1. Click on Window -> Preferences
2. Select Team -> Ignored Resources
3. Click on Add Pattern and enter "bin"
4. Click on Add Pattern and enter "target"
   
   Generatly the pattern will be:
   .project
   .checkstyle
   .classpath
   .settings (directory)
   target (output directory)
   bin (directory)
   
5. Click on Apply and then OK