Previously, if the checkpoint interval was 40 steps, the checkpoint directories would be named
Checkpoint40
Checkpoint80
Checkpoint120
etc.

It is often preferable to have all the step numbers written with the same width, padding with zeros as necessary:
Checkpoint040
Checkpoint080
Checkpoint120
etc.

Accordingly, I added a parameter to HyPerCol, checkpointIndexWidth, to control this behavior. For example, setting checkpointIndexWidth to 3 will generate the behavior above. For time step 1000, the directory will still be Checkpoint1000: the step number is never truncated.

Setting checkpointIndexWidth=0 or 1 recreates the old behavior: step numbers are never truncated, and padding zeroes are never added.

If you set checkpointIndexWidth to a negative number, checkpointWrite will compute the total number of steps from the startTime, stopTime, and dt parameters, and use the number of digits in the number of steps when creating the directory name.

The default value of checkpointIndexWidth is -1 (to automatically choose the width).