Add proper documentation for tools/modify_input_files

[samsrabin]

What sort(s) of documentation issue is this?

• Something is missing.
• Something is (or might be) incorrect or outdated.
• Something is confusing.
• Something is broken.

What part(s) of the documentation does this concern?

• Technical Note (science and design of the model)
• User's Guide (using the model and related tools)
• Somewhere else (e.g., README file, tool help text, or code comment): There are two existing README files that should be obsoleted and deleted.
• I don't know

Describe the issue

There are two README files in tools/modify_input_files/. These should be turned into proper documentation in the User's Guide, then deleted so there's only one source of truth.

Additional context

Related:

• Review 1.3. Using CLM tools #3882
• User's Guide: Creating sparse-grid mesh and surface files #3109

[samsrabin]

@slevis-lmwg I assigned you so that you can delegate, as the CLM6 docs push coordinator.