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Why does WScript work when I run my script from the desktop, but not when run as part of Setup.exe?

I've been working on this issue for about 6 hours now and feel like I'm getting nowhere. I have a vbscript to write to the windows registry that I want to use during the installation of a .net Visual Studio program. It writes to the Local Machine part of the registry, so permissions have to be edited to accomplish that. The code in question is as follows:
If Not WScript.Arguments.Named.Exists("elevate") Then
CreateObject("Shell.Application").ShellExecute WScript.FullName _
, WScript.ScriptFullName & " /elevate", "", "runas", 1
WScript.Quit
End If
The code works perfectly when I just run the script from my desktop, and does exactly what I need it to do. But when I run the setup.exe that includes the script (even if I run setup.exe from my desktop), I get an Object Required error from the WScript code above. I need to know either 1) why I am getting this error and how to allow access to the WScript object, or if that is impossible 2) how to give my script the proper admin privileges required to write to the Local Machine Registry without using WScript.

If you are running this script as a VBScript custom action, then Windows Installer uses a custom VB script host. Unlike wscript.exe and cscript.exe, this host does not provide the WScript object, so any references to it will fail. You could choose to launch it as an EXE action via wscript.exe instead. I would not recommend this, at least not without reading my third paragraph.
Also, as a general recommendation, you should avoid elevating within a custom action, as doing so leads to the potential of multiple UAC prompts during a single installation. So to write to per-machine areas of the registry you should prefer using the Registry view, and thus entries in the Registry table. If you need custom values, note that you can specify property references in the view/table, and they will be evaluated when writing the values.
If you absolutely need to write to the registry through a custom action, consider carefully the rollback scenarios, and prefer to use an action that is "deferred in system context," as this kind of custom action will have access to administrative privileges if the installation is per-machine. Note that deferred custom actions do not have access to most properties.

Use PolicyKit to give my application access to restricted files

I'm writing an application for Ubuntu, which allows you to customize the Unity 2D desktop environment.
Some settings, I can change using Dconf, which is user-specific. So if one user changes a setting, it only applies for that user.
For other settings, however, I need to edit text files which are located in /usr/share/unity-2d/, to which a normal user can't write. To solve this problem, I thought it was a good idea to have users run the application as root, which makes sure they have access to /usr/share/unity-2d/. Only, when the application is running as root, and one of the Dconf settings is changed, it gets changed in the root user's Dconf, so the changes don't apply to the actual user.
I need to find a solution to this problem, and my first realistic idea was to use PolicyKit. I need to make sure that my application runs as the current user (so not always as root), but that it does have access to /usr/share/unity-2d/ and the files inside it. I'm writing the application in C#, using the Mono framework. I don't really have any experience with PolicyKit, and to be honest this is my first attempt in making a serious Linux application.
My idea was PolicyKit, but if one of you has another (realistic) way to achieve this, that fine with me as well. If it comes down to using PolicyKit, I'd like to have a bit more information on how to do this, and what everything does, please. I know I can probably just run my application using pkexec, but I was actually thinking more among the lines of a button in my application to unlock the features which need access to that directory, which at that moment asks for a password to get writing access to the files in the folder. In this way, people who don't have special permissions on the system the application is running on, can still customize some basic settings.

Well, the obvious solution is to have two processes, one normal user app with the GUI, and something that runs as root that manipulates files as root.
E.g. as an analog "commandline only" issue would writing a file as root:
sudo echo Hello World >/root/hello.txt
Does not work because the redirection is done by the interactive shell and it does not have root's access.
The classical solution is to use two processes:
echo Hello World | sudo tee /root/hello.txt
Now the /root/hello.txt file is opened by tee which runs as root (via sudo), which is allowed.

Using ClickOnce when i need to generate several large files?

I'm building a digital signage application and I want to deploy it using ClickOnce. (I feel this is the best approach.) When I start the application from Visual Studio (VS) it works great. The application downloads a lot of images from my web service and saves them to disk:
string saveDir = new FileInfo(Assembly.GetExecutingAssembly().Location).Directory.FullName;
When I start my deployed application, it shows the splash screen and then disappears. The process keeps running, but the UI doesn't display. I'm wondering if my saveDir as shown above is giving me trouble?
How do I locate my installed application? (I need to make license files, etc.)

I'm not sure if this is the root of your problem, but I highly recommend you change the structure of how you store your application information.
When an application is installed through ClickOnce, the application is installed within the User's folder, and it's considerably obfuscated. Furthermore, locations may change with subsequent application updates, so you can not be guarantee than any cached, downloaded file will exist from update to update.
To solve this problem, ClickOnce does provide a Data directory, that is not obfuscated and can be used for caching local data. The only caveat is this directory is not available for non-ClickOnce instances of your application (like the version that is running within the VS debugger.)
To get around this, you should write a function that you can use to get your data directory, regardless of your method of distribution or execution. The following code is a sample of what the function should look like:
//This reference is necessary if you want to discover information regarding
// the current instance of a deployed application.
using System.Deployment.Application;
//Method to obtain your applications data directory
public static string GetAppDataDirectory()
{
//The static, IsNetworkDeployed property let's you know if
// an application has been deployed via ClickOnce.
if (ApplicationDeployment.IsNetworkDeployed)
//In case of a ClickOnce install, return the deployed apps data directory
// (This is located within the User's folder, but differs between
// versions of Windows.)
return ApplicationDeployment.CurrentDeployment.DataDirectory;
//Otherwise, return another location. (Application.StartupPath works well with debugging.)
else return Application.StartupPath;
}

Embed individualized code into ClickOnce setup.exe?

