docs: Remove targets of the form dir/BUILD:target which cause errors

ValueError: Spec tests/java/com/pants/examples/hello/greet/BUILD:greet
has BUILD as the last path part and BUILD is reserved files

Reviewed at https://rbcommons.com/s/twitter/r/853/
Migrate some reasonable default values from pants.ini into 'defaults' in the pants source.  This covers scala-compile, jvm-compile, protobuf-gen, and a few others.

Testing Done:
CI is baking at: https://travis-ci.org/pantsbuild/pants/builds/32014416

Bugs closed: 455, 456, 458

Reviewed at https://rbcommons.com/s/twitter/r/852/
Miscellaneous fixes to protobuf codegen.

Sorted protobuf paths and resources, and handled collisions deterministically. This process generates
copious warning/error log output where appropriate, as protobuf collisions are something the user should
definitely be aware of.

The imports property of java_protobuf_library was changed slightly to not cache its list of jars if it doesn't
manage to resolve one of its targets. This solves a problem where it incorrectly saves an empty list if it's
poked before the build graph loads.

Modified the log outputs of ivy imports to be more accurate/helpful.

Reduced occurance of extraneous/incorrect 'unconsumed gen targets' warning (it still happens, not as much).