OK. I've found the cause of both problems:
Ad. 2. The "Region not found" problem - while adding trim I've also changed throw to log and it masked me loading animation twice, first with wrong atlas (apparently it was not causing a crash in older versions or got uncommented while I updated the code to match newer runtime).
Ad. 1. It crashed on r-item attachement which has empty attachementName in function setAttachment in Skeleton.java after loading - to set empty attachement I followed your (or Shiu) advice π and used setAttachment("r-item", "") to make the knight have empty hand (null crashed the old version, apparently right now you have to use null instead of empty string).
Not related to Java project setup as you can see, just one bug in my code and one change in spine runtime. Feel free not to answer and ignore my posts if you don't have time - I post it so other users can answer if they had similar problems while at the same looking for an answer myself (and now everything is stable with Spine in my project, so expect a long silence until the next big update π ).