Add setup-repo documentation to the index.

The documentation for the setup-repo command was included in the tree
but was not specified in the index.txt, preventing it from appearing in
the list of commands. The documentation page was reachable by URL, but
not really discoverable.
Merge branch 'release-0.5.x'
Remove duplicate --p4-* options from 'rbt diff'.

We fixed a bug with missing options twice on different branches, which meant
when we merged, we ended up with these defined twice. Trivial fix.