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Add source set information to dependencies in Eclipse model

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Back-port wtp classpath attribute calculation to Gradle core

This commit unifies how the Tooling API and the eclipse-wtp plugin defines

deployment classpath attributes for Eclipse project classpath entries.

The commit aims to fix GRADLE-2123, but also introduces a breaking

change because it changes the content of the Eclipse descriptors generated

by the eclipse and eclipse-wtp plugin. For more elaborate explanation check

out https://github.com/gradle/buildship/issues/7.

As a side-effect the Tooling API now considers the manipulations done

in eclipse.project.beforeMerged and eclipse.project.whenMerged closures.

+review REVIEW-6015

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Fix some oversites from the commons-collections 3.2.2 update.

+review REVIEW-5870

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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!

https://web.nvd.nist.gov/view/vuln/detail?vulnId=CVE-2015-8103

https://commons.apache.org/proper/commons-collections/security-reports.html

http://foxglovesecurity.com/2015/11/06/what-do-weblogic-websphere-jboss-jenkins-opennms-and-your-application-have-in-common-this-vulnerability/

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set target runtime explicitly in eclipse classpath

- introduce eclipse.jdt.javaRuntimeName to tweak runtime name and allow overwriting of computed default

+review REVIEW-5723

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change ide classpath mapping

- all transitive repository deps are mapped as direct dependencies

- all (transitive) project dependencies are mapped as direct project dependencies

- deprecated EclipseClasspath.noExportConfigurations

- deprecated AbstractLibrary.declaredConfigurationName and ProjectDependency.declaredConfigurationName

- TODO

- add all transitive file only dependencies

- fix temporally ignored IdeaIntegrationTest / IdeaMultiModuleIntegrationTest

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GRADLE-1422: do not add test* configuration dependencies by default

Removed the type directory from the artifact filestore layout.

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Fix integration test for new cache path

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Update IDE integration tests for new cache layout

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Integration test fixes for new cache location and layout.

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Meaty check-in :/ Updated the package names to be consistent with the convention we have. Updated docs accordingly.

  1. … 393 more files in changeset.