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Yes, you are right!
Few weeks ago i had situation, when the disk was full.
So now i just recreate repository:
emca -deconfig dbcontrol db -repos drop
emca -config dbcontrol db -repos create
Now EM works fine, but do you know any solutions to restore only server.xml file without drop-and-create all repository?
Sorry but I am not finding the metalink note 746250.1
The server.xml is empty .. Reason I do not really know... As you describe above I was having some issues with the space in the file systems.