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/config/schema/experimental.ts

@@ -0,0 +1,20 @@
+import { z } from "zod"
+import { DynamicContextPruningConfigSchema } from "./dynamic-context-pruning"
+
+export const ExperimentalConfigSchema = z.object({
+  aggressive_truncation: z.boolean().optional(),
+  auto_resume: z.boolean().optional(),
+  preemptive_compaction: z.boolean().optional(),
+  /** Truncate all tool outputs, not just whitelisted tools (default: false). Tool output truncator is enabled by default - disable via disabled_hooks. */
+  truncate_all_tool_outputs: z.boolean().optional(),
+  /** Dynamic context pruning configuration */
+  dynamic_context_pruning: DynamicContextPruningConfigSchema.optional(),
+  /** Enable experimental task system for Todowrite disabler hook */
+  task_system: z.boolean().optional(),
+  /** Timeout in ms for loadAllPluginComponents during config handler init (default: 10000, min: 1000) */
+  plugin_load_timeout_ms: z.number().min(1000).optional(),
+  /** Wrap hook creation in try/catch to prevent one failing hook from crashing the plugin (default: true at call site) */
+  safe_hook_creation: z.boolean().optional(),
+})
+
+export type ExperimentalConfig = z.infer<typeof ExperimentalConfigSchema>