Switch a bunch of migrated tasks to read option values the new way.

Note that this also allowed us to get rid of some explicit fallbacks
to the config file, as new options do this automatically, assuming
the right naming conventions.

Some configs were renamed and added to the config migration script,
to align them with these conventions.

Note that this slightly changes the semantics of one flag. Previously
--extension in MarkdownToHtml would overwrite the default values of
['.md', '.markdown']. Now it appends to those two defaults. So the
default extensions will always be processed, plus whatever is added.

Testing Done:
CI pending.

Reviewed at https://rbcommons.com/s/twitter/r/1281/
Sync of https://github.com/pantsbuild/pants/commit/ee0732a42bdd614baf0e065326f1f6872a041d3a