ToME WikiNerdanelVampire: There is a persistent bug that makes a savefile completely unusable, causing the game to exit with the same error message every time you try to resume the game:
./tome3: Too many abilities
This appears related to the new abilities you can get from the dojo challenges. I've seen the bug with two different such abilities, and it seems completely reproduceable.
BucketMan: Ouch. That's a show stopper. Thank you for the report. As DarkGod has pointed out, I was doing some rather naughty things with new_ability. I don't see a good way to selectively load abilities at startup, so I'm scrapping the default ability system and building my own. It's not as complicated as it sounds; it's mostly just the purchasing interface that needs doing. I've got it basically working now, but there are still some issues to resolve. I should have this taken care of by the next release. Thanks!
DarkGod: 
On the other hand I added a way to hide abilities for the next alpha6 release, if you wish to use that it should work for your needs I believe