You will not be able to choose the user's download location with javascript. This can only be set from the user's end, otherwise it would violate user's security.
If your app is for an intranet only there are various ways you can push a config onto the user's browsers (depending on which web browser they are running in the intranet). But that would make ALL downloads go to that location.
Most browsers also have a configuration that allow the user to define a location for every download as covered here and here's more specifics for different browsers. The user would be able to (and have to) select the download location for every download.
If this is for an intranet app, and if your intranet is running Firefox, there is also this add-on. You would have to push it out to all your user's computers (or manually install it on them all). I haven't tried it yet but I was planning on using it should a situation like yours arise (all my ExtJS work is for an intranet running Firefox - I push out things like this using a logon script whenever a user logs into the network to automatically install them).
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