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It's reproducible on the clean install of S1S RC2 on Win2000. In 'Tools->Options' find 'System->Modules->Web- >Tomcat Server'. In Property window switch 'Enabled' to 'False'. It will ask to disable 'Web Services' module ( choose 'OK' button). Now try to enable 'Tomcat Server' back. You will get the error window with the following text: "The server.xml file in "...." directory cannot be recognized as the Tomcat configuration file. It might be corrupted." Anyway 'Tomcat Server' module can be enabled and works fine after this message.
I don't understand why it requires disabling of Web services module. This needs to be investigated. server.xml could be already recognized by different data loader (generic XML likely) and thus the warning can be printed. Probably will disappear after restart.
The issue is caused by the fact that in a certain moment (when Temcat is disabled and enabled) the server.xml file is not recognized as a Tomcat configuration file but as a regular XML file. Fortunately,this doesn't cause any subsequent troubles. The server.xml is recognized correctly later. However, the message is not proper for that case. The issue is somehow related to web services module because I was not able to reproduce the issue with Netbeans3.5.
Tomcat4 plugin was replaced by Tomcat5 plugin. This issue isn't relevant to new plugin. There is no specific DataObject created for server.xml any more.