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Updating application using msi fails to update dll project reference

I am creating a setup msi using a Project Output (Say Project-A), which refers another project (Say Project-B).
When i update application using new msi, dll of Project-B does not get updated though latest build contains some changes in Project-B
Note: When i uninstall the application, dll of Project-B remains in installation folder( not deleted).

It's not clear what you mean by "update ... using new msi" but the way you upgrade using Visual Studio installer projects is to increment the setup project's version and accept the changes, which include generating a new ProductCode. RemovePreviousVersions also needs setting to true. This should help and is still relevant:
https://www.simple-talk.com/dotnet/visual-studio/updates-to-setup-projects/
In addition you must increment the file versions of files you need replacing - it's not enough that they are just different.

Upgrade and add new features with MST transform

I am trying to update my application and while doing so also enabling some new features. The features existed in the previous version as well, they were just turned off.
I create an MST file using Orca where I have set INSTALLEVEL to 4 and all the features that I want to install to 1, the ones I don't want to install I set to 5 or above. Everything works as it should.
After this I would like to do an upgrade of the application the same way as I did the install with the difference that I would like to turn on additional features using INSTALLEVEL. After the installation is finished my application is in fact the new version but the newly added features are missing.
What I can do to resolve this issue is using ADDLOCAL=feature1,feature2 in command line, but I would avoid doing so because on large scale this solution won't work.
I've tried adding ADDLOCAL in the property table of the msi and generated a mst file from it using Orca. Doing so will install the features,but the problem with this solution is that:
a) MSDN doesn't recommend it
b) After install if I go to Add/Remove programs and try and change the application, I can't any more, because it is in some sort of repair mode...
SO my question is, how do I update a product enabling new features in it using mst file?
EDIT
It is worth noting that if a feature was installed previously after the upgrade it will be there, this only fails if it wasn't installed previously.

You could try to set a false condition on the standard action MigrateFeatureStates, to never execute. I suspect this is the one that overwrites the install levels of your features. (You can check this by creating a verbose log and searching for the action name in it)

Visual Studio Setup Project not removing DLL

I have a problem regarding the Visual Studio Setup Project and uninstalling an application.
This is a very basic installer, installing an ApplicationLauncher.exe C# .NET 4.0 console application and an Application.Common.dll (a dependency of the application ApplicationLauncher.exe).
The installation is a success, copying both the exe and DLL into the program files folder C:\Program Files (x86)\Company\ApplicationLauncher\.
My problem comes when uninstalling the application (through the MSI) - the uninstall seems successful, however it leaves Application.Common.dll behind, and doesn't remove it as I would expect.
I've used ProcessExplorer to make sure nothing else is using the DLL, no explorer windows are open during the uninstall.
Is this the expected functionality and do I have to create a custom action to remove this DLL? Or have I done something wrong? :S

It seems I was able to fix this issue by renaming the solution and product name of the application, I'm not sure how this fixed it, but it did.
My only thoughts here is this traversed through to the installer, where the application installed into a different folder, thus not applying the same permissions to the DLL..

It's not expected, no. It will happen if you ever done any of the following with your setup and installed it:
Marked the file Permanent.
Marked the file SharedLegacyFile true.
These are project settings, but if you set either of them and do the install it will stay behind. You can unset them in the setup project but that's too late - you've marked that component permanent or sharedlegacy on the system. If you use a brand new system, like a fresh virtual machine, reset these values if they are set and rebuild the MSI and do the install/uninstall does it still happen?

I had the same problem. Then I have tried to install and unistall my app on Windows XP and that had worked.

Renaming the ProductCode is treating the symptoms not the cause. The problem occurs when the uninstaller doesn't remove the dll. The next install will use the dll again and can't remove it on an uninstall event because it's still used by the other program.
These steps hopefully solve the problem:
Install your Software
Open CMD (with admin privileges) and run:
msiexec /x {ProductCode} /L*V "C:\CustomPath\FileName.log"
The ProductCode can be found when hitting F4 on the Setup Project
Open the log file and search for the lines that look something like this:
Disallowing uninstallation of component: {6CEC09F6-9108-7062-A692-2BCBACEE3BD8} since another client exists
Disallowing uninstallation of component: {A0A0FA84-CC0D-C5C4-1F57-169788C4482D} since another client exists
Disallowing uninstallation of component: {XXXXXXXX-XXXX-XXXX-XXXX-XXXXXXXXXXXX} since another client exists
All these components have to be removed from the registry by hand. To do this the GUID (e.g. {6CEC09F6-9108-7062-A692-2BCBACEE3BD8}) first has to be converted into a packed/compressed GUID (e.g. 6F90CEC6801926076A29B2BCCAEEB38D). I found a Website where one can run a script to do this. Find the following code on the website and replace the right side with the GUID from the log.
string inStrGUID = "{6CEC09F6-9108-7062-A692-2BCBACEE3BD8}";
Open the registry (as an administrater) and search (Edit -> Find...) for the compressed GUID (uasually it's somewhere in HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Installer\UserData\S-1-5-18\Components\)
Delete the folder that is equal to the compressed GUID. The values inside the folder should be a path to the dll.
Once deleted select the parent folder (...\S-1-5-18\components) and hit Edit -> Find...
Repeat these steps (4-7) for all components from the log file.
It's also a good idea to delete all files still present in the original folder that weren't uninstalled.
Can one prevent this from happening?
I don't know. This really isn't that easy to reproduce. Some other post on SO have suspected the install/uninstall option in Visual Studio to be the cause of the problem but I have a different theory:
This bug might be the result of RemoveExistingProducts in InstallExecuteSequence in the Setup being executed too late and therefore not removing dlls at the right time. This bug is known for years and can be fixed by doing this. If you need help with Orca this explains how to install it.

