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copy files to a machine in local network in java with authentification

I've used Commons IO to write a program that copy files and other things. But I want to copy a file to a local ip address \\10.x.x.x, but the user doesn't have rights to do the copy, so I need to put an ID and password to access it. However I cannot find a way I can do that.
To move file I use :
FileUtils.moveFileToDirectory(fichier, destDir,true);
But my directory is something like \\10.x.x.x\files and only a few users can write in that directory so I have an ID & password that let you move files there. I want that even if the users don't have rights to move files to that directory my program can do it.

It is not really the way Windows security works. If you really want to do it that way, you will have to use Java Native Interface or Java Native Access, and manage to call the WNetAddConnection function from Mpr.dll (and do not forget to call WNetCancelConnection when done).
But you would have to store a password in your program, which is poor security practice.
The standard way to do that would be to start a service that would run under a user that has access to the desired directory, and have your program to communicate with it using whatever you want, the simplest way being probably TCP/IP. But unless you have special requirement for that I would not recommend to use Jave for those kinds of program.
A more Java alternative would be to start a Tomcat service on server machine running under a user having access to the directory. That way you just have to develop a standard Java Web Application able to upload files that would save the files to the proper directory. But it would be a traditionnal and portable Java application with no need for JNI nor JNA.
If cannot use a Tomcat and do not want to invest to much on it, you could split the program in pieces :
one client program that copies files on a directory (on server machine) with File creation rights for everybody - can decays to the copy utility if nothing more has to be done or can easily written in Java
one server program that will run on server machine under a user that has full write permissions on target directory. This one can also be easily written in Java
you can easily install the server program as a service on the server machine with sc and srvany according to this answer on ServerFault
If you use a client program, you could easily add a digital signature file with each copied file, but as I said above, it is poor security practice and add little if any security. At least the program should be executable and not readable, and the sources should be kept hidden. It is better to log the users that copied the file and ask them what happened is you find a problem.

Is there a way to read contents of a directory from web app

I have a web application built on the JVM. In this application the users are able to upload files. I read the contents of the file and do "something" with it.
In addition to this, I would like to give option to the users to put in a directory path. This directory path will be read by the application and the directory will be scanned for all relevant files (.CSV). And each will be processed.
Questions
Will the web-application be able to scan the directory located on the users machine? Or the directory path need to be in a network to which the web-app has access to?
I will be using the Commons IO package to scan the directory for files and process the files, is there a better approach?

You cannot access file system of user machine from pure web application. This task can be implemented using trusted applet or java application executed via java web start or trusted flash component or other native component (browser plugin).
Applets are almost obsolete and require JVM on client side. Java web start still requires JVM. All signed components (java based, flash, native code) require user approval.
I think that better and more modern way is to use a great feature of HTML 5 that allows not navigation to specific location on disk (that was possible since HTML 1.0) but also selecting a full directory.
Take a look on the following discussion for details: Does HTML5 allow drag-drop upload of folders or a folder tree?

Allow user to download a file generated by Java applet using Javascript API

I have a Java applet embedded into a web page which generates a file that the user must download. I understand there is a way to do this by communicating with a Javascript API.
Could somebody please explain to me how to do it this particular way?

Javascript doesn't allow file saving just yet, and the hacks that "work" need modern browser that understands data URI:s. In that case you would simply send the binary data as base64 and make the browser navigate to the data URI by setting document.location.href = 'data:application/octet-stream...' The download prompt would look like this in firefox:
http://img824.imageshack.us/img824/5080/octetstream.png
Flash allows for real download/save dialogs though so you could also look into that... or find out if java applets have that too.

If the user can be expected to have (or be willing to upgrade to) a Plug-In 2 architecture JRE (e.g. Sun's 1.6.0_10+)1, it is possible to launch the applet using Java Web Start. When an app. is launched using JWS, it can access the JNLP API, that offers file services that allow even sand-boxed code to save information to the local file-system.
Here is a demo of the JNLP files services.
That is if the applet needs to be embedded. JWS could launch applets free-floating since it was introduced in 1.2.

