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/messages-reader.ts

@@ -0,0 +1,27 @@
+import { existsSync, readdirSync, readFileSync } from "node:fs"
+import { join } from "node:path"
+import type { StoredMessageMeta } from "../types"
+import { getMessageDir } from "./message-dir"
+
+export function readMessages(sessionID: string): StoredMessageMeta[] {
+  const messageDir = getMessageDir(sessionID)
+  if (!messageDir || !existsSync(messageDir)) return []
+
+  const messages: StoredMessageMeta[] = []
+  for (const file of readdirSync(messageDir)) {
+    if (!file.endsWith(".json")) continue
+    try {
+      const content = readFileSync(join(messageDir, file), "utf-8")
+      messages.push(JSON.parse(content))
+    } catch {
+      continue
+    }
+  }
+
+  return messages.sort((a, b) => {
+    const aTime = a.time?.created ?? 0
+    const bTime = b.time?.created ?? 0
+    if (aTime !== bTime) return aTime - bTime
+    return a.id.localeCompare(b.id)
+  })
+}