The comments below are very minor and do not cause any issues with understanding the paper.

Pages 1, 7, 8, 10: (PDF only). Most of the URLs print correctly, but
the link you get on a mouse-over is often truncated if the URL wraps a
line. This may just be an issue with the PDF viewer. I don't expect
many people will follow URLs from the PDF and the html/xml versions
are fine.

Page 3 right column: There is an extraneous space in the setence
"For other tools we either modified them to omit specific data
types (Samcomp ) or produced multiple ..."

Table 3, 4, 5: (Pages 5, 6): These tables would benefit from the
a few vertical or horizontal bars separating the sections. Eg vertical
in table 3 to distinguish the SRR003177 group from the SRR007215 group,
or horizontal in tables 4 and 5 to separate the clustering of
values. See the original PDF for examples. If this is not possible
then maybe extra white space could be used as separators?

Tables 3, 4, 5: The numerical values would benefit from being right
justified in columns instead of left justified. Also I note that the
bold font is coming out larger than the non-bold ones, making
visual alignment poor, although that last point is extremely minor.

Pages 7, 8: The two groups of equations would look better if the floor
function (the large square bracket with the top horizontal portion
missing) spanned the full height of the equations (see the original
for an example). (Very minor formatting - just a nicety.)