When someone answers this I will most likely have a duh moment.
I have been having this problem since I started with eclipse. I use hibernate and have a hibernate.cfg.xml file in the bin directory. Sometimes when I do a compile and every time I do a clean the hibernate.cfg.xml is deleted from the bin so I have to copy it back to get my project to run. My question is how can I stop it from being deleted? There is a log4j.properties file in the same bin directory that does not get deleted, so there must be a way.
Never put those files in the bin directory. Use src/resources directory depend on your build system. If you use Maven build it automatically copy those config files from resources directory to the build directory. For Ant builds you can customize the target to do the same.