when you will run your application on Server without eclipse, getServletContext().getRealPath("/") will return you the context path of your application.
To get the Folder of your web server, you can try -
In the path that you are getting, wtpwebapps is the deployment folder of eclipse.
Webapps shouldn't know nor care where the web server is located. You can obtain and read a webapp's resources using the HttpServletRequest getResource() and getResourceAsStream methods. You should not attempt to access other webapp's resources, and you should NEVER attempt to write within a deployed webapp's directories. Always use external directories.
Likewise, you shouldn't attempt to access any of the webapp server's files or directories within a webapp.
There is, of course, one exception to the above, and that's the case where the webapp in question is a server control webapp such as the Tomcat Manager webapp. But for normal business apps, no.
An IDE is no substitute for an Intelligent Developer.
+1 for comment of Tim. Doing this should be avoided upto the maximum possible limit. If you have something like file upload, better use some other location/machine for storage. Avoid using deployment/server folder, even for temporary storage purposes.