I didn't understand the manifest part. Can I add the other jars (the ones that are located in lib/ext) to the manifest of my web-application's jar? What is the way to do it? (I couldn't understand from the links that you sent me.)
There is no need to put anything into the ext directory, or fiddle around with manifests. Put all jar files on the remote server, and reference them in the archive attribute of the applet tag. More information on that can be found here.
Also, the policy file only needs to be changed if the applet does something that's not normally allowed (like file I/O). Otherwise, don't change it. [ September 14, 2006: Message edited by: Ulf Dittmer ]
Like I said before! There are two ways of handling your first issue. Referencing via the manifest (which is a bit more complex, I agree) or adding stuff to the classpath via the archive attribute (in the html page). Maybe it is best if you use the second alternative like Ulf said. So follow his link and you will be able to fix your problem.
Ulf also has a point when he says that no policy file editing is necessary when no IO tasks are done (or other secure tasks). I assumed however that you altered your policy file because of security issues. Maybe the following link is useful for you to determine whether or not you need to do this.
One important thing I would like to mention is this: The classes that your web application can/may use have nothing to do with the classes that the applet use. The web application is running in a different virtual machine than the applet. The applet is running on the client that is accessing the web application. The only thing the webserver does is allow the applets' jars to be downloaded to the client. The applets'jars are not included in the classpath of the server. This means that there is nothing you can do in the lib/ext folder of the webapp that will have any result on the applets'classpath. So if your applet and webserver share classes you will have to put those classes in the applets'jars (classpath) AND in the web-apps'classpath.