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/cli/config-manager/opencode-config-format.ts

@@ -0,0 +1,17 @@
+import { existsSync } from "node:fs"
+import { getConfigJson, getConfigJsonc } from "./config-context"
+
+export type ConfigFormat = "json" | "jsonc" | "none"
+
+export function detectConfigFormat(): { format: ConfigFormat; path: string } {
+  const configJsonc = getConfigJsonc()
+  const configJson = getConfigJson()
+
+  if (existsSync(configJsonc)) {
+    return { format: "jsonc", path: configJsonc }
+  }
+  if (existsSync(configJson)) {
+    return { format: "json", path: configJson }
+  }
+  return { format: "none", path: configJson }
+}