"resources", "help" and "doc" being included in jalview.jar and shadowJar twice, one copy without $$text$$ replacements

The gradle build is written to process the files in "resources", "help" and "doc" into the "classes" dir with some $$text$$ replacements and in the case of help also some indexing. This whole classes structure is included in the jalview.jar. This is how the ant build worked.

However, for buildship/eclipse reasons, the raw resources found in "resources", "help" and "doc" are also listed in sourceSets.main.resources.srcDirs.

It turns out that the in-built gradle Java plugin's "jar" task automatically includes resources.srcDirs into the jar, alongside anything found in "classes" (sourceSets.main.java.outputDir). It also does not report on conflicting files -- it simply includes both in the jalview.jar. This also follows through to the shadowJar task.

The correctly processed files appear first in the jalview.jar so hopefully are the ones being used, although this is less than certain!
If unzipping the jalview.jar with NO replacements, you get