More thoughtful use of input and output files in tests and examples

[RobertPincus]

As noted by @skosukhin in #319 the treatment of input and output files in tests/ and examples/ is inconsistent and sometimes makes file management during testing more complicated than it needs to be.

At a minimum we should have check_variants write to a separate output file rather than directly to the input file.

• Should we do this programmatically (i.e. make a new output files with the same coordinates as the input) ormake a blank template file to copy over (any thoughts @skosukhin ?)

In general I should look over the use of files in testing and examples.