Added outputs to Muscle. Hooked into Thelen2003Muscle and added Thelen2003Muscle to testComponents. TODO: repeat for Millard2012EquilibriumMuscle.
Merge branch 'master' of https://github.com/opensim-org/opensim-core into addOutputsToMuscles
Outputs should now be available for Millard2012EquilibriumMuscle as well. Note that Millard2012AccelerationMuscle makes testComponents kerplode ("testComponents.exe has stopped working" error on Windows). Probably not worth investigating at this time, since nobody uses the Acceleration model.
Ignoring issues with the Acceleration muscle.
Update to latest lepton from openmm.

This fixes the size_t warnings from VS2013.
Made a bunch of change to Model, adding output and replace old property construction with new property construction

clean up old convention in Model

Fix a bunch of bugs, take care of string property parsing so that it treats the whole property value as a single string in case that the property allows only one value.

clean Model a little bit
Un-duplicate comments for properties.
Fix typo

[ci skip]
Fix typo in comment.

[ci skip]
Converted output names from `CamelCase` to `lowercase_with_underscores`.
Made modifications according to comments for the PR
Merge branch 'hackathon_Justin_7_17' into hackathon_Justin
Hold onto Output's and Input's using unique_ptrs.
Remove comparisons of int to NULL.

Fixes clang warnings introduced by the use of ReferencePtr.
Fix python wrapping bug.

The _opensim target needs the source output of the PyWrap target. There was a bug in the CMakeLists that caused the _opensim target not to depend on this source output unless CMake was re-run after PyWrap was build.

Also added a fix to get python wrapping working on APPLE Mac OS X, and improved error handling.
In java wrapping: fix bug, improve error handling.

1. Avoid using GLOB for osimJavaJNI target, as the _wrap.cxx files doesn't exist until after cmake configures.
2. Set up the JavaWrap target so it doesn't build each time CMake runs; it will only build when it is out of date.
Fix mistakes in Java wrapping CMake.

Added variable for the swig-generated header file. Added back the
explicit dependency on JavaWrap.
Fix CMake syntax error.

Clean up another CMake file. Remove _wrap.h from repository.
Add comment in Java wrapping cmake.
Update CoordinateAxis with Simbody's changes.

CoordinateAxis::assertIndexIsValid is gone in Simbody, but it still existed in
our copy of it that we use for SWIG.