This is already encapsulated in:
and, to different extent, in:
… but I cannot comment on this there. This is indeed the problem. It is preventing us from moving to Buildship at this time (and we would very much like to move to it). There seem to be more issues surrounding this kind of behaviour…
We absolutely have to separate the command-line Gradle build from the Eclipse one. Builds are very different, with different levels of debug info in code and compilation style that affects optimizations and ability to debug / put breakpoints and step through code and to perform incremental compilation, for example. Note that languages other than Java are used as well - in our case Scala, for example.
I have yet to confirm whether this is Buildship only or related to something we do “less appropriately” but (command line) test output folders are being added to (main, not test) Eclipse project classpaths. There are multiple issues with this. (a) This is a command-line variant, not an Eclipse one, (b) tests should not be in the main classpath (but you may handle that differently) and ©, this may need to be a project reference, not a folder one, depending on how Buildship does tests (Eclipse wants separate projects to be clean).