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/session-recovery/storage/orphan-thinking-search.ts

@@ -0,0 +1,43 @@
+import { THINKING_TYPES } from "../constants"
+import { readMessages } from "./messages-reader"
+import { readParts } from "./parts-reader"
+
+export function findMessagesWithOrphanThinking(sessionID: string): string[] {
+  const messages = readMessages(sessionID)
+  const result: string[] = []
+
+  for (const msg of messages) {
+    if (msg.role !== "assistant") continue
+
+    const parts = readParts(msg.id)
+    if (parts.length === 0) continue
+
+    const sortedParts = [...parts].sort((a, b) => a.id.localeCompare(b.id))
+    const firstPart = sortedParts[0]
+    const firstIsThinking = THINKING_TYPES.has(firstPart.type)
+
+    if (!firstIsThinking) {
+      result.push(msg.id)
+    }
+  }
+
+  return result
+}
+
+export function findMessageByIndexNeedingThinking(sessionID: string, targetIndex: number): string | null {
+  const messages = readMessages(sessionID)
+
+  if (targetIndex < 0 || targetIndex >= messages.length) return null
+
+  const targetMessage = messages[targetIndex]
+  if (targetMessage.role !== "assistant") return null
+
+  const parts = readParts(targetMessage.id)
+  if (parts.length === 0) return null
+
+  const sortedParts = [...parts].sort((a, b) => a.id.localeCompare(b.id))
+  const firstPart = sortedParts[0]
+  const firstIsThinking = THINKING_TYPES.has(firstPart.type)
+
+  return firstIsThinking ? null : targetMessage.id
+}