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/recover-thinking-block-order.ts

@@ -0,0 +1,36 @@
+import type { createOpencodeClient } from "@opencode-ai/sdk"
+import type { MessageData } from "./types"
+import { extractMessageIndex } from "./detect-error-type"
+import { findMessageByIndexNeedingThinking, findMessagesWithOrphanThinking, prependThinkingPart } from "./storage"
+
+type Client = ReturnType<typeof createOpencodeClient>
+
+export async function recoverThinkingBlockOrder(
+  _client: Client,
+  sessionID: string,
+  _failedAssistantMsg: MessageData,
+  _directory: string,
+  error: unknown
+): Promise<boolean> {
+  const targetIndex = extractMessageIndex(error)
+  if (targetIndex !== null) {
+    const targetMessageID = findMessageByIndexNeedingThinking(sessionID, targetIndex)
+    if (targetMessageID) {
+      return prependThinkingPart(sessionID, targetMessageID)
+    }
+  }
+
+  const orphanMessages = findMessagesWithOrphanThinking(sessionID)
+  if (orphanMessages.length === 0) {
+    return false
+  }
+
+  let anySuccess = false
+  for (const messageID of orphanMessages) {
+    if (prependThinkingPart(sessionID, messageID)) {
+      anySuccess = true
+    }
+  }
+
+  return anySuccess
+}