I'm not sure why you would want to run the CMIS Workbench on a schedule. The Workbench is a developer tool intended to be used to access CMIS repositories via the Apache Chemistry client to test queries, browse the data dictionary, and see what nodes in the repository look like from a CMIS perspective.
If you want to run scripts on a schedule that leverage CMIS you could:
Write a Groovy script which you then kick off on a schedule using cron
Similarly, write a Python script and kick it off from cron
Write a Java class that uses OpenCMIS and then schedule it with the Quartz Scheduler
Write a RESTful endpoint using the language and framework of your choice. The endpoint can use CMIS to do what you need to do with the repository. A shell script can be written and scheduled using cron that invokes the RESTful endpoint.
The CMIS Workbench is a useful tool to make sure that your queries work and that your objects are being created as you intend, but if you need to do anything CMIS-related on a schedule, consider using one of the options listed above.