Sam flexible control files

Allows the user to specify control file regex, and changes default control file regex slightly. Existing user code should continue to compile and run without changes (except the control file regex has changed slightly, but hopefully not in a way that will cause problems).

If accepted, this would close #193.

I would like to review the changes to the default regex with @jagatsingh before merging this code to master.

In my opinion we need to make it easier to add parameters like this regex to upload while maintaining source backwards compatibility.
I always thought the `|` only applies to a single character or a group specified via `()`?

Should the regex be changed to match the whole file name as well instead of just a subpart to make it more robust?