Fix source deps bug in dependency analysis.

- Not all dependencies were getting computed correctly, because the source_deps section
 of the analysis relations file wasn't getting used. (It was removed because it appeared
 to be redundant, and caused some trouble with error message generation.) This reinstates
 source_deps in the analysis.

Auditors: benjy
Make missing dep errors actual errors.

Remove some commented-out code that wouldn't even work
any more if it were uncommented.

Auditors: markcc
Merge branch 'master' into new_reporting
WIP
Revert "Make missing dep errors actual errors."

This reverts commit b5f47ae1cc4b5889b8a50bfd767e7848cca275f4.
Fix scala artifact merging bug.
Dependency analysis fixes.

- Add a filter parameter for eliminating missing dependency errors that
  shouldn't be reported.
- Only return missing dependency errors if they were reported to the user.
- Throw exception when missing deps are detected.
- Eliminate redundant retrievals of parameters.

Auditors:  benjy
Address review comments.
Merge branch 'source-deps-fix'
Merge remote-tracking branch 'origin/master' into new_reporting

Conflicts:
	src/python/twitter/pants/tasks/jvm_dependency_cache.py
	src/python/twitter/pants/tasks/scala/zinc_artifact.py
Merge branch 'master' into new_reporting

Conflicts:
	src/python/twitter/pants/tasks/jvm_dependency_cache.py
WIP