Separate them, clarify their differences. Also, fix some links which weren't being properly populated.
Depends on: https://github.com/matrix-org/matrix-doc/pull/212 https://github.com/matrix-org/matrix-doc/pull/208 https://github.com/matrix-org/matrix-doc/pull/207 for the actual rendered output to not throw javascript errors at runtime.
As a side effect, I got rid of all of the horrible symlinks and just put in all of the proper relative paths. Because the horrible symlinks were horrible.