Add an HtmlDependencyReportTask task
- implements (hopefully) the ideas detailed in http://forums.gradle.org/gradle/topics/add_an_html_dependency_report
- generates a report for the current project, or for a set of projects
- combines the dependency report features with the dependency insight features
Add entries in the docs for the HtmlDependencyReportTask
Fix bug in HTML dependency report generation
- insight dependencies were matched with a "contains" spec instead of an "equals" spec
GRADLE-2886 fix placement of jar manifest when generating war and ear files
Only apply source directory conventions as a default

- If a srcDir is explicitly configured, don't apply the source convention
Minor improvement to sample to avoid linking unused source set to binary
Test that custom layout replaces conventional default source locations
More test coverage for native binaries plugins
Improved HelloWorldApps and generic language tests

- Tests no longer apply plugins for unused languages
- Tests no longer configure the cppCompiler when cpp isn't used (and same for c)
NativeBinary.getLibs() is now responsible for including libs from source sets
Keep source set library dependencies separate when compiling

- dependencies added to one DependentSourceSet are no longer available when
  compiling another source set
Remove unused compiler arg
Report the searched locations when Visual Studio or the Windows SDK cannot be located
Tidied up a couple of TODOs
fix test on windows
GRADLE-2906/GRADLE-2900: Different handling for directories.
Some changes on build init types based on REVIEW-3243
- start composing different init descriptors
- seperate init ids from descriptors
- move file generation into seperate util class for better testing
Fixed broken link in user guide to Maven reference.
Attempt to fix C++ integ test on windows

- Ensure stream content is flushed for library
Removed the type directory from the artifact filestore layout.