It’s quite hateful that Eclipse always generates hidden files .project and .classpath in project folder. Sometimes you’re not awared if something goes wrong in these files.
After upgrading your Eclipse and if you found the following compile error, I’d suggest you to check .classpath in your project folder.
The project was not built since its build path is incomplete. Cannot find the class file for java.lang.Object. Fix the build path then try building this project
Most likely you would see a line like this.
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/ org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/j2re1.4.2_03"/>
The stupid Eclipse appended this for no reason. Just simply remove it to make it work again. ;)