Stop your server before you start to clean.
Stopping a server
You can stop the server from the Servers view.
To stop the server:
- In the Servers view ( Window > Show View > Other > Server >
Servers > OK), select the server that you want to stop.
- Click the Stop the server icon
in the toolbar. In the Servers view, the status of the server
changes to Stopped.
If for some reason the server fails to stop, you can terminate the
process as follows:
a. Switch to the Debug perspective.
b. In the Process view, select the server process that you want to stop.
c. Click the Terminate
icon in the toolbar.
Note: When terminating a server, the server process will end and the server will not go through the normal routine of stopping, for example calling the destroy() method on a servlet.
Source: Eclipse Help