refactor: update plugin handlers and shared utils

Minor updates to config handler, plugin detector, index entry, and builtin command templates.

Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-opencode)

Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>

src/features/builtin-commands/templates/init-deep.ts

@@ -275,8 +275,8 @@ For each generated file:
 Mode: {update | create-new}
 
 Files:
-  ✓ ./AGENTS.md (root, {N} lines)
-  ✓ ./src/hooks/AGENTS.md ({N} lines)
+  [OK] ./AGENTS.md (root, {N} lines)
+  [OK] ./src/hooks/AGENTS.md ({N} lines)
 
 Dirs Analyzed: {N}
 AGENTS.md Created: {N}