In the latest Buildship milestone, the build folder is no longer excluded. Any source folders inside it will compile as expected.
You can show/hide the build folder in the Project Explorer, Package Explorer and Navigator like this:
Please note, that in order to make it work you have to refresh your Gradle project.
We plan to release Buildship 1.0.10 with the fix next week. If you want to evaluate you can install the latest milestone build from the following update site: http://download.eclipse.org/buildship/updates/e45/milestones/1.0/1.0.10.v20160309-1150-m
We appreciate any feedback.