Add changes to support the presence of ellipses

The code to scale the coordinates was not considering the case where
ellipses are present in the scene.
Merge branch 'issue_5' into light_fixes
Merge branch 'light_fixes' into issue_11
Change format_pcoa data to write ellipses data

This is a change that will only happen if ellipses data is available,
else no ellipses data will be written to the output.
Add option to perform jackknifing on the pcoa data

Test suite was updated accordingly.
Add jackknifing option to the script interface

The script interface is now capable of producing jackknifed plots, an
option to select what method you want to use for this calculation was
added as well.

The main input option, no longer takes a single file only, now it is
capable of taking a directory with multiple files in it. Several
different checks are being performed from the script interface.

This should fix #11