Add doxygen to remaining repository routines.

[GeorgeGayno-NOAA]

Add basic doxygen to remaining repo routines. Doxygen would not work
with the Fortran include files in orog.fd. So I removed unused include file
resovod.h and converted machine.h to a Fortran module. Update to use
full paths for better online display.

See: https://georgegayno-noaa.github.io/UFS_UTILS/index.html

Resolved #191.

[GeorgeGayno-NOAA]

One thing I can't figure out. There are routines with the same name in multiple programs. And doxygen creates a single merged file from them. Very confusing. For an example, see model_grid (and go to bottom of page): https://georgegayno-noaa.github.io/UFS_UTILS/classmodel__grid.html

[edwardhartnett]

I don't (yet) have an answer for the problems of duplicate file names.

However, this still does not complete the issue, though this is great progress. We still need to write a mainpage which the user can use to navigate all these utilities and functions...

[GeorgeGayno-NOAA]

I don't (yet) have an answer for the problems of duplicate file names.

However, this still does not complete the issue, though this is great progress. We still need to write a mainpage which the user can use to navigate all these utilities and functions...

Do you want the mainpage as part of this PR? Is there a good example of a mainpage in one of our repos?

[edwardhartnett]

Nice!

[GeorgeGayno-NOAA]

After the merge, should I update the official 'gh-pages' branch? I think we forgot to do that after the last few merges.

[edwardhartnett]

Yes, good idea, please do update them.

The way I do that is to build the code, with --enable-docs, as usual.

Then, I clone another copy of the repo. In that clone I do:

git checkout gh-pages
git status        **<------------------------check to ensure you are on gh-pages branch!**
git rm -rf *
cp -R /other/clone/docs/* .
git add *
git commit -m "updated" -a && git push

*MAKE SURE you are on the gh-pages branch before doing git rm -rf !

On the gh-pages branch, you remove everything, then copy the new html there, then add it. You really want to be sure you are on the gh-pages branch before doing git rm -rf *. I really can't say that enough! ;-)

[GeorgeGayno-NOAA]

Yes, good idea, please do update them.

The way I do that is to build the code, with --enable-docs, as usual.

Then, I clone another copy of the repo. In that clone I do:

git checkout gh-pages
git status        **<------------------------check to ensure you are on gh-pages branch!**
git rm -rf *
cp -R /other/clone/docs/* .
git add *
git commit -m "updated" -a && git push

*MAKE SURE you are on the gh-pages branch before doing git rm -rf !

On the gh-pages branch, you remove everything, then copy the new html there, then add it. You really want to be sure you are on the gh-pages branch before doing git rm -rf *. I really can't say that enough! ;-)

Done!