One of the problems I had was also that the project/tomcat/application root subdirectory was not saved, and I edited that manually in the context file. I do not have Automatically compute checked, but instead have checked the wanted projects checked individually. Sounds almost like there is a rights issue with regards to some files.
Ok, solved it. Turns out I had misconfigured Tomcat trying to fix another issue by Turning on Add Java pojects to Tomcat Classpath for one of the projects.
So, if I really quickly start Tomcat right after Eclipse launches it works. But if I wait for 5 seconds after that it will not. Nor will it restart, both with the error above.
java.lang.ClassNotFoundException: org.apache.catalina.loader.DevLoader on second start
Ok, all set. Turns out Tomcat_HOME is a bit unexpected when you install with hom...
Hmm, that ws dumb. The saving issue was due to not ticking "is a tomcat project"....
Tomcat won't start and settings won't save
Maven snapshot version numbering