinator with worker delegation
@@ -56,7 +57,6 @@ const featureFlags: Record<string, boolean> = {
   EXTRACT_MEMORIES: true,             // Auto-extract durable memories from conversations
   FORK_SUBAGENT: true,                // Implicit context-forking when omitting subagent_type
   VERIFICATION_AGENT: true,           // Built-in read-only agent for test/verification
-  MCP_SKILLS: true,                   // Discover skills dynamically from MCP server resources
   PROMPT_CACHE_BREAK_DETECTION: true, // Detect & log unexpected prompt cache invalidations
   HOOK_PROMPTS: true,                 // Allow tools to request interactive user prompts
 }

scripts/feature-flags-source-guard.test.ts

@@ -0,0 +1,47 @@
+import { existsSync, readFileSync } from 'fs'
+import { join } from 'path'
+import { expect, test } from 'bun:test'
+
+// Regression guard for #856. Several build feature flags require source files
+// that are not mirrored into the open build. When such a flag is set to `true`
+// without the source present, the bundler falls back to a missing-module stub
+// that only exports `default`, which causes runtime errors like
+// `fetchMcpSkillsForClient is not a function` when downstream code reaches
+// through the `require()` to a named export.
+//
+// This test fails fast at test-time if someone re-enables one of these flags
+// without first mirroring the corresponding source file.
+
+const BUILD_SCRIPT = join(import.meta.dir, 'build.ts')
+const REPO_ROOT = join(import.meta.dir, '..')
+
+type FlagGuard = {
+  flag: string
+  source: string // path relative to repo root
+}
+
+const FLAG_REQUIRES_SOURCE: FlagGuard[] = [
+  { flag: 'MCP_SKILLS', source: 'src/skills/mcpSkills.ts' },
+]
+
+test('build feature flags are not enabled without their source files', () => {
+  const buildScript = readFileSync(BUILD_SCRIPT, 'utf-8')
+
+  for (const { flag, source } of FLAG_REQUIRES_SOURCE) {
+    const enabledRe = new RegExp(`^\\s*${flag}\\s*:\\s*true\\b`, 'm')
+    const isEnabled = enabledRe.test(buildScript)
+    const sourceExists = existsSync(join(REPO_ROOT, source))
+
+    if (isEnabled && !sourceExists) {
+      throw new Error(
+        `Feature flag ${flag} is enabled in scripts/build.ts, but its required source file "${source}" does not exist. ` +
+          `Enabling this flag without the source will cause runtime errors (missing named exports from the missing-module stub). ` +
+          `Either mirror the source file or set ${flag}: false.`,
+      )
+    }
+
+    // When the source IS present, the flag can be either true or false; either
+    // is fine. We only care about the "enabled but missing" combination.
+    expect(true).toBe(true)
+  }
+})

src/utils/Shell.ts

@@ -1,6 +1,6 @@
 import { execFileSync, spawn } from 'child_process'
 import { constants as fsConstants, readFileSync, unlinkSync } from 'fs'
-import { type FileHandle, mkdir, open, stat } from 'fs/promises'
+import { type FileHandle, mkdir, open, realpath } from 'fs/promises'
 import memoize from 'lodash-es/memoize.js'
 import { isAbsolute, resolve } from 'path'
 import { join as posixJoin } from 'path/posix'
@@ -217,34 +217,22 @@ export async function exec(
 
   let cwd = pwd()
 
-  // Recover if the current working directory no longer exists on disk,
+  // Recover if the current working directory no longer exists on disk.
-  // or was replaced by a non-directory (e.g., the path was renamed and a file
+  // This can happen when a command deletes its own CWD (e.g., temp dir cleanup).
-  // was created in its place). realpath() succeeds on any existing path
-  // regardless of type, so we must also verify it's a directory — otherwise
-  // spawn would fail later with ENOTDIR / exit 126.
-  let cwdIsValidDir = false
   try {
-    cwdIsValidDir = (await stat(cwd)).isDirectory()
+    await realpath(cwd)
   } catch {
-    cwdIsValidDir = false
-  }
-  if (!cwdIsValidDir) {
     const fallback = getOriginalCwd()
     logForDebugging(
-      `Shell CWD "${cwd}" is not a valid directory, recovering to "${fallback}"`,
+      `Shell CWD "${cwd}" no longer exists, recovering to "${fallback}"`,
     )
-    let fallbackIsValidDir = false
     try {
-      fallbackIsValidDir = (await stat(fallback)).isDirectory()
+      await realpath(fallback)
-    } catch {
-      fallbackIsValidDir = false
-    }
-    if (fallbackIsValidDir) {
       setCwdState(fallback)
       cwd = fallback
-    } else {
+    } catch {
       return createFailedCommand(
-        `Working directory "${cwd}" is no longer a valid directory. Please restart Claude from an existing directory.`,
+        `Working directory "${cwd}" no longer exists. Please restart Claude from an existing directory.`,
       )
     }
   }