Why is it that when CodeQL generates a database, some source code is not analyzed?

When I add the CodeQL-generated source code analysis database (referred to as "jeecgdb source archive") to the workspace in VS Code for viewing, I notice that some source code files are missing in the generated database structure. What could be the reason for this situation?

The missing file is：/Users/fqy/Desktop/CodeAudit/JAVA/jeecg-boot-3.5.0/jeecg-module-system/jeecg-system-biz/src/main/java/org/jeecg/modules/api/controller/SystemApiController.java，In the generated database file, none of the files under the "api" directory have been included.

Start by examining the CodeQL-generated database in the VS Code workspace and compare its structure with the Java project path ending in jeecg-system-biz/src/main/java/org/jeecg/modules/api/controller/SystemApiController.java. Check why files under the api directory are absent; done means identifying and documenting the cause of the incomplete database.

Written by the indexing model from the issue text.