For 4.6, we have decided on following

• by default, pegasus-plan will look for pegasus.properties file in the current working directory
• the catalog files also by default will be picked up from cwd directory.
• --sites option if not specified, used to mean all sites in site catalog. For 4.6 it will be updated to mean all sites other than local in the site catalog

For condor sites, universe as vanilla will be automatically associated unless site is local , or user already has universe specified.