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/dynamic-context-pruning.ts

@@ -0,0 +1,55 @@
+import { z } from "zod"
+
+export const DynamicContextPruningConfigSchema = z.object({
+  /** Enable dynamic context pruning (default: false) */
+  enabled: z.boolean().default(false),
+  /** Notification level: off, minimal, or detailed (default: detailed) */
+  notification: z.enum(["off", "minimal", "detailed"]).default("detailed"),
+  /** Turn protection - prevent pruning recent tool outputs */
+  turn_protection: z
+    .object({
+      enabled: z.boolean().default(true),
+      turns: z.number().min(1).max(10).default(3),
+    })
+    .optional(),
+  /** Tools that should never be pruned */
+  protected_tools: z.array(z.string()).default([
+    "task",
+    "todowrite",
+    "todoread",
+    "lsp_rename",
+    "session_read",
+    "session_write",
+    "session_search",
+  ]),
+  /** Pruning strategies configuration */
+  strategies: z
+    .object({
+      /** Remove duplicate tool calls (same tool + same args) */
+      deduplication: z
+        .object({
+          enabled: z.boolean().default(true),
+        })
+        .optional(),
+      /** Prune write inputs when file subsequently read */
+      supersede_writes: z
+        .object({
+          enabled: z.boolean().default(true),
+          /** Aggressive mode: prune any write if ANY subsequent read */
+          aggressive: z.boolean().default(false),
+        })
+        .optional(),
+      /** Prune errored tool inputs after N turns */
+      purge_errors: z
+        .object({
+          enabled: z.boolean().default(true),
+          turns: z.number().min(1).max(20).default(5),
+        })
+        .optional(),
+    })
+    .optional(),
+})
+
+export type DynamicContextPruningConfig = z.infer<
+  typeof DynamicContextPruningConfigSchema
+>