Yes, absolutely. You can have multiple files in different folders uploaded to the same project.
You can include files by their exact path or by using standard path wildcards ? (single character), * (anything except path separator), ** (anything including path separators).
You can control files you want to upload with exclusion rules and conditions.
Example:
"upload": {
"type": "json",
"files": "modules/**/en.json"
}
}
The above configuration will scan for files named en.json in all subfolders of the modules folder.