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Housekeeping: Added deprecation warning for sourceSets.outpu.classes -> Fixed the human description of the SourceSet's output.

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Moved the classesDir and resourcesDir properties to the so that it is clearer

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- Fixed case where duplicate source directories were added to eclipse project when the java source directory was also configured as a resource directory. - Changed SourceSet.allJava, allGroovy, allScala and allSource to return a SourceDirectorySet instead of a generic FileTree. Removed code from ide plugins which reached into the implementation types for these properties, and use the api instead. This will later allow us to have per-directory include/excludes, and allow arbitrary file collections to be added to source sets.

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Renamed subprojects/gradle-(.+) to subprojects/$1

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