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/auto-update-checker/checker/pinned-version-updater.ts

@@ -0,0 +1,53 @@
+import * as fs from "node:fs"
+import { log } from "../../../shared/logger"
+import { PACKAGE_NAME } from "../constants"
+
+export function updatePinnedVersion(configPath: string, oldEntry: string, newVersion: string): boolean {
+  try {
+    const content = fs.readFileSync(configPath, "utf-8")
+    const newEntry = `${PACKAGE_NAME}@${newVersion}`
+
+    const pluginMatch = content.match(/"plugin"\s*:\s*\[/)
+    if (!pluginMatch || pluginMatch.index === undefined) {
+      log(`[auto-update-checker] No "plugin" array found in ${configPath}`)
+      return false
+    }
+
+    const startIndex = pluginMatch.index + pluginMatch[0].length
+    let bracketCount = 1
+    let endIndex = startIndex
+
+    for (let i = startIndex; i < content.length && bracketCount > 0; i++) {
+      if (content[i] === "[") bracketCount++
+      else if (content[i] === "]") bracketCount--
+      endIndex = i
+    }
+
+    const before = content.slice(0, startIndex)
+    const pluginArrayContent = content.slice(startIndex, endIndex)
+    const after = content.slice(endIndex)
+
+    const escapedOldEntry = oldEntry.replace(/[.*+?^${}()|[\]\\]/g, "\\$&")
+    const regex = new RegExp(`["']${escapedOldEntry}["']`)
+
+    if (!regex.test(pluginArrayContent)) {
+      log(`[auto-update-checker] Entry "${oldEntry}" not found in plugin array of ${configPath}`)
+      return false
+    }
+
+    const updatedPluginArray = pluginArrayContent.replace(regex, `"${newEntry}"`)
+    const updatedContent = before + updatedPluginArray + after
+
+    if (updatedContent === content) {
+      log(`[auto-update-checker] No changes made to ${configPath}`)
+      return false
+    }
+
+    fs.writeFileSync(configPath, updatedContent, "utf-8")
+    log(`[auto-update-checker] Updated ${configPath}: ${oldEntry} → ${newEntry}`)
+    return true
+  } catch (err) {
+    log(`[auto-update-checker] Failed to update config file ${configPath}:`, err)
+    return false
+  }
+}