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/tools/background-task/message-dir.ts

@@ -0,0 +1,17 @@
+import { existsSync, readdirSync } from "node:fs"
+import { join } from "node:path"
+import { MESSAGE_STORAGE } from "../../features/hook-message-injector"
+
+export function getMessageDir(sessionID: string): string | null {
+  if (!existsSync(MESSAGE_STORAGE)) return null
+
+  const directPath = join(MESSAGE_STORAGE, sessionID)
+  if (existsSync(directPath)) return directPath
+
+  for (const dir of readdirSync(MESSAGE_STORAGE)) {
+    const sessionPath = join(MESSAGE_STORAGE, dir, sessionID)
+    if (existsSync(sessionPath)) return sessionPath
+  }
+
+  return null
+}