Merge branch 'master' of https://github.com/Electrostatics/apbs-pdb2pqr

(issue #64) Finished updating the test_cases.cgf file to contain the intermediate results.

apbs/doc/ChangeLog.md

@@ -1,15 +1,22 @@
 APBS 1.4.2 CHANGELOG
 ====================
 
-These are notes for APBS version 1.4.2.
+These are notes for APBS version 1.4.2.1.
 ---------------------------------------
 
 * Binary releases may be found on
  [GitHub](https://github.com/Electrostatics/apbs-pdb2pqr/releases) and
  on [SourceForge](http://sourceforge.net/projects/apbs/files/apbs/).
 
-###New Features
-* Poisson-Boltzmann Semi-Analytical Method (PB-SAM) packaged and built with APBS
+### Changes from 1.4.2
+* Actually included PB-AM binary, examples and documentation -- note that this is Linux and OS X only!
+* Fixed Windows build so that it is not a Debug build, and ensured that no DLLs are missing
+
+### New Features
+* Poisson-Boltzmann Semi-Analytical Method (PB-AM) packaged and built with APBS
+  * the binary is called `mpe` and colocated with the apbs binary
+  * documentation is with the APBS documentation, and called PBE_Manual_V1.docx
+  * examples are located with APBS examples in a pb-am directory
 * New Geometric flow API and improvements in speed (#235)
 * Support for BinaryDX file format (#216)
 * SOR solver added for mg-auto input file option
@@ -21,8 +28,7 @@ These are notes for APBS version 1.4.2.
   * Intermetiate result testing (#64)
 * Example READMEs onverted to markdown and updated with latest results
 
-
-###Bug Fixes
+### Bug Fixes
 * OpenMPI (mg-para) functionality restored (#190)
 * Fixed parsing PQR files that contained records other than _ATOM_ and _HETATM_ (#77, #214)
 * Geometric Flow boundary indexing bug fixed
@@ -33,15 +39,15 @@ These are notes for APBS version 1.4.2.
   * Pull requests merged
 * Removed irrelevant warning messages (#378)
 
-###Notes
+### Notes
 The following packages are treated as submodules in APBS:
 * Geometric Flow has been moved to it's own [repository](https://github.com/Electrostatics/geoflow_c)
 * FETk has been [cloned](https://github.com/Electrostatics/FETK) so that we have could effect updates
 * PB-SAM lives [here](https://github.com/Electrostatics/PB-SAM)
 
 Added [chat feature](https://gitter.im/Electrostatics/help) for users.  This can also be found from the support tab on http://www.poissonboltzmann.org/.
 
-###Known Bugs
+### Known Bugs
 * Travis CI Linux builds are breaking because Geometric Flow relies on C++11 and Travis boxen have an old GCC that doth not support C++11.  This is also an issue for CentOS 5
 * BEM is temprarily disabled due to build issues
 * Geometric Flow build is currently broken on Windows using Visual Studio

apbs/doc/ReleaseNotes.md

@@ -1,6 +1,6 @@
 Dearest APBS users,
 
-We are pleased to announce the latest release of APBS 1.4.2.  The latest
+We are pleased to announce the latest release of APBS 1.4.2.1.  The latest
 version of APBS includes several notable features and bug fixes.  This
 release includes a major rewrite of the geometric flow code for
 easier modification and testing. We are also packaging the code to run