Change certain core configs into registered options.

These are options like pants_workdir, whose values can be interpolated
into pants.ini to create values for other options. So we treat them
specially: We refer to them as "bootstrap options" and we determine their
values in an early pass before getting the values for all the other options.

This allows, e.g., overriding --pants-workdir on the cmd line, like any other
option, but still having %(pants_workdir)s interpolations in config files
work as expected.

Testing Done:
CI passed.

Reviewed at https://rbcommons.com/s/twitter/r/1373/
Minor docs fix: ./pants.d -> .pants.d

Fix path in the http://pantsbuild.github.io/tshoot.html page: ./pants.d  -> .pants.d

Testing Done:
./build-support/bin/publish_docs.sh -d tmp -o; verified the fix.

Reviewed at https://rbcommons.com/s/twitter/r/1387/
Sync of https://github.com/pantsbuild/pants/commit/4f36df6475691dc847da2587110656b453ddff11