I know that it is possible to pass in parameters via URL to ClickOnce apps launched online. However, most users downloads setup.exe and launch it from their machine. Is there any way that I can re-write setup.exe at download, insert a code (let's say the user's email address), and then have the app launch with knowledge of the code? Assume that we can somehow re-sign setup.exe so that it is legit.
Assume .NET 3.5.
Update The goal here is to pass on either email address and/or referrer information to setup.exe so that even when the user runs the installer from a different machine and a different ip we can figure out who did the referral.
Update 2 Assume .NET 3.5 SP1, does it help? Apparently one can now pass parameters to .application while offline. Is it possible to embed parameters into the setup.exe so that it calls .application?ref=someone right when setup.exe is run?

Well, if your goal is to embed a customer id (email, code, etc) into the exe, the easiest way I can think of is using the IPropertyStorage and IPropertySetStorage interfaces. If you are feeling brave, you could call methods directly on IPropertySetStorage via p/invoke, or you could go the easy route and use Microsoft's prepared COM wrapper, which is called dsofile.dll.
Note that while dsofile is intended for office documents, it does indeed work on any file - including .exe files - you are just stuck with the pre-defined property names. Why not throw your customer id into something like the .Comments property. Just do it in such a way that you can parse it out again.
Here's a sample:
var doc = new OleDocumentPropertiesClass();
doc.Open(pathToFile);
doc.SummaryProperties.Comments = "joe#test.com";
doc.Save();
Of course, you need to first copy it to a temp location, and some time after the user downloads it you'll want to delete it.
You can bundle dsofile.dll with your application and register it as a dependancy and use it in your installer to read the property back out. Or if you can p/invoke the IPropertyStorage without it, then you won't have the dependancy.
The other thing to look into would be using the extended file properties that are read by the Shell32.dll. I just haven't been able to find a clean way to write them easily. If you go this route, please share how you wrote the properties to your .exe.

Have a look whether InPlaceHostingManager class can help you in this case. It won't probably do exactly what you have asked for. But may be able to help...
Any ClickOnce application based on an .exe file can be silently
installed and updated by a custom installer. A custom installer can
implement custom user experience during installation, including custom
dialog boxes for security and maintenance operations. To perform
installation operations, the custom installer uses the
InPlaceHostingManager class.
Walkthrough: Creating a Custom Installer for a ClickOnce Application
EDIT
I am not sure whether you could achieve what you want exactly in the way that you have described in the question. Check whether these threads help you.
Accessing Local and Remote Data in ClickOnce Applications
How to include custom data files in ClickOnce deployment?
How to: Retrieve Query String Information in an Online ClickOnce Application

How would you imagine to "rewrite" setup.exe at download? if instead of opening your application with the provided link (url) users are downloading the file locally directly from the network share, you can't intercept this.
I would try to play with permissions and have the users to execute it from the link provided to them, but unable to connect directly to the share or web address and download it. Not sure this is possible anyway.

You can try embedding that information as a resource into the exe.
Here's a c++ example of updating a resource of an exe. http://msdn.microsoft.com/en-us/library/ms648008(v=vs.85).aspx#_win32_Updating_Resources

You should combine approach by Charith and Josh - essentially, configure your web server so that you can generate a new setup based on URL parameters. Use custom installer to read from the referral information from resource for setup.exe. Check this link for how to manipulate resources for a native application in C# - you have to write to resource file while generating setup and need to read it from your custom installer.
Yet another way of generating custom setup would be to build your executable or helper assemblt from command line embedding the necessary information. And then build the setup from command line tools (see http://msdn.microsoft.com/en-us/library/xc3tc5xx.aspx). It appears to be quite cumbersome and will take long time to generate the custom setup as opposed to modifying the resource of already built setup.
A completely different approach would be to email the unique referral code (registration code) whenever user downloads the application. In the setup (or application), use custom installer to prompt user for this code. If the setup is invoked via URL then the code will be available from there and in such case Custom Installer need not ask for the code. The email that you send when user download the setup should inform user to preseve the code into some text file along with the setup file.

Run.Cs or.Vb files without calling the in asp.net

By security reason I ask this... Can .cs or .vb files to run in any way without calling those in asp.net?

C# and VB script requires a host to interpret the code. Windows Explorer wont interpret C# or VB script. However, there are applications which can be launched which will interpret the script. For example, cscript.exe can interpret *.vbs files and execute the code within it.
There are also other more malevolent techniques to trick applications into executing script. This is particularly used in getting Microsoft office to open exploits on computers via scripting.

they can be compiled using csc.exe or vbc.exe and then run as .exe, but this can be done only if malevolent user has logged in at your server.
And if so he can do mostly anything his windows account permits.