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Java applets are no longer supported - what's the alternative? (File manipulation - shell commands)

I have a question about how to manipulate files from the browser, currently we are using a java applet. To create some folders, replace/delete save some files/folders and execute a shell command with parameters. As we know Chrome no longer supports the npapi and therefor java applets, FireFox will soon follow and my guess is that IE will not stay behind forever.
So the actual question is what's the best way to go?
Should we think about creating plugins (but this then should be done for all major browsers - a lot of work)
Or do you recommend to install an external program, what we can launch on the users system? By for instance associating a specific extension, or by adding a url scheme?
What about this Java Web Start? Does this allow us to communicate with the domino api?
Any other technologies that would be better?
The website we are building is using IBM Domino 9.0.1 XPages (JSF).

Answering to your use case: content management system.
For adding files the HTML5 files API should do all you need. There are plenty of examples including multi file uploads.
It gets trickier when you want to provide a round-trip edit experience. Like you click something and Word, Excel, Impress, Photoshop opens and you edit. When you save it all goes back to Domino.
The solution here is wevDAV. You can even expose Domino views as folders in Explorer / Finder / Nautilus.
For Domino there is a project on OpenNTF that implements WebDAV for documents/attachments on Domino (I wrote it). It might be your best bet.

I think we should be making a distinction here:
things like file access can be done using HTML5 file access, but
things like local administration definitely aren't something that need or should be done from within the browser.
In fact, I always hated that Java suggested that users "need not install any software" to do this and that on their machine, which was a straight lie, considering they downloaded Java Software, had to tell their Java Policy framework to trust that and then that software was able to make local changes. That's just as unsecure as downloading any (signed) executable and making your user execute it.
Java's portability¹ doesn't apply to your use case, as it seems; "executing a shell command" sounds as non-portable as it gets. So, in the end, you either only have one platform you address, or one solution for every platform, in which case you gain no portability by the fact that the same Java executable can run on all JREs (given that's the case, even).
I'd say: It's a good time to let Java for Desktops die, especially since you don't seem to be doing anything that Java is good at² in your application.
As it sounds, the average installer framework can do what you want without you writing any code. There's plenty out there, especially for Windows, which you seem to be addressing; take microsoft's .MSI as an example. You'd end up with a two click, signable, trustable, updateable solution that wouldn't need the user to keep a JRE installed or secure at all.
CLARIFICATION: I really don't hate Java; I don't find it's the greatest language or has the best ecosystem, but whatever makes your application work is fine.
Now, you mention:
To be clear, we are creating a Document Managing System, which used to be on the Lotus Notes client and that we are trying to port to the Web.
That does in fact sound like it might be a good idea to chose any browser and embed that. In fact, Firefox is "merely" an application around a browser core, and you might just modify it (e.g. by writing an extension) to fit your needs. It's not really a "web application", that way, but it would meet your requirements of integration with a web application and local administrative access. I furthermore recommend thinking twice about the shell scripts you need to run locally -- maybe their job can be more easily replaced by another program or even something that is "web compatible" than calling them with local privileges from your web application.
¹ (which was a big thing back in the day, but honestly, Java applications nowadays are about as portable as your average .Net or Qt based application on desktop OSes, but never quite feel completely like home -- it's like portabilities ugly sister if you're portable, but only offer the minimal common subset of functionality and look and feel on each platform)
² ... whatever that might be!

Java Application Deployment/Installer Options?

I'm looking for advice on good options to deploy Java applications on end user systems.
Our end users are not tech savvy experts but casual computer users who can't be expected to figure out directories and version conflicts.
Runnable jar is not practical because we need to provide VM parameters. Batch files are not practical because for whatever reason, java.exe is not on the $PATH in a huge amount of Windows system.
Webstart is an option, but our users commonly complain that no shortcuts are created (a feature that's apparently broken), every click on the website prompts a new download, and a plethora of other issues make this option seem incredibly unprofessional to the end user.
Many of the things one finds when googleing for Java deployments are themselves built with Java, which means they won't run either on a system with a missing or broken Java installation.

If you do not want to spend any money, a popular solution is izpack.
If you're looking for a commercially supported solution, there is install4j (Disclaimer: My company develops install4j). The installer is a Java application here as well. However, it is started by a native launcher that can download a JRE bundle from your server on the fly. You can also statically bundle a private JRE. See here for more information on JRE bundles.

Webstart is an option, but our users commonly complain that no shortcuts are created (a feature that's apparently broken), every click on the website prompts a new download, and a plethora of other issues make this option seem incredibly unprofessional to the end user.
Many webstart deployments are quite unprofessional. Make sure any deployment that is showing problems is validated using JaNeLA. For the shortcuts specifically, look into the IntegrationService of the JNLP API for establishing them after launch, with feed-back.
Ultimately though, APIs will have bugs. If you find one in web start, please report it on the bug database (v. broken at the moment, but you have to try).
Many of the things one finds when googleing for Java deployments are themselves built with Java, which means they won't run either on a system with a missing or broken Java installation.
As to missing or too low version Java, use deployJava.js to ensure a suitable JRE is present. No ideas on the broken installs.
I doubt you will swing back to JWS for this immediate deployment, but please investigate it according to the ideas outlined above, for future use.