How to get the publish version of a WPF application

I want my WPF application publish version. I tried using the answer for this question. It works but the problem is we can manually change the values there. I want to know how many times my project was actually published (don't need version number. Just how many times did I publish my application). Can this be done?

Using Click Once, each time you publish, Visual Studio will change the number automatically. It will increment the value each time you publish. Your problem is that you have manually changed the number. The solution is to publish and just let Visual Studio update the value... you should notice that your project needs to be saved once you have published. This is because Visual Studio just incremented the value for you.
UPDATE >>>
If you want to access the published version from code (which you should have made clear in your question), then you can use this code, but you have to ensure that the application is network deployed first... that means that it has actually been published, so it won't work while you are debugging. Try this:
private string GetPublishedVersion()
{
if (System.Deployment.Application.ApplicationDeployment.IsNetworkDeployed)
{
return System.Deployment.Application.ApplicationDeployment.CurrentDeployment.
CurrentVersion.ToString();
}
return "Not network deployed";
}

You may be confused by 2 sets of numbers. Please note that you can set version of your WPF app in TWO different places:
Project Properties / Publish tab / Publish Version
AssemblyVersion declared in AssemblyInfo.cs file, which you can find if you expand Project Properties node in Solution Explorer.
They are similar in the sense that they both provides 4 numbers: major, minor, build and revision. The difference is that Publish Version is only available if the app was actually Published (i.e. Installed). It is not available in your debug session nor if you just copy the executable to another machine and run it there. SO, if you just need to track version of your EXE file, use AssemblyInfo.cs.
Correspondingly, to read the data use the following code:
1 To read Publish version (declared in Publish tab)
using System.Deployment.Application;
ApplicationDeployment.CurrentDeployment.CurrentVersion.ToString();
Note that in this case: a) you need to add reference to System.Deployment assembly, b) if the app was not deployed, it won't work.
2 To read Assembly Version (declared in AssemblyInfo.cs)
Assembly.GetExecutingAssembly().GetName().Version;
This one always works.

Universal solution if we get application version from not startup assembly:
var version = System.Reflection.Assembly.GetEntryAssembly().GetName().Version;
string appVersion = $"{version.Major}.{version.Minor}";
GetEntryAssembly give version of startup project.

var obj=Assembly.GetExecutingAssembly().GetName().Version;
string version= string.Format("Application Version {0}.{1}", obj.Build, obj.Revision);
OR
string version= string.Format("Application Version {0}.{1}", obj.Major, obj.Minor);
whichever properties suits you.

c# Check if there is a file on server with specific name

I making a program and wanted to make an update function... So lets say I make one update and put it on my dropbox.. When someone click on update, the program will check if there any file with different name (no same version) on the server and if there is, then start to download it.. Is it possible?
And my second problem I installed my program on my computer but when start the installer again it says:
Another version of this product is already installed. Installation cof this version cannot continue. To configure or remove the existing version of this product use add/remove programs on the control panel.
I want when I run second time installer a confirmation message appear if he want to delete previous version to install this one (I need this for the update)

You could create a web service that provides an index / manifest of a directory that you want to synchronize. The web service could also provide methods for uploading and downloading the synchronized files and folders.
If you are using a Visual Studio Setup Project (.msi) you can simply change the installer version. Visual Studio sees the change and asks you if you want to change the product code. You would say 'yes'. The installer should then remove previous versions before installing the latest. You would also want DetectNewerInstalledVersion = true and RemovePreviousVersions = true.
Not sure if it works for this scenario but you may want to look at a ClickOnce deployment. It may solve both of your problems. ClickOnce Deployment