Initial work on bug #35

Added the RobotTrajectory object to the methods that need to be
converted to test the new code against the results obtained from using
JointTrajectory.

Converted applyVelocityConstraints to use only data from the
RobotTrajectory object.

Made the JointTrajectory versions of computeTimeStamps private to ensure
that they are not used anywhere.
Migrated applyAccelerationConstraints to use RobotTrajectory.
Still working on issue #35.

When updating the "updateTrajectory" function to not use
trajectory_msgs::JointTrajectory I ended up in some code that seems old
and not longer in use.  I think that velocities and accelerations
calculated in this function are not used anywhere, that's why I created
a new updateTrajectory which just updates the time between waypoints
using the previously calculated time_diff vector.
More work on issue #35. Updating updateTrajectory.

Discarded the timestamps-only updateTrajectory and updated the original
one to update the time_from_previous waypoints in the RobotTrajectory
and the velocities and accelerations in every joint / waypoint.
Working on issue #35. No more JointTrajectory msg.

This commit should finish the transition from the previous
Joint Trajectory based timestamps calculations to making the calculations
in place in RobotTrajectory.

The new wrappers which take a JointTrajectory are still missing.
Removed some code duplication.

While working on issue #35, three functions generated the active_joints
string vector. Now it is only generated in updateTimestamps and passed
as reference to the functions that use it.
Merge pull request #62 from tulku/issue35

issue #35 almost complete