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/deep-merge-record.ts

@@ -0,0 +1,29 @@
+export function deepMergeRecord<TTarget extends Record<string, unknown>>(
+  target: TTarget,
+  source: Partial<TTarget>
+): TTarget {
+  const result: TTarget = { ...target }
+
+  for (const key of Object.keys(source) as Array<keyof TTarget>) {
+    const sourceValue = source[key]
+    const targetValue = result[key]
+
+    if (
+      sourceValue !== null &&
+      typeof sourceValue === "object" &&
+      !Array.isArray(sourceValue) &&
+      targetValue !== null &&
+      typeof targetValue === "object" &&
+      !Array.isArray(targetValue)
+    ) {
+      result[key] = deepMergeRecord(
+        targetValue as Record<string, unknown>,
+        sourceValue as Record<string, unknown>
+      ) as TTarget[keyof TTarget]
+    } else if (sourceValue !== undefined) {
+      result[key] = sourceValue as TTarget[keyof TTarget]
+    }
+  }
+
+  return result
+}