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AMOEBA extrapolated polarization

More acos protections in Amoeba

Remove Jenkins badges from README.md

errors.

This copies the fix for the AmoebaTorsionTorsionForce over to the other two
forces that calculate angles via the inverse cosine -- specifically the in-plane
angle force and the stretch-bend force.  The TorsionTorsion fix did not
completely solve the occasional simulation blowup, although it did make it a
*lot* less frequent (it went from happening within 5 minutes to happening ~once
per day).

Fix push of dev user and developer guide HTMLs to S3

Also build the HTML user guide in travis

Document how to turn on API docs building

Add hooks for parameterizing unmatched residues in ForceField

AmoebaTorsionTorsionForce avoids singularity in acos()

Fix testInstallation, and simplify the error handling

Fix ambiguous overloaded function in Visual Studio 2015

Python 3 does not have dict.itervalues

Really we should move to using six and importing the iterator versions of dict
methods and range/zip from there, but for now just use "values" since using a
raw list doesn't seem like it will cause memory or performance problems here.

Conflicts:
	.travis.yml

Rewrite run-ctest.py