Improve build system for Sphinx

Improve build system for Sphinx

If one switches between various commits that add .rst files to the
documentation, the old ones get left in the sphinx-input/ directory in
the build tree and generate spurious warnings when building the
documentation after switching to a commit where the file no longer
exists.

Make CMake remove the obsolete files.  There are still issues if someone
removes or renames a 'gmx' subcommand, but those cases should be rarer
than reorganizing or adding to the manually maintained .rst files.

Use a more reasonable logic for REGRESSIONTEST_MD5SUM.

Change-Id: If3fcef162af1936217ee36238aa1876a110473be