If graphs output is set to a custom directory, like $rootDir/graphs, then the files for each sub-module are supposed to be put into relative paths from that root directory, like:

./graphs/lib-1/main.dot
./graphs/lib-1/test.dot
./graphs/lib-2/api/main.dot
./graphs/lib-2/api/test.dot
./graphs/lib-2/impl/main.dot
./graphs/lib-2/impl/test.dot

Instead, we get this thing:

./graphs/build/reports/modulecheck/graphs/main.dot
./graphs/build/reports/modulecheck/graphs/test.dot
./graphs/build/reports/modulecheck/graphs/testFixtures.dot

There are two problems:

1. Every module has the same relative output path (build/reports/modulecheck/graphs/<source set>.dot), so they all just overwrite each other.
2. The parent directories build/reports/modulecheck/graphs should not be there. This is especially bad because the inclusion of /build/ means that the report will be automatically ignored by many .gitignore files.