Skip volatile directories when copying the repository into a test scratch dir

[AdzerKI]

Problem

AnnotatorBaseCoreTest.setup copies the whole repository into the test's scratch dir:

FileUtils.copyDirectory(repositoryDirectory.toFile(), outDirPath.resolve("Annotator").toFile());

That walk includes build/, .gradle/ and .git/, which the outer Gradle build keeps writing into while the tests run, and four test forks walk them at once. When a file disappears between list() and opening it the copy throws and the test dies before it starts:

DeepTest > paramPassTest FAILED
    java.lang.RuntimeException at AnnotatorBaseCoreTest.java:88
        Caused by: java.io.FileNotFoundException at FileUtils.java:2719

It is a race, so it lands on whichever tests happen to be running: build-without-cache took DeepTest, AnalysisModeTest and CoreTest on one run of #279, and build-with-gradle-build-action-cache failed the same way on master at 63074f6.

Changes

The copy skips build, .git and .gradle. The copy exists to run ./gradlew library-model-loader:jar --rerun-tasks against the sources, which rebuilds what it needs, so none of the three is read from it. It also stops copying the build outputs of the whole repository into a temp dir once per test.

Verification

DeepTest.paramPassTest, CoreTest.multipleReturnNullable, AnalysisModeTest and Java21Test green on JDK 21; spotlessCheck clean.

[AdzerKI]

Correction on my own claim above: the copy filter alone does not stop the failure. The run on this branch still lost CoreTest > multipleReturnNullable to the same FileNotFoundException, so at least one source of the copy still changes under it, and it is not build, .git or .gradle.

What the filter does do is worth keeping on its own: it stops copying the build outputs and the VCS metadata of the whole repository into a scratch dir 59 times, once per test, for a copy that only feeds ./gradlew library-model-loader:jar --rerun-tasks.

To find the rest I added a second commit to this branch: Archive test report now runs on failure too, and its path points at where Gradle actually writes the reports. Today it is build/reports/tests/test — the root project, which has no test task — so the artifact has been empty on every green run and absent on every red one. With the reports and the XML results collected per subproject, the next occurrence names the file that vanished instead of just the exception type.

I did not reproduce it locally: the whole annotator-core suite is green here both serially and with four forks (JDK 17, 59 tests).