refactor: wave 2 - split atlas, auto-update-checker, session-recovery, todo-enforcer, background-task hooks

- Extract atlas/ into 15 focused modules (hook, event handler, tool policies, types, etc.)
- Split auto-update-checker into checker/ and hook/ subdirectories with single-purpose files
- Decompose session-recovery into separate recovery strategy files per error type
- Extract todo-continuation-enforcer from monolith to directory with dedicated modules
- Split background-task/tools.ts into individual tool creator files
- Extract command-executor, tmux-utils into focused sub-modules
- Split config/schema.ts into domain-specific schema files
- Decompose cli/config-manager.ts into focused modules
- Rollback skill-mcp-manager, model-availability, index.ts splits that broke tests
- Fix all import path depths for moved files (../../ -> ../../../)
- Add explicit type annotations to resolve TS7006 implicit any errors

Typecheck: 0 errors
Tests: 2359 pass, 5 fail (all pre-existing)

src/cli/config-manager/format-error-with-suggestion.ts

@@ -0,0 +1,39 @@
+interface NodeError extends Error {
+  code?: string
+}
+
+function isPermissionError(err: unknown): boolean {
+  const nodeErr = err as NodeError
+  return nodeErr?.code === "EACCES" || nodeErr?.code === "EPERM"
+}
+
+function isFileNotFoundError(err: unknown): boolean {
+  const nodeErr = err as NodeError
+  return nodeErr?.code === "ENOENT"
+}
+
+export function formatErrorWithSuggestion(err: unknown, context: string): string {
+  if (isPermissionError(err)) {
+    return `Permission denied: Cannot ${context}. Try running with elevated permissions or check file ownership.`
+  }
+
+  if (isFileNotFoundError(err)) {
+    return `File not found while trying to ${context}. The file may have been deleted or moved.`
+  }
+
+  if (err instanceof SyntaxError) {
+    return `JSON syntax error while trying to ${context}: ${err.message}. Check for missing commas, brackets, or invalid characters.`
+  }
+
+  const message = err instanceof Error ? err.message : String(err)
+
+  if (message.includes("ENOSPC")) {
+    return `Disk full: Cannot ${context}. Free up disk space and try again.`
+  }
+
+  if (message.includes("EROFS")) {
+    return `Read-only filesystem: Cannot ${context}. Check if the filesystem is mounted read-only.`
+  }
+
+  return `Failed to ${context}: ${message}`
+}