the current explanation in github's FAQ says:

For compiled languages, if you want to limit code scanning to specific directories in your project, you must specify appropriate build steps in the workflow. The commands you need to use to exclude a directory from the build will depend on your build system. For more information, see "Configuring the CodeQL workflow for compiled languages."

however, there's no example or explanation how to actually do it.
inside codeql's runner there is an exclude configuration for java code:

$ ./codeql resolve extractor --language=java --format=betterjson
{
  "extractor_root" : "/Users/me/codeql/codeql/java",
  "extractor_options" : {
    "exclude" : {
      "title" : "A glob excluding files from analysis.",
      "description" : "A glob indicating what files to exclude from the analysis.\n",
      "type" : "string"
    }
  }
}

however, i couldn't find a way to send this configuration to codeql workflow.