Documentation and reorganizing repo

[dputtick]

• Previously made a new branch called "old-version" to capture state of project before these changes.
• Delete /fs from the repo since it's no longer used (has been replaced by fs_filecheck)
• Move several utility shell scripts into /shell_utils and delete ones that are no longer relevant because they were for /fs
• Add CONTRIBUTING.md
• Edit README_setup.md for clarity and update with recent changes
• Move some notes and extra documentation into /doc in preparation for adding to the project wiki
• Update README.md to correctly describe how Circlean handles various file types