Add passthru arg support in the new options system.

Anything after a double-dash is captured as-is. Future changes will
plumb them through to tasks that want them.

This is useful e.g., for passing args through to a tool invoked by a task.

Testing Done:
Ran option tests. CI passed.

Reviewed at https://rbcommons.com/s/twitter/r/1270/
Refactor protobuf parsing logic out of protobuf_gen

This is in preparation of adding support for the Wire generator which also uses .proto files as sources.

Testing Done:
CI is green: https://travis-ci.org/pantsbuild/pants/builds/39766434

Bugs closed: 762

Reviewed at https://rbcommons.com/s/twitter/r/1273/
Correctly parse named_is_latest entries from the pushdb

The named_is_latest entry was being implicitly str()d on the way into the database, but was defaulting to a boolean on the way out. Strings are "truthy", so the "False" string would be treated as true.

Reviewed at https://rbcommons.com/s/twitter/r/1245/
Migrate jar_publish to new options.

Testing Done:
CI passed. Ran jar_publish's unit and integration tests. The integration tests exercise most of the flags.

It's a bit hard to test manually because parts of jar_publish are broken for other reasons. But we're pretty confident about migration changes at this point.

Reviewed at https://rbcommons.com/s/twitter/r/1276/
Migrate dependencies, depmap, detect_duplicates and check_published_deps to new options

Testing Done:
https://travis-ci.org/pantsbuild/pants/builds/39655628

Reviewed at https://rbcommons.com/s/twitter/r/1269/
Deeper selection of internal targets during publishing

The current behavior of selecting directly declared Jarable targets broke ages ago during Patrick's target refactor. In order to appropriately walk through intermediate jar_library/target declarations, we need to recurse.

It's common practice internally to have a top-level alias (a 'target' declaration) to point deeper into the directory structure to an actual java_library or scala_library. This meant that publishing was 1) ignoring those deps during fingerprint calculation and 2) not including them via DependencyWriter in written poms.

Testing Done:
test publishes; will follow up to add unit tests here if things look sane.

Reviewed at https://rbcommons.com/s/twitter/r/1213/
Add Task.workdir docs.

Testing Done:
CI went green here: https://travis-ci.org/pantsbuild/pants/builds/39909933

Bugs closed: 766

Reviewed at https://rbcommons.com/s/twitter/r/1277/
Fix DetectDuplicate's handling of an 'append'-type flag.

Testing Done:
Ran the broken tests, verified that they succeed with this change.

Reviewed at https://rbcommons.com/s/twitter/r/1282/