The myrug v2 software is now available from the homepage http://www.purplepixie.org/myrug.
This version includes a much nicer command-line interface, a web interface for the first time and also now supports non-primary indexes.
General (MUL) indexes are now added using explicit CREATE INDEX fieldname (fieldname) ON table. This will fail if the index is already created (which it should) and so gets round the reason indexes were pulled in v1 - the creation of duplicates problem.
However - this relies on your indexes being named the same as the field. If you run the script on a table with existing indexes with names other than the fields then duplicate field-named indexes will be created (you can turn index creation off in the options).