Changed RigidBodyManipulator.bodies from std::vector<RigidBody> to std::vector<std::unique_ptr<RigidBody>> in preparation for adding a std::unique_ptr<DrakeJoint> member to RigidBody.

Conflicts:
	systems/plants/constructModelmex.cpp
Now creating DrakeJoints in constructModelMex and storing std::unique_ptrs to them in RigidBody objects.

Conflicts:
	systems/plants/constructModelmex.cpp
Now setting DrakeJoint in URDFRigidBodyManipulator as well.

Conflicts:
	systems/plants/constructModelmex.cpp
Cleanup.
Add missing include.
Make warnOnce warn once per instance.

The disabled_msgids map was being default initialized in the classdef of
WarningManager. Because containers.Map is a handle class, this means that all
WarningManager objects shared the same disabled_msgids map. So rather than
warning once per instance of a class containing a WarningManager, we were only
warning once ever. The fix is to initialize the disabled_msgids in the
constructor instead.
Update CollisionFilterGroups for removed links

The child links need to be removed from any collision filter groups they belong
to and the names of the parent links need to be updated.

Fixes #164.
Add warning for discarded CollisionFilterGroups.

If the child link in a removed joint belongs to a filter group and the parent
does not, then
  * if the parent has no contact shapes, the welded link will belong to the group
  * if the parent has contact shapes, the welded link will not belong to the
    group and the user will be warned.
Added HybridTrajectoryOptimization, with minor updates to DirectTrajectoryOptimization. Added example using this to the Compass Gait.
Added comments.
Don't add parents of removed links to all CFGs
Silence warnings in bullet_collision_zero_rad_sphere_test
Fix typo in CollisionFilterGroup.

Bad copy and paste. testCollisionFilterGroups passes on my machine now.
adds integral option to qtraj block
Merge pull request #1 from mitdrc/add-integ-to-qtraj-block

adds integral option to qtraj block
removed deprecated call
Merge pull request #2 from mitdrc/fix-num-dof-call

removed deprecated call
Updates after feedback.
Fixed compile errors on GCC (missing <memory> include and ambiguous call to isinf, see https://bugs.webkit.org/show_bug.cgi?id=59249 for info).
add name field to geom