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Changed JavaBasePlugin to create compile and process resources tasks using the legacy types rather than the software model type. This allows the software types to be created later (ie as rules require them).

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Some unit test coverage for handling of task dependencies for various FileCollection implementations.

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Some cleanup of native services initialization in unit tests

+review REVIEW-5378

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rewordings and test fixes related to improving string representation for source sets

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added method SourceSet.getJarTaskName()

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- Changed JavaBasePlugin to add a compile and runtime configuration for each source set. - Changed DependencyHandler so that a configuration can be used as the right-hand side of a dependency declaration. Simply a shortcut for extendsFrom(), but keeps all the dependencies grouped in one place. - Reworked some samples to simplify.

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Fixed deprecation warnings related to sourceSet.classes -> sourceSet.output in the remaining files

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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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