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/part-content.ts

@@ -0,0 +1,28 @@
+import { THINKING_TYPES, META_TYPES } from "../constants"
+import type { StoredPart, StoredTextPart } from "../types"
+import { readParts } from "./parts-reader"
+
+export function hasContent(part: StoredPart): boolean {
+  if (THINKING_TYPES.has(part.type)) return false
+  if (META_TYPES.has(part.type)) return false
+
+  if (part.type === "text") {
+    const textPart = part as StoredTextPart
+    return !!textPart.text?.trim()
+  }
+
+  if (part.type === "tool" || part.type === "tool_use") {
+    return true
+  }
+
+  if (part.type === "tool_result") {
+    return true
+  }
+
+  return false
+}
+
+export function messageHasContent(messageID: string): boolean {
+  const parts = readParts(messageID)
+  return parts.some(hasContent)
+}