Hi. Regarding Community Edition, yes, it IC2 can be used with the free versions, but you do lose first-class JavaScript and CSS support (as well as a few other things). Please see this for more details:
Regarding automatic removal of supporting meta.xml files, I'm not aware of such a bug, but I'll check it out on Monday and take care of it for the next build if it's present. Apologies for the inconvenience, and thank you for bringing it to my attention.
Regards,
Scott Wells