Update README.md
Update README.md
Added --resume option, output respects --verbose, cleaned up interface, added PKA specific exception.
Added DEBUG option to compile scripts.
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.
Merge branch 'monson-dev' of https://github.com/Electrostatics/apbs-pdb2pqr into monson-dev
Added the icons that Minju Chun provided for us.  Yay Minju!
Fixed typo and crash while running extentions with --clean in some cases.
Minor code cleanup.
Fixed handling of unrecognized residues.
Fixed executable name in spec file.
Added first Henderson Hasselbalch detection unit test
Merge branch 'monson-dev' of https://github.com/Electrostatics/apbs-pdb2pqr into monson-dev
Fixed flipped acid/base in Henderson-Hansselbalch detection.