I'd rather have a limited number of projects (3) with unlimited references. But I understand why it isn't that way, Catavi doesn't track projects beyond maintaining an MRU list.
Catavi can merge projects, so if managing multiple projects with Free became too onerous (because of only 100 references) one could raid the piggy bank and buy Pro.
Windows 7Pro 64bit Desktop,
Mint UL portable with Firefox & EpubReader