Java installer for Swing based project

I worked on a Java project in which web services are used, values are to be modified in registry and there are some DLLs to be register with system. there are some environment variables to set, at the time of installation, keeping in mind these requirements , which Java installer is best, i also need a installer which is platform independent as my Java project is platform independent.
I think i may use IzPack
but i think you guys can help me better and suggest me an installer.

If a commercial product is an option, you could take a look at install4j, but I can't say anything about it.
IzPack seems to be the only open source Java installer that's still being actively developed. I've recently used it myself, and it has a lot of powerful features, but is not easy to get started with. There's a lot of documentation that describes some things in great detail, but unfortunately no simple "how to" for the most common case. Expect to spend a lot of time on trial-and-error.

I would use IzPack, its a great tool which bundles your installer in a jar. platform independent and with the possibility to only use some routines when special conditions a present. For example, only install DLL on Windows, mess with the registry (Custom Action) and so on.
I always enjoyed using IzPack and suggest you should give it a try.
The doc is also a great resource for the possibilities Doc

How to distribute Java-based software?

Now, don't get me wrong, I am a very competent programmer, but when I program, I typically develop things for the web using scripting languages like JavaScript, PHP, Python, SQL, etc. If I want to develop Java software (I am relatively experienced in Java), how do I distribute it?
Is there any good way to package up Java software in a nice little executable, send it out, and have it run? Alternatively, is there any good way to package up Java in some sort of installer, and send it out to be installed and run?

I'm using Launch4J http://launch4j.sourceforge.net/ it will generate an .exe executable for Windows, if the targeted system don't have JVM, it will tell user to download and get JVM.

You can package Java applications in so called jar-files using the jar tool or any competent Java IDE. These jar-files are self-contained and seldom need any installer.
These .jar files can easily be distributed and executed.
If you're used to web-development, you may also be interested in the Java Webstart technology.
Some links to get you started.
Export to a .jar-file in Eclipse
Lesson: Java Webstart

I have found two approaches to work well, depending on the needs of the end user.
1) Java WebStart - allows for central distribution and easy maintenance, but works best for online users. Require you to have a web site to locate the files - these days this is easy to do on the Google Application Engine.
2) Wrapping up the Java program in a single jar using one-jar, and then using jsmooth to generate an .EXE file which ensures Java is available, extracts the jar-file and invokes Java on it. This works well for users not always on the net, where you want the launch process to be transparent, but is less easy to upgrade than the webstart approach.

I use Maven to handle all the dependencies of my projects and that way when you utilise Maven to build your projects they will compile into one nice executable jar that contains everything so you dont need to worry about getting all your third-party jars in the right place etc.

There are a couple of ways: one is to create an installer that allows your user to install and run it. For this you can take a look at NSIS.... or you can just use Java Web Start where your user can just click the link and launch your application.

Here you will find a large set of options: Open Source Installers Generators in JavaIt is very useful for the "naive" customer or user of your application, to make the installation process as painless as possible. Let them install whatever is needed, DBMS, JVM, JMF and additional options via one installer.

You can also consider use one of the rich client platforms available for Java. The learning curve is probably a lot higher than just creating a jar file and ship it, but you will get a lot for free when it comes to distribution. (Think Eclipse with auto update through an update site).
Do a search for "Eclipse RCP" and "Netbeans RCP" and you'll find the two biggest contenders here. I also performed a serach for "eclipse RCP installer" and one of the hits seems interesting:
http://download.instantiations.com/RCPPackagerDoc/integration/latest/docs/html/gettingstarted/GenInstaller.html

I personally like izpack. It generates a jar file installer that you could wrap up in launch4j, supports things like windows specific shortcuts, is highly customisable through XML and hooks directly into ant.
OneJar is great for smaller stuff, but for larger programs or applications it's nowhere near as flexible and in my experience is rather slow.

Hello you can make an installer for your application.
In the link below you will find a nice help about izpack installer.
http://www.imrantariq.com/blog/?p=89
Link below contains a detailed pdf to make installer with izpack.
http://www.imrantariq.com/blog/?attachment_id=112
cheers

What language / platform would you use for a shareware / freeware desktop application?

