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Convert groovy samples to lazy tasks API

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Sample projects should provide root project name as best practice (#3730)

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Remove usage of --no-search-upwards and deprecate

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Use separate output directories for all JVM languages

- Introduce an outputDir on SourceDirectorySet

- Default output directory is now `build/classes/<source directory set name>/<source set name>`

- Example: Java compilation goes to build/classes/java/main instead of build/classes/main

- Adapt JDepend, FindBugs, Test and ValidateTaskProperties tasks to handle multiple class directories

- Deprecate setClassesDir/getClassesDir on SourceSetOutput

- Calling setClassesDir restores old behavior (shared output directory)

- Introduce addClassesDir and getClassesDirs on SourceSetOutput

- OSGi plugin needs a single classes directory, so introduce 'osgiClasses' task that syncs all classes to a single directory

Most of the changes to integration tests are find classes in their new location. Helper methods in AbstractIntegrationSpec

can locate class files vs hardcoding a path.

Squashed commit of sg-split-jvm-classes branch for REVIEW-6502

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Upgrade Apache Commons Collections to v3.2.2

Version 3.2.1 has a CVSS 10.0 vulnerability. That's the worst kind of

vulnerability that exists. By merely existing on the classpath, this

library causes the Java serialization parser for the entire JVM process

to go from being a state machine to a turing machine. A turing machine

with an exec() function!




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Use Junit 4.12 in samples

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More IDE friendly sample.

Make integrationTest task exposed as public in ToolingAPI.

update default library versions used in tests and samples

- JUnit -> 4.11

- Groovy -> 2.0.5

- Scala -> 2.9.2

- use short instead of long dependency notation

- eliminate usage of `scalaTools` configuration

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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 the deprecation warnings in our own build. Deprecated sourceSet.xxx.classesDir in favor of sourceSet.xxx.output.classesDir (still pending fixing deprecation in the code itself).

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Updated to JUnit 4.8.2, TestNG 5.14.10, asm 3.3.1, commons-lang 2.6

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

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