Some of the important aspect of this change:

* Remote repos in the execution root are under output_base/execroot/repo_name, so the prefix is ../repo_name (to escape the local workspace name).
* Package roots for external repos were previously "output_base/", they are now output_base/external/repo_name (which means source artifacts always have a relative path from their repository).
* Outputs are under bazel-bin/external/repo_name/ (or similarly under genfiles). Note that this is a bit of a change from how this was implemented in the previous cl.

Fixes #1262.

RELNOTES[INC]: Previously, an external repository would be symlinked into the
execution root at execroot/local_repo/external/remote_repo. This changes it to
be at execroot/remote_repo. This may break genrules/Skylark actions that
hardcode execution root paths. If this causes breakages for you, ensure that
genrules are using $(location :target) to access files and Skylark rules are
using http://bazel.io/docs/skylark/lib/File.html's path, dirname, etc.
functions.

Roll forward of bdfd58a8.

--
MOS_MIGRATED_REVID=133606309