chore(lint): move cmd handling to lint rules

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

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

Author: tae2089

.ccg.yaml

@@ -19,9 +19,6 @@ exclude:
   - "testdata/.*"
   - ".*\\.gen\\.go$"
   - "scripts/.*"
-  - "root.go"
-  - "main.go"
-  - "cmd/.*"
 
 comment_tags:
   standard:
@@ -55,3 +52,9 @@ rules:
   - pattern: npm/.*
     category: orphan
     action: ignore
+  - pattern: "cmd/.*"
+    category: missing
+    action: ignore
+  - pattern: "cmd/.*"
+    category: unannotated
+    action: ignore