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In my projects written under F2 java ECLIPSE_HOME was used in classpath. Now (F4) if you go to the project properties -> Java Build Path -> Libraries -> Add variable, you will see no ECLIPSE_HOME variable. It is not great bug. The bug is in following: When create ECLIPSE_HOME variable there manually it becomes lost again. Create library path based on ECLIPSE_HOME, then try to create second entry - you will see that there is no ECLIPSE_HOME again.
I've just found that this is because Window->Preferences->Plug-In development- >TargetPlatform -> all plugins was unchecked here
ECLIPSE_HOME is managed by PDE. Moving to PDE.
*** This bug has been marked as a duplicate of 20197 ***