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/atlas-hook.ts

@@ -0,0 +1,25 @@
+import type { PluginInput } from "@opencode-ai/plugin"
+import { createAtlasEventHandler } from "./event-handler"
+import { createToolExecuteAfterHandler } from "./tool-execute-after"
+import { createToolExecuteBeforeHandler } from "./tool-execute-before"
+import type { AtlasHookOptions, SessionState } from "./types"
+
+export function createAtlasHook(ctx: PluginInput, options?: AtlasHookOptions) {
+  const sessions = new Map<string, SessionState>()
+  const pendingFilePaths = new Map<string, string>()
+
+  function getState(sessionID: string): SessionState {
+    let state = sessions.get(sessionID)
+    if (!state) {
+      state = { promptFailureCount: 0 }
+      sessions.set(sessionID, state)
+    }
+    return state
+  }
+
+  return {
+    handler: createAtlasEventHandler({ ctx, options, sessions, getState }),
+    "tool.execute.before": createToolExecuteBeforeHandler({ pendingFilePaths }),
+    "tool.execute.after": createToolExecuteAfterHandler({ ctx, pendingFilePaths }),
+  }
+}