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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/

  1. … 54 more files in changeset.
set target runtime explicitly in eclipse classpath

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

+review REVIEW-5723

  1. … 16 more files in changeset.
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

  1. … 23 more files in changeset.
GRADLE-1422: do not add test* configuration dependencies by default

Removed the type directory from the artifact filestore layout.

  1. … 12 more files in changeset.
Fix integration test for new cache path

  1. … 12 more files in changeset.
Update IDE integration tests for new cache layout

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Integration test fixes for new cache location and layout.

  1. … 13 more files in changeset.
Meaty check-in :/ Updated the package names to be consistent with the convention we have. Updated docs accordingly.

  1. … 393 more files in changeset.