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/atlas/is-abort-error.ts

@@ -0,0 +1,20 @@
+export function isAbortError(error: unknown): boolean {
+  if (!error) return false
+
+  if (typeof error === "object") {
+    const errObj = error as Record<string, unknown>
+    const name = errObj.name as string | undefined
+    const message = (errObj.message as string | undefined)?.toLowerCase() ?? ""
+
+    if (name === "MessageAbortedError" || name === "AbortError") return true
+    if (name === "DOMException" && message.includes("abort")) return true
+    if (message.includes("aborted") || message.includes("cancelled") || message.includes("interrupted")) return true
+  }
+
+  if (typeof error === "string") {
+    const lower = error.toLowerCase()
+    return lower.includes("abort") || lower.includes("cancel") || lower.includes("interrupt")
+  }
+
+  return false
+}