Allow for configuring the deletion of the project directory in cleanup of ProjectSpec

* Needed this functionality for a different project.
* Also fixed a compilation issue on `ClasspathAddingInitScriptBuilder` (missing closing parenthesis). When running the whole test suite, there are some other failures related to the creation of the init script. These ones I didn't fix. Let me know if I should have a look at it.
Just checked. It also fails on the command line with Gradle. The line was changed three days ago.