I ran into this problem when using ProjectBuilder in a unit test for a gradle plugin task and found this issue when searching for similar issues before reporting it. It was not clear (at least to me) how to "specify an explicit temporary directory", but some trial and error resulted in this, which at least performs the expected cleanup in Spock&JUnit:

    @Rule
    public TemporaryFolder folder = new TemporaryFolder();

    def setup() {
        ProjectBuilder builder = ProjectBuilder.builder()
        Project project = builder.withProjectDir(folder.newFolder()).build()
        //Project project = builder.build() --> this was the old code
        ....
    }

Without that cleanup, one temp folder with some minor content was left behind for every test method defined in the specification/testcase.

As announced on the Gradle blog we are planning to completely migrate issues from JIRA to GitHub.

We intend to prioritize issues that are actionable and impactful while working more closely with the community. Many of our JIRA issues are inactionable or irrelevant. We would like to request your help to ensure we can appropriately prioritize JIRA issues you’ve contributed to.

Please confirm that you still advocate for your JIRA issue before December 10th, 2016 by:

• Checking that your issues contain requisite context, impact, behaviors, and examples as described in our published guidelines.
• Leave a comment on the JIRA issue or open a new GitHub issue confirming that the above is complete.

We look forward to collaborating with you more closely on GitHub. Thank you for your contribution to Gradle!

Thanks again for reporting this issue. We haven't heard back from you after our inquiry from November 15th. We are closing this issue now. Please create an issue on GitHub if you still feel passionate about getting it resolved.