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/todo-continuation-enforcer/index.ts

@@ -0,0 +1,58 @@
+import type { PluginInput } from "@opencode-ai/plugin"
+
+import { log } from "../../shared/logger"
+
+import { DEFAULT_SKIP_AGENTS, HOOK_NAME } from "./constants"
+import { createTodoContinuationHandler } from "./handler"
+import { createSessionStateStore } from "./session-state"
+import type { TodoContinuationEnforcer, TodoContinuationEnforcerOptions } from "./types"
+
+export type { TodoContinuationEnforcer, TodoContinuationEnforcerOptions } from "./types"
+
+export function createTodoContinuationEnforcer(
+  ctx: PluginInput,
+  options: TodoContinuationEnforcerOptions = {}
+): TodoContinuationEnforcer {
+  const {
+    backgroundManager,
+    skipAgents = DEFAULT_SKIP_AGENTS,
+    isContinuationStopped,
+  } = options
+
+  const sessionStateStore = createSessionStateStore()
+
+  const markRecovering = (sessionID: string): void => {
+    const state = sessionStateStore.getState(sessionID)
+    state.isRecovering = true
+    sessionStateStore.cancelCountdown(sessionID)
+    log(`[${HOOK_NAME}] Session marked as recovering`, { sessionID })
+  }
+
+  const markRecoveryComplete = (sessionID: string): void => {
+    const state = sessionStateStore.getExistingState(sessionID)
+    if (state) {
+      state.isRecovering = false
+      log(`[${HOOK_NAME}] Session recovery complete`, { sessionID })
+    }
+  }
+
+  const handler = createTodoContinuationHandler({
+    ctx,
+    sessionStateStore,
+    backgroundManager,
+    skipAgents,
+    isContinuationStopped,
+  })
+
+  const cancelAllCountdowns = (): void => {
+    sessionStateStore.cancelAllCountdowns()
+    log(`[${HOOK_NAME}] All countdowns cancelled`)
+  }
+
+  return {
+    handler,
+    markRecovering,
+    markRecoveryComplete,
+    cancelAllCountdowns,
+  }
+}