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I'd like to integrate a application into a web site which allows user to manipulate files on their local machine via the web browser.
Flash and Silverlight run at with low permissions and no file system access.
Are there alternatives to using a java applet?
You could use Java Web Start or if you could get away with a desktop app, use Adobe Air.
You could use an ActiveX control but it will run only on IE.
I am no expert on Java Web Start but I have used JWS deployment on a project in a similar way. Given that the application is signed and JNLP file grants full access, you should be able to access local files. It is worth noting that in JWS deployment the application is not sandboxed within the browser, the permissions are set via a JNLP file. For further read you should check out the JWS tutorial at Oracle.