Fixed bug in app where 'useDispersionCorrection' for AMOEBA was being cast to int instead of bool.
Added AMOEBA test system and tests for ForceField fin setting up AMOEBA system.
Fixes to tests.
XmlSerializer generates XML directly rather than going through TinyXml
Merge pull request #484 from peastman/xml

XmlSerializer generates XML directly rather than going through TinyXml
Fix Clang warning about unhandled enum values.

Clang had been generating the following warning:

```
ParsedExpression.cpp:123:13:
warning:
      30 enumeration values not handled in switch: 'CONSTANT', 'VARIABLE',
      'CUSTOM'...
            [-Wswitch]
                switch (node.getOperation().getId()) {
                                ^
                                1 warning generated.
```

To get rid of this warning, I added a default case, which does nothing.
In travis, use multiple cores.

Travis VM's have up through 2 cores. Passing a -j2 flag should make/ctest the builds/tests faster.
Merge pull request #486 from chrisdembia/travis-parallel-build

In travis, use multiple cores.
Merge pull request #485 from chrisdembia/fix-parsed-expression-warning

Fix Clang warning about unhandled enum values.
Merge remote-tracking branch 'upstream/master'
Committed updated Makefile and doxyfile.  (These don't need to be in here.)
Fixed examples/Makefile.
Reverted Doxyfile to upstream master.
Removed 'void' declarations from getCutoff/getCutoffDistance methods so that swigInputBuilder.py would correctly wrap return values.
Changed cutoff test for AmoebaVdwForce/AmoebaMultipoleForce.
Added dispersion correction flag handling to NonbondedGenerator.
Merge pull request #491 from jchodera/fix-amoeba

Fix error in setting up AMOEBA systems when useDispersionCorrection is specified (retry)
Fixed a rare memory corruption error when roundoff causes tile indices to be wrong
Fixed some test failures
Merge pull request #495 from peastman/unsigned

Fixed a rare memory corruption error when roundoff causes tile indices to be wrong