You can specify wildcard and glob patterns in digger.yml to include multiple directories into a project. A common use case for this is if you have multiple environment folders and they import from a common modules directory:
The path of include / exclude patterns is relative to the digger.yml location - NOT the project location
If you wanted to trigger plans for all modules/ folder in both dev and prod projects you would include them in the include_patterns key. Similarly you put anything which you want to ignore in the exclude_patterns key ( exclude takes precedence over includes).