Switch global option registration to the new options system.

Also fix a couple of small issues that arose while testing this.

Also switch the --graph option in list_goals to be read from the
new location, to verify that this all works together.

Note that add_global_options is still used when generating the
build dictionary, so we can't get rid of it yet. We'll do so
in a pending change.

Testing Done:
Ran ci.sh. Ran manual command lines to verify that flags still work.

Reviewed at https://rbcommons.com/s/twitter/r/1109/
Add transitive jar dependencies to depmap project info goal for intellij plugin.

Add transitive jar dependencies to depmap goal for Pants Intellij plugin

When creating projects using the plugin, the depmap showed direct dependencies for 3rdparty jar libraries.
This change add the trasitive dependency jars to the depmap output.
The transitive jars are required to correctly configure intellij modules.

Testing Done:
yes.

Added integration tests but need to verify the contents.

PR created here:
https://github.com/pantsbuild/pants/pull/626
{Coverage increased (+0.04%) when pulling 09790ec on add_transitive_jar_deps into ad7d09d on master.}

Locally tested
./pants tests/python/pants_test/tasks:depmap_integration

Reviewed at https://rbcommons.com/s/twitter/r/1047/
oh, it had tests? I guess I should fix those
Merge branch 'master' into buildsyms
checkstyle