Renamed some of the files

The naming schemes I used changed over the course of development, and I wanted
to standardize them a bit before submitting a manuscript.

Signed-off-by: Ted Gibbons <ted.codes@gmail.com>
Tweaked file names, fixed a bug, and halved the pipeline

The eckPipeline.sh script no longer analyzes the set of dimensionless graphs
produced by blast2graph.py because the resulting clusterings are identical to
the dimensioned set. The dimensionless graphs are still produced, however,
because they are useful for comparative analyses.

Signed-off-by: Ted Gibbons <ted.codes@gmail.com>