Removed printing the source file in most debug prints

All of the recurring debug prints now don't print the source file.
Added FIXME line as a reminder
Removing the source bounds check. May not be correct solution

I remember adding it for a reason, but it may have just been while
debugging something unrelated. I'll check the logs for why it was
changed.
Removed FIXME. If the problem resurfaces it will be looked into more
Organized example files; tracking Makefile, .gitignore, examples