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From JavaErrors

You can get the error message

 The hierarchy of the type Foo is inconsistent

if something in the hierarchy is broken. For example, if you have

WRONG

 public abstract class Superclass implements NonExistentInterface { // interface doesn't exist
   // stuff
 }
 public abstract Foo extends Superclass {
   // stuff
 }

then you will get an error in Foo.java saying that the hierarchy of the type Foo is inconsistent.

This error will also be displayed if your imports are out of sync, perhaps caused by a re-build using an external builder like Ant. To remedy this, hit 'Refresh' (F5) on your Project in Eclipse's Package Explorer.

Another way to get this error in Eclipse is by running an Ant build that instantiates a hierarchy that is really a reference to another project. If the build fails (or was written incorrectly) the hierarchy is not cleaned up. I found I had to go to the Navigator tab (which shows the directories on disk - Windows/Show View/Navigator) and clean things up. Another way to clean it up, if you are running with source control, is to delete the project and bring it back (Thanks Subversion).