Adjustments to the beautifier to make it run on the Foldit branch

[roccomoretti]

Assorted adjustments to the beautifier to allow it to work properly on the Foldit branch.

• Fix handling of R"(....)" style strings
• Add support for brace-initialized variables at file scope.
• Add option for better debugging output for beautify_specific_files.py
• Add Foldit-specific Macros to the known macro list
• Add an exclusion list of files not to beautify (e.g. external files)

These allow the beautifier to run cleanly on the Foldit branch

These changes still work on master, and cause no formatting changes. They could potentially be included in whole or in part (if there's certain changes which are counter-indicated for master, we can still keep them in a foldit-specific branch.)

[roccomoretti]

@aleaverfay Do you see issues with merging this (in whole or in part) to the master branch of Rosetta?

[aleaverfay]

Please do!