I've to access to files on the software user and I don't know if it's better to use a full JS app with HTML5 File Api rules or use Java and communicate with it ?
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If you have the option to use the HTML file api and you are not worried about browser compatibility then you should avoid using 3rd party things like java as a far as possible and keep as close as possible to bare bones.
Java requires a JRE to be installed on the client PC, which adds a deployment layer, however simple it may be.