I frequently switch between Clojure and Java projects in my workspace. For some reason Clojure support keeps being added automatically to my Maven-based Java project, even though it doesn't seem to contain anything that would cause it to look like a Clojure project. This causes my .project and .classpath files to be updated. For the most part this doesn't cause any problems, except that the target/classes entry added to the .classpath file causes an error when I try to run unit tests (because the directory doesn't exist).
I'm guessing if I disable "Automatic detection of Clojure project" it will cure the problem. But I thought I'd report it since automatic detection (if it can be made to work well) is a nice feature.