How does eclipse deploy web applications using WTP?

It's just all definied in the context. Xml which Eclipse has given to Tomcat. If you want to configure this behaviour, then doubleclick the Tomcat instance in the servers view and check the Server locations section.

To achieve what you initially want/expected, you need to select Use Tomcat installation and if necessary also specify the Deploy path .

I recently have to figure out more detail on this topic to troubleshoot application startup issues so I note it here.

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