Restarting the server will take some time but surely reload the files if they exist on the file system. I am not sure about calling Clean from the Servers view.
If you call Publish within Servers view, RAD will restart the application on the server. Thereby changes normally get picked up.
You need to understand what kind of change you did and see what WebSphere Application Server requires to load the change. If you scroll to the bottom of the linked help entry, you can see for each JavaEE module type a link to a document which describes what needs to be done to pickup the changes.
http://publib.boulder.ibm.com/infocenter/wasinfo/v7r0/index.jsp?topic=/com.ibm.websphere.base.doc/info/aes/ae/trun_app_hotupgrade.html
Otherwise, you should understand the whole lifecycle of what happens from the change to picking it up in the browser, e.g. change on the file, file gets compiled, prepare for deployment runs, classloader sees the change, notices that application needs to be restarted, user calls Republish to restart the application on the server, user refreshes the web page, Firefox shows within Firebug that the Last-Modified timestamp in HTTP header changed.
I am not sure what hot-swap means but when debugging the server, hot code method replacement can replace a class within the debugged server if there is no reference held to the class or the class structure has not changed.
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