Uploading the contents of a directory in JSP

I'm developing a JSP application, and I want to be able to upload the contents of a directory to the server. So the user will select the directory he wants to upload, and somehow all its contents will be uploaded.

Can't be done with regular HTML/Javascript, you have to use either Java or Flash.

There is no support for this in HTML (only uploading of a single file) so there is nothing you can do in your JSP. If you want to do this in java you will have to have something client side, like a signed Applet or a jar that the user downloads and runs.

Looks like it's time for a Framework! Struts2 can handle this type of jobs well and is easy to start with. Here you can take a look at a File Upload sample.

As said, there is no way to do this in JavaScript/HTML.
If you do not want to use a Java Applet (they are clunky and your users may not have Java installed), you can let people upload a zip file and extract it on the server (there is support for this in the Java standard API). Both Windows and Mac OS allow the clients to zip a folder by right-clicking.

Cross-platform executable/runtime delivery method

I need assistance finding a delivery method that best fulfills the following requirements:
We wish to deliver a single file to my clients.
Clients should be able to launch this file from the operating system shell - much like running an '.exe' on Windows.
After being launched, the program/script should be able to display a window with HTML content. this may be done using a stand alone program, a runtime or by running within a browser.
We need the ability to embed a resource within the delivered file, such as an mp3 file, which i can later extract programmatically.
Optimally, the solution should run on Windows, Mac and Linux machines. Less than perfect cross-platform interoperability is acceptable, but we want as broad a penetration as possible.
Clients should not need to pre-install anything (unless it is done transparently), pre-configure anything, or approve any thing for this to happen.
For example:
We could use a regular executable file, written in C++ to do this, but it will not be cross-platform.
We could use a sliverlight XAP file, an adobe Flex file or a Java JAR, but internet explorer warns users when local content is launched. In addition these approaches mean that we have less than perfect penetration, even though it is acceptable in these cases.
We could use a python (or equivalent) script, but the installed-base (penetration) of the python interpreter is not good enough.
Using a standard HTML is not enough because of the difficulty of embedding resources in it. Embedding Silverlight XAML or uuencoded content in HTML causes IE to display a warning.
Using something along the lines of a jpeg as a delivery method is not rich enough since we need to display HTML.

..but internet explorer warns users when local content is launched..
I don't get it, what's the problem with IE saying "Hey this app is trying to run your files!"
I don't mean you don't have a good reason for this, it is just, I don't get it.
IE will only warn the user if the app has not been downloaded and try to access local resources, for instance if running from an applet or a JNLP like this one:(click on the first orange button you see )
But if the users download the jar and run it from the computer ( double click on it ) the app is local and can run without problems.
The jar file is a zip file after all, so you can attach your mp3 file with it. Double click is supported in the desired platform, and the HTML content could be either a local file ( un-packed along with the mp3 file ) or an internet web page.
Java is preinstalled on those OS already.

"internet explorer warns users when local content is launched"
There's a reason for this. How can they distinguish your excellent, well-behaved, polite application from a virus?
Since the line between your app and a virus is very, very blurry, go with any of Silverlight XAP file, an adobe Flex file or a Java JAR.
The IE business is a good thing, not a bad thing.

You could try using the 'Jetty' application server.
This supposes there is a working java environment on the target machine.
Jetty is java servlet container but it is possible to configure
everything (web server, html templates, applications, etc.) in a
single executable jar, which launches the web server and opens a default page.
Exactly how the jar file is launched will vary from platform to platform
but otherwise the user interface will be identicle, and, as its a java application
you can do pretty much anything one it has started.

Sounds like MIME HTML does exactly what you want - unfortunately, it is not supported by many browsers other than IE.

I'd investigate Adobe AIR. It can display both HTML and Flex content in a desktop application without using a web browser. However this will require installation of the AIR runtime, also I'm not sure if the Linux version is out of the beta stage.
http://www.adobe.com/products/air/

You can also use a binary for each platform.
As per your description the app is very simple, and porting from one platf to another sounds like just matter of re-compile and offer binary based on the dist.
Is this an option?