organize scripts

[c-dilks]

Some are at the top level, others are in scripts. Some scripts are only meant to be called by another script.

• leave build_*.sh and check_*.sh at the top level, since they are for general maintenance
• top level should also have simulate.py and reconstruct.sh
• all other scripts go to the scripts/ directory; it would be nice to categorize them but some scripts may fit in multiple categories
• put any scripts which are meant to be called only by other scripts in scripts/src
• consider moving ruby/ to scripts/src/