Loop-step

* Added ability to get all configurations for each system, as well as using matching
or regexps for the names of configurations to select.

* For loops now use the value of loop index as the subdirectory
* Improved handling of lists for ForEach loops so blank-delimited lists work
properly. Quotes can be used for values with embedded blanks, much like the Linux
commandline.

* The subdirectories now start at 1, not 0, to make counting more normal
* When looping over systems, now have the option to name the directories
after the system or configuration name, not the iteration number.

* For loops could crash writing to write final_structure.mmcif before the directory
had been made.

* Remove 'iteration.out' if it already exists.