Document how to customize the build options

I couldn't find a lot of documentation on how the CIME build works in the CIME User's Guide nor in README's or comments in the code.

From what I see the options for customization are:

1. Modify: Macros.cmake, Macros.make, or env_mach_specific.xml for your case (use --keep on case.setup to preserve your changes if you have to rerun case.setup)
2. Explicitly set any of these environment variables for the build:
USER_SLIBS
USER_CPPDEFS
USER_INCLDIR
USER_CMAKE_MODULE_PATH
USER_CMAKE_OPTS
USER_MKDEPENDS_OPTS
3. Customize the files in your ccs_config in your checkout for the given machine
4. Customize specfic file compilation by adding files to the Depends.$COMPILER file in ccs_config
5. Use your own .cime directory to customize your settings
For "1" I just filed bugs: #4971 #4972

For "2" I showed that setting $USER_SLIBS does work correctly. But, haven't tried the others.

For "3" I've of course shown this works

I haven't done anything with "4", but obviously this is working.

I haven't tried "5" for a machine that ccs_config already has a definition for.