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/thinking-strip.ts

@@ -0,0 +1,27 @@
+import { existsSync, readdirSync, readFileSync, unlinkSync } from "node:fs"
+import { join } from "node:path"
+import { PART_STORAGE, THINKING_TYPES } from "../constants"
+import type { StoredPart } from "../types"
+
+export function stripThinkingParts(messageID: string): boolean {
+  const partDir = join(PART_STORAGE, messageID)
+  if (!existsSync(partDir)) return false
+
+  let anyRemoved = false
+  for (const file of readdirSync(partDir)) {
+    if (!file.endsWith(".json")) continue
+    try {
+      const filePath = join(partDir, file)
+      const content = readFileSync(filePath, "utf-8")
+      const part = JSON.parse(content) as StoredPart
+      if (THINKING_TYPES.has(part.type)) {
+        unlinkSync(filePath)
+        anyRemoved = true
+      }
+    } catch {
+      continue
+    }
+  }
+
+  return anyRemoved
+}