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/skills.ts

@@ -0,0 +1,45 @@
+import { z } from "zod"
+
+export const SkillSourceSchema = z.union([
+  z.string(),
+  z.object({
+    path: z.string(),
+    recursive: z.boolean().optional(),
+    glob: z.string().optional(),
+  }),
+])
+
+export const SkillDefinitionSchema = z.object({
+  description: z.string().optional(),
+  template: z.string().optional(),
+  from: z.string().optional(),
+  model: z.string().optional(),
+  agent: z.string().optional(),
+  subtask: z.boolean().optional(),
+  "argument-hint": z.string().optional(),
+  license: z.string().optional(),
+  compatibility: z.string().optional(),
+  metadata: z.record(z.string(), z.unknown()).optional(),
+  "allowed-tools": z.array(z.string()).optional(),
+  disable: z.boolean().optional(),
+})
+
+export const SkillEntrySchema = z.union([z.boolean(), SkillDefinitionSchema])
+
+export const SkillsConfigSchema = z.union([
+  z.array(z.string()),
+  z
+    .record(z.string(), SkillEntrySchema)
+    .and(
+      z
+        .object({
+          sources: z.array(SkillSourceSchema).optional(),
+          enable: z.array(z.string()).optional(),
+          disable: z.array(z.string()).optional(),
+        })
+        .partial()
+    ),
+])
+
+export type SkillsConfig = z.infer<typeof SkillsConfigSchema>
+export type SkillDefinition = z.infer<typeof SkillDefinitionSchema>