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/tools/background-task/time-format.ts

@@ -0,0 +1,30 @@
+export function formatDuration(start: Date, end?: Date): string {
+  const duration = (end ?? new Date()).getTime() - start.getTime()
+  const seconds = Math.floor(duration / 1000)
+  const minutes = Math.floor(seconds / 60)
+  const hours = Math.floor(minutes / 60)
+
+  if (hours > 0) {
+    return `${hours}h ${minutes % 60}m ${seconds % 60}s`
+  }
+  if (minutes > 0) {
+    return `${minutes}m ${seconds % 60}s`
+  }
+  return `${seconds}s`
+}
+
+export function formatMessageTime(value: unknown): string {
+  if (typeof value === "string") {
+    const date = new Date(value)
+    return Number.isNaN(date.getTime()) ? value : date.toISOString()
+  }
+  if (typeof value === "object" && value !== null) {
+    if ("created" in value) {
+      const created = (value as { created?: number }).created
+      if (typeof created === "number") {
+        return new Date(created).toISOString()
+      }
+    }
+  }
+  return "Unknown time"
+}