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/cli/config-manager/parse-opencode-config-file.ts

@@ -0,0 +1,48 @@
+import { readFileSync, statSync } from "node:fs"
+import { parseJsonc } from "../../shared"
+import { formatErrorWithSuggestion } from "./format-error-with-suggestion"
+
+interface ParseConfigResult {
+  config: OpenCodeConfig | null
+  error?: string
+}
+
+export interface OpenCodeConfig {
+  plugin?: string[]
+  [key: string]: unknown
+}
+
+function isEmptyOrWhitespace(content: string): boolean {
+  return content.trim().length === 0
+}
+
+export function parseOpenCodeConfigFileWithError(path: string): ParseConfigResult {
+  try {
+    const stat = statSync(path)
+    if (stat.size === 0) {
+      return { config: null, error: `Config file is empty: ${path}. Delete it or add valid JSON content.` }
+    }
+
+    const content = readFileSync(path, "utf-8")
+    if (isEmptyOrWhitespace(content)) {
+      return { config: null, error: `Config file contains only whitespace: ${path}. Delete it or add valid JSON content.` }
+    }
+
+    const config = parseJsonc<OpenCodeConfig>(content)
+
+    if (config === null || config === undefined) {
+      return { config: null, error: `Config file parsed to null/undefined: ${path}. Ensure it contains valid JSON.` }
+    }
+
+    if (typeof config !== "object" || Array.isArray(config)) {
+      return {
+        config: null,
+        error: `Config file must contain a JSON object, not ${Array.isArray(config) ? "an array" : typeof config}: ${path}`,
+      }
+    }
+
+    return { config }
+  } catch (err) {
+    return { config: null, error: formatErrorWithSuggestion(err, `parse config file ${path}`) }
+  }
+}