I have a DVD cataloging application that I wrote a few years ago with MFC. Records are saved in a sqlite database, so basically it's a CRUD app. UI-wise, it has a tree view on the left, a list view (grid) on the top right, and an HTML view (embedded IE) on the bottom right. Nothing fancy.
I wanted to update the app with more features, but I've been using Java EE for the past couple of years and I realized that I wasn't productive at all with MFC. So I'm thinking maybe I should use something else to boost my productivity. Cross-platform would be a big bonus, but it's not absolutely required.
Here are the options based on my research:
Java / Swing: I can utilize my Java knowledge; great third party libraries (such as Spring for IoC and Hibernate for ORM); cross-platform. Downside is, JRE required for users; Swing seems to be in the "maintanence" mode and it's not getting much attention from Sun.
C++ / Qt: native application;
cross-platform. But I'm new to Qt so
I have to learn it first.
C# / WPF: WPF seems to be the future
of Windows GUI development and I'm
impressed by some WPF sample apps. I
have some experience with C# but I
need learn WPF. Downside is, Windows
only; .NET 3.5 runtime required.
So what would you use if you were in my situation? Thanks in advance for any suggestions.

If you want to learn some new skills while developing this application, then C# / WPF, and LINQ in C# 3.0 is really great if you didn't have it in Java.
If you just want to get on speed, then you already answer your own question, Java / Swing. It is what you are good at.

I'm actually a big C# fan, but since you said that cross-platform would be a huge bonus, I think that Qt might actually be better for that. C# can be cross-platform via Mono, but I've had better results with Qt in that respect. They also have real good documentation in QtAssistant to get you started.

Consider PyQt + Python as well if your productivity is a big issue. Trust me when I say the learning curve for Qt is well worth it, and not as hard as it may seem at first.
Sqlite support is in both the Python standard libraries and the QSql module in Qt if you prefer to use that.
PyQt + Python is a cross-platform option as well, since Python is available for many platforms and Qt's cross-platform to begin with.
The controls you mentioned you used in your application are all available in Qt.

The only other tool apart from raw C++ is Delphi. Period.
With other tools you will have problems in the deployment.
With Delphi you will produce native exes, self-contained. Also, the database connectivity is great.
You never will be dissapointed by lack of controls or 3d party tools, a lot with source code and with free/commercial toolset.
And the compiling times are the fastest in this galaxy ;)
So, if you are serious in provide no-hasle app for your customers, and that customers are not tech-oriented like developers so could be confused because which one of the 4 .NET runtimes install, want minimal support, easy downloads, click-click-install-go, apps that work instanly like Skype,TopStyle (made with Delphi) and others,then Delphi/C++ is are your only option. Seriously. The ONLY options.
If you want a cross-plataform solution, then FreePascal/Lazarus could work if your GUI is minimalist.

In most cases, as long as the scope of the project is reasonably small, and the computational needs are modest, I tend to favor using TCL/Tk. I have not yet learned a gui api in which I'm more productive than tk (not to say that there isn't one, just that I've tried several and found them slower). TCL is not the most wonderful language to program in, to be sure, although there are a number of add-ons that help a lot, specifically [incr tcl] and tcllib.
The reason I choose this instead of other systems, I prefer coding in python, for instance, is because deployment with tcl/tk is close to unbeatable. With Starkit, you end up with a single file double clickable application that requires no installer, and is trivially portable.

Well if you really want a class platform type of application, I would convert it into a web application and host it. That way if one user uploads dvd information or a dvd cover picture another user could take advantage of that information already input into the system.
If your going to develop for the desktop try to make feel like its an application made for that platform by utilizing the OS UI tools. And for windows, pick your 3rd option C# /WPF.

If you have some non UI code in your MFC app that you would like to reuse then consider QT. Otherwise pick whatever you prefer to learn.

Instead of C#/WPF you could give Silverlight a look. You app seems simple enough that it would not take a lot to get up and running. Similar to the demos that are shown off at conferences.
Once you get the basics down it will be fairly easy to add some cool features like animations, movie clips, album art, coverflow like interface etc.
You will be able to target Windows/Mac users and possibly Linux with Moonlight. But I haven't looked at Linux in the past 8 years so I really can't say much about it.

With Eclipse RCP, you get Java, cross-platform development (see Delta Pack), native look (via SWT) and a great framework collection for desktop development (declarative UI, plugin management etc.). You should definitely give that a try.

I went the C++/wxWidgets (but you could do Qt) route a few months back when presented with almost the exact same scenario (upgrade an app with a SQLite db). wxWidgets was fairly easy to pick up, had everything I needed, and was way easier than MFC. The best part was I found a good C++ wrapper for SQLite on CodeProject (e.g., CPPSQLite) and had the whole thing up an running in no time... The project sold me on wxWidgetss, in case you couldn't tell.

I would actually look very closely at something like adobe air. It is cross platform and can be html/javascript based so chances are you won't have a heck of a lot to learn except maybe a javascript library or two. It has the ability to talk to a local datastore or over the interweb to a webservice or RESTFUL service. Development is free with aptana. Check out some of the stuff written in it:
http://www.adobe.com/products/air/showcase/