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/hooks/todo-continuation-enforcer/session-state.ts

@@ -0,0 +1,62 @@
+import type { SessionState } from "./types"
+
+export interface SessionStateStore {
+  getState: (sessionID: string) => SessionState
+  getExistingState: (sessionID: string) => SessionState | undefined
+  cancelCountdown: (sessionID: string) => void
+  cleanup: (sessionID: string) => void
+  cancelAllCountdowns: () => void
+}
+
+export function createSessionStateStore(): SessionStateStore {
+  const sessions = new Map<string, SessionState>()
+
+  function getState(sessionID: string): SessionState {
+    const existingState = sessions.get(sessionID)
+    if (existingState) return existingState
+
+    const state: SessionState = {}
+    sessions.set(sessionID, state)
+    return state
+  }
+
+  function getExistingState(sessionID: string): SessionState | undefined {
+    return sessions.get(sessionID)
+  }
+
+  function cancelCountdown(sessionID: string): void {
+    const state = sessions.get(sessionID)
+    if (!state) return
+
+    if (state.countdownTimer) {
+      clearTimeout(state.countdownTimer)
+      state.countdownTimer = undefined
+    }
+
+    if (state.countdownInterval) {
+      clearInterval(state.countdownInterval)
+      state.countdownInterval = undefined
+    }
+
+    state.countdownStartedAt = undefined
+  }
+
+  function cleanup(sessionID: string): void {
+    cancelCountdown(sessionID)
+    sessions.delete(sessionID)
+  }
+
+  function cancelAllCountdowns(): void {
+    for (const sessionID of sessions.keys()) {
+      cancelCountdown(sessionID)
+    }
+  }
+
+  return {
+    getState,
+    getExistingState,
+    cancelCountdown,
+    cleanup,
+    cancelAllCountdowns,
+  }
+}