I am using eclipse with tomcat. On the server (right-click)tab you have the options:
Clean, Publish and Clean Tomcat Work directory, What do these options really do a
Clean, Publish and Clean Tomcat Work directory options work on server files, on the other hand Project>build work on workspace files (projects are inside workspace folder). Server files and workspace files are usually in separated folders, it depends on how do you have configured your server.