fix(shell): drop now-unused realpath import

Closes #844.

When the session's cached working directory is renamed on disk and
a file is subsequently created at the old path (e.g. `mv orig renamed
&& touch orig`), every Bash tool invocation failed with
`ENOTDIR: not a directory, posix_spawn '/usr/bin/zsh'` (exit 126),
and `!`-prefixed commands silently failed. No recovery was possible
without restarting the session.

Root cause: the pre-spawn guard in `src/utils/Shell.ts:exec()` used
`realpath(cwd)` to detect a missing CWD. `realpath()` succeeds on
any existing path — file or directory — so a path that was replaced
with a regular file slipped past the check. spawn() was then called
with `cwd` pointing at a non-directory and failed with ENOTDIR.

Fix: replace `realpath()` with `stat().isDirectory()` for both the
primary CWD check and the `getOriginalCwd()` fallback check. When
the cached CWD is no longer a directory, fall back to the original
CWD (as before) and update state so subsequent tools recover
transparently.

Verification:
  - Repro: `mkdir -p /tmp/x/orig && mv /tmp/x/orig /tmp/x/renamed
    && touch /tmp/x/orig`, then exec with stale cwd=/tmp/x/orig
  - Before: exit 126, stderr "ENOTDIR: not a directory, posix_spawn"
  - After:  exit 0, cwd transparently recovered to originalCwd
  - `bun test` — no new regressions (pre-existing model/provider
    test failures are unrelated and present on main)

scripts/build.ts

@@ -34,7 +34,6 @@ 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
@@ -57,6 +56,7 @@ 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

@@ -1,47 +0,0 @@
-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, realpath } from 'fs/promises'
+import { type FileHandle, mkdir, open, stat } from 'fs/promises'
 import memoize from 'lodash-es/memoize.js'
 import { isAbsolute, resolve } from 'path'
 import { join as posixJoin } from 'path/posix'
@@ -217,22 +217,34 @@ 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,
-  // This can happen when a command deletes its own CWD (e.g., temp dir cleanup).
+  // or was replaced by a non-directory (e.g., the path was renamed and a file
+  // 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 {
-    await realpath(cwd)
+    cwdIsValidDir = (await stat(cwd)).isDirectory()
   } catch {
+    cwdIsValidDir = false
+  }
+  if (!cwdIsValidDir) {
     const fallback = getOriginalCwd()
     logForDebugging(
-      `Shell CWD "${cwd}" no longer exists, recovering to "${fallback}"`,
+      `Shell CWD "${cwd}" is not a valid directory, recovering to "${fallback}"`,
     )
+    let fallbackIsValidDir = false
     try {
-      await realpath(fallback)
+      fallbackIsValidDir = (await stat(fallback)).isDirectory()
+    } catch {
+      fallbackIsValidDir = false
+    }
+    if (fallbackIsValidDir) {
       setCwdState(fallback)
       cwd = fallback
-    } catch {
+    } else {
       return createFailedCommand(
-        `Working directory "${cwd}" no longer exists. Please restart Claude from an existing directory.`,
+        `Working directory "${cwd}" is no longer a valid directory. Please restart Claude from an existing directory.`,
       )
     }
   }