You might want to consider a multi-user environment over a secured web application. Each users have their roles, permissions and views. This would be much easier to deploy with a java webapp and is much more secure than allowing everyone to access the files with the encryption key. A centralized database server with web and application server would allow you to scale up as well if necessary and the web is a common protocol. If you need security, you can have your own internal CA and do your own SSL/TLS connections. Since users connect via intranet, more control would be available over the users.
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