Add support for custom windows

[pashadag]

Currently, the MAKE_WIN stage runs make_masked_win to divide the genome up into windows with a given target size. We should allow the user to generate their own window files and pass them to cnfind.pl. When this option is invoked, cnfind should check that the windows are "proper" (non-overlapping, and within the bounds of the chromosome lengths defined in the companion package.