Presently when using a filter type of dir, the integration will read all files within that directory and all files within sub-directories. It will not ignore the files in the sub-directories. Therefore you have three options:
a. In github move the sub-directories that you don’t want read by the integration into another location.
b. In the Github configuration, use the filter type of file and specify each file individually.
c. Use our classic Github integration which uses the CLI client as described here.