Code cleanup

[rdaly525]

• [ ] Apply .clang-format to all files
• [ ] Replace all headers with #pragma once
• [ ] (tentative) Move Simulator into separate repo
• [ ] Update build-system
  • [ ] Use external projects directly
  • [ ] catch.hpp
  • [ ] json.hpp
  • [ ] Dillon's bitvector code
• [ ] Write style guide for CoreIR
• [ ] Organize Issues
• [ ] Reorganize tests
  • [ ] move outputs to build directory
  • [ ] move golds to gold/ directory
  • [ ] cleanup .gitignore to ignore build dirs

[rsetaluri]

I am beginning this process. I hope to have something to show for this by end of summer. And all of what you mentioned above should be included.