Putting a jar in <tomcat_home>/server/lib makes it accessible to the code running on the server. It does not make it visible as a file to the user. Long term you may want to consider making a file-based module to put your applet in (see https://www.labkey.org/wiki/home/Documentation/page.view?name=simpleModules).

For short term, you might copy the file to the 'files' area in your home project.

* Go to the menu item "/Admin/Go to Modules/FileConent"
* Upload your jar file
* Select the file you uploaded
* the URL is shown in the details area it will look something like

   {my server}/_webdav/labkey/home/%40files/JavaTreeView.jar

Hope that helps,
Matt