Change defaults to support ZAP.
Remove some cruft.
Cleaned up geoflow test case.
The percent error computation was broken, and producing negative values
which passed because they were below the threshold.
Removing standalone directory.  It's still in the finish-geoflow branch.
Updated log
Remove silly code that required a MALOC hack-patch and replace it with something that does not.
Minor readme tweak.
Fix psize to better check for errors.
Improved missing backbone error message.
Update README.md
Update README.md
The GCC compiler complains about (and rightly so, IMO) size_t not
being defined.  Clang and the Intel compiler don't say anything, which
is how the problem snuck in at all.
Valist_readPQR maintenance.

* Cleaned up a bit by removing some unused variables
* Removed unnecessary code at the end of the main loop that reads
lines from the PQR file.
The ion radius was 6.00 and should be 3.00.
Update copyright date in the source code.
Improve .gitignore a tad.
Update copyright in files that are involved in generating other files.

Rampant out of control file generation.  We need some Lynx!
Updated results from testing with the 1.4.1-binary release.
Added the icons that Minju Chun provided for us.  Yay Minju!