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/empty-text.ts

@@ -0,0 +1,55 @@
+import { existsSync, readdirSync, readFileSync, writeFileSync } from "node:fs"
+import { join } from "node:path"
+import { PART_STORAGE } from "../constants"
+import type { StoredPart, StoredTextPart } from "../types"
+import { readMessages } from "./messages-reader"
+import { readParts } from "./parts-reader"
+
+export function replaceEmptyTextParts(messageID: string, replacementText: string): boolean {
+  const partDir = join(PART_STORAGE, messageID)
+  if (!existsSync(partDir)) return false
+
+  let anyReplaced = 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 (part.type === "text") {
+        const textPart = part as StoredTextPart
+        if (!textPart.text?.trim()) {
+          textPart.text = replacementText
+          textPart.synthetic = true
+          writeFileSync(filePath, JSON.stringify(textPart, null, 2))
+          anyReplaced = true
+        }
+      }
+    } catch {
+      continue
+    }
+  }
+
+  return anyReplaced
+}
+
+export function findMessagesWithEmptyTextParts(sessionID: string): string[] {
+  const messages = readMessages(sessionID)
+  const result: string[] = []
+
+  for (const msg of messages) {
+    const parts = readParts(msg.id)
+    const hasEmptyTextPart = parts.some((part) => {
+      if (part.type !== "text") return false
+      const textPart = part as StoredTextPart
+      return !textPart.text?.trim()
+    })
+
+    if (hasEmptyTextPart) {
+      result.push(msg.id)
+    }
+  }
+
+  return result
+}