Fix alignment problems in Skel and SDF parsers
Exemplary clean-up of one function in Geometry.cpp
Clean-up of geometric functions in Geometry.cpp
Make Joint::updateTransform() and Joint::updateVelocity() protected

Body node automatically calls these functions when necessary.

TODO: Make Joint::updateAcceleration() protected too.
Merge branch 'master' of github.com:dartsim/dart
Fix compiler error in GCC caused by 11aad6bd4975848e1306984c962ed910b1589e9b
Remove undefined joint and shape types. Remove P_ prefix from shape types for consistency.
Fix unit tests after commit 11aad6bd4975848e1306984c962ed910b1589e9b broke them
Clean-up Joint:
- Remove Joint::mV, mdV and rename Joint::updateVelocity().
- Rename Joint::updateAcceleration() to updateJacobian() and updateJacobianTimeDeriv(), respectively.
- Make Joint::updateJacobianDeriv() protected
(need more work)
Clean-up Joint (fix compiler errors)
Clean up Skeleton and World
Fix runtime errors caused by last commit
Merge branch 'cleanup_joint'
Make BodyNode::setDependDofList() as protected function
Merge BodyNode::init(), setSkeleton(Skeleton*) as init(Skeleton*)
Fix comment
Merge branch 'bodynode_init'
Merge branch 'origin/master'