So what does it mean now? Just generally 'outside the (perceived) establishment'?
Yeah, pretty much? At least when it comes to video games. I mean, Skullgirls has always had a publisher at various points, but it's always been referred to as an indie fighter. TFH is still being called an indie fighter. These games are made by a generally small team of people, and they (and likely the publishers) are not under the umbrella of any of the major "AAA" game publishers or console developers. That's enough for people to consider games to still generally be considered indies. Obviously there are some games that are FULLY independant, as in self-published, but even so. In the minds of many, simply having some publisher support doesn't automatically strip the "indie" tag from you.
Meanwhile you look at something like We Happy Few, a game that was crowdfunded, was in Early Access for a while, and was generally an indie game people were looking forward to whenever it got finished. Then it got picked up by Gearbox Software and was run through the AAA-game grinder, checking off every damn tickbox on the checklist: $60 price tag, preorder bonuses, season pass, gameless collector's edition, etc etc. That right there ain't an indie game anymore; it went too far up the industry ladder and got swept up by a AAA publisher.