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To start with, using

subprojects { ... }

(as well as

allprojects { ... }

,

project(...) { ... }

and similar) is highly discouraged and bad practice as it immediately introduces project coupling, disturbs more sophisticated Gradle features, and reduces clarity and maintainability. Instead you should use convention plugins in

buildSrc

or an included build, for example implemented as precompiled script plugin. Regarding the actual problem, if you configure for

configDirectory

the root directory, that is extremely bad, as then the whole directory tree becomes input files for the checkstyle tasks which has very bad consequences, including those warnings you get and the suggestions in those warnings are actually non-sense symptom treatment instead of fixing the root cause. So if you want to set

configDirectory

, make sure this is a dedicated directory like

config/checkstyle

that only has the Checkstyle configuration as content and nothing else. Otherwise, do not set the

configDirectory

, but only the

configFile

. To configure the suppressions file, you probably need to use some variable like in your "first" branch and set the property from the build script.

Thanks.