use step instead of stepInTime

[jbphet]

Many of the model elements use the function stepInTime to advance their state. This was PhET's convention back in the "Java days", but we generally just use "step" now. These should be updated.

For the most part, this will be a simple search and replace, but there are some files that have both a step and stepInTime function. I looked through these, and at least initially it appears that these should be fairly easy to consolidate. When doing so, be sure to consider #67.

[aadish]

discussed with @jbphet and left the stepInTime functions where play pause functionality is required and removed at other places in above commit

[aadish]

fixed, closing