rtd scans the project for a conf.py file so we cannot name it conf.py.in
unless we get rtd to run cmake before building.
The easier option is to have doc/conf.py be the file used by rtd and all
other builds use cmake to first configure it.
This also moves the doc generation completely into cmake (no more
Makefile).
To generate the docs the project needs to first be configured and then
`make doc` can be run.
The approach used is leaned on the cmake's project own use of Sphinx:
Utilities/Sphinx/CMakeLists.txt
This allows us to also have the manual as part of the generated html
documentation.
The syntax is also easier to use.
Right now the man page installed on the system is not replaced with the
rst file, this will come in a later step
Patrick Ziegler