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MSIX not packaging all dependencies

I've been looking into packing my WPF .Net Core 3.1 application into an MSIX installer using the packaging project.
However upon debugging or testing the output manually, the app crashes at launch due to it missing the Microsoft.EntityFrameworkCore.Design dll that my app is depending on. I can't quite understand why this is happening.
I do not reference this package directly, just the Microsoft.EntityFrameworkCore.Sqlite and Microsoft.EntityFrameworkCore.Tools packages, but when i do try to reference it directly, the behavior doesn't change.
I tried to follow this guide to setting it up for reference: https://learn.microsoft.com/en-us/windows/apps/desktop/modernize/modernize-wpf-tutorial-5
I can see the dll is absent from the folder, is there something extra I need to do on top of this guide to get my app to run? The dll is provided in the build directory for the app itself, just not in the build directory for the package.
Any suggestions would be really helpful

So after fiddling with settings I discovered that the Microsoft.EntityFrameworkCore.Tools package which was referencing the Microsoft.EntityFrameworkCore.Design package that was missing had some properties blocking it from being included in the package projects output.
When pressing F4 on the EFC.Tools reference I found that its Private assets property was set to "all". Looking at the the documentation for this I can see that it would prevent the dll from passing to the package project where it would be needed.
Removing this attribute appears to have fixed everything. Considering though that it was a default setting, it would be helpful to know if this was the right solution however, feels more like a workaround to me.

When added to solution NuGet packages restore/install to multiple locations

I'm using Visual Studio 2017, building a .Net framework (not core) v4.6.1 ASP.Net MVC project and when I added packages to my single project inside my solution the packages are seemingly restoring/installing to multiple different locations. I am installing packages from multiple feeds, some are internal to my company and others are public.
Some packages are located at my solution root and others seemingly are landing at %userprofile%.nuget\packages\
One package even installed and its hintpath was in a completely different location from the two of them. The package was installed there but I don't know why it didn't install to what I consider the solution's local package folder.
I'm not sure if these are the right questions to ask yet, but these are what I'm trying to answer for now:
For VS2017, .Net framework, ASP.Net MVC what is the default package install location?
How do I specify which feed a package comes from for CI/CD purposes?
Does NuGet look for packages already installed on my computer?
If yes, where does NuGet look for packages and where can I find its list of locations it looks for.
Thanks!

1.For VS2017, .Net framework, ASP.Net MVC what is the default package install location?
It depends on which package management method you using. If you are use package.config, the default package install location is solution root, if you are use PackageReference, the default package install location is %userprofile%.nuget\packages\. That is the reason why you added packages to single project inside the solution the packages are seemingly restoring/installing to multiple different locations. You can unload and edit your project, check the project file .csproj, you will find following:
<ItemGroup>
<PackageReference Include="xxxxx">
<Version>x.x.x</Version>
</PackageReference>
</ItemGroup>
To resolve this issue, you can accept the advice of Lex. If you want to unify, make the choice and change the files. You can uninstall those packages which using PackageReference(or package.config), then change the nuget settings(Tools->Options->NuGet Package Manager->General->Default package management format->Packages.config), then reinstall those packages, make sure they use a uniform form.
2.How do I specify which feed a package comes from for CI/CD purposes?
You can not do such things and you do not need to do things. As we know, when we install nuget packages from multiple feeds, all the packages are downloaded to the local host, Visual Studio will use those packages on the local, Nuget does not care which feed it comes from.
3.Does NuGet look for packages already installed on my computer?
4.If yes, where does NuGet look for packages and where can I find its list of locations it looks for.
Yes, you can use the command line nuget locals all -list to find its list of locations.
See Managing the global packages, cache, and temp folders for some more details.
Hope this helps.

ClickOnce Application with PackageReferences auto to Prerequisites

How can I get PackageReference packages to be included with the ClickOnce automatically?
I am trying to convert a ClickOnce application from packages.config to use PackageReferences as I have a good 30+ nuget packages (mostly dependencies) and it it makes it a lot easier to upgrade the few I actually need to reference.
The issue is that once I did that, all the nuget package assemblies are now considered "Prerequisites (Auto)" instead of "Include (Auto)", making ClickOnce deployments skip them. It also gives me the "...must be strong signed in order to be marked as a prerequisite" for any custom nuget packages.
Update:
It turned out that this didn't work at all. Assemblies like System.Runtime was not included by ClickOnce, period. There was no option to include it, and it ended up breaking the deployment (due to a FileNotFoundException for System.Runtime) even after setting all assemblies to Include manually. I had to revert back to packages.config. I'd love to see ClickOnce updated to work with PackageReferences

NuGet package refuses to uninstall in .NET Core library

I'm creating a .NET Core xUnit test project library in VS2017. I accidentally installed the System.Collections.Immutable NuGet package, and now I want to uninstall it.
First, I tried editing the csproj file and removing this line:
<PackageReference Include="System.Collections.Immutable" Version="1.3.1" />
That didn't work, since the types from that package were still highlighted in the editor. So I tried running Uninstall-Package System.Collections.Immutable in the Package Manager Console.
The console said it couldn't find the package, so I tried putting the <PackageReference... line above back and running Uninstall-Package again. The console said the uninstall succeeded, but VS still recognized the types.
I tried closing VS, deleting .vs/, and reopening. It still recognized the types.
I tried git stashing my changes, running git clean -xdf, and running dotnet restore from the command line. Somehow, it still outputs
$ dotnet restore
Restoring packages for C:\cygwin64\home\james\Code\cs\BlockList\src\BlockList\BlockList.csproj...
Restoring packages for C:\cygwin64\home\james\Code\cs\BlockList\src\BlockList.Tests\BlockList.Tests.csproj...
...
Installing System.Collections.Immutable 1.2.0.
Installing System.Collections.Immutable 1.3.0.
...
I also tried restoring from Visual Studio instead of the command line. Still no luck.
When I searched all the files in my repo for the word Immutable, the only thing popping up is project.assets.json in the obj directory. Not a single source file contains the word Immutable. I'm confused, then, as to how it's still being referenced. How can I uninstall it?
A few other things:
I checked the 'Dependencies' drop-down for my project in Solution Explorer, and it's not listed there.
I don't want to delete my local copy of the repo and re-clone it, since I have other work stashed.
System.Collections.Immutable.dll doesn't show up at all in the bin/ directory, yet when I use one of the types in my library and run it, it works fine.
Thanks!
edit: Adding this line to the library:
System.Diagnostics.Debug.WriteLine(typeof(ImmutableArrayExtensions).GetTypeInfo().Assembly.Location);
And running it says that the assembly is located in this location:
C:\Program Files\dotnet\shared\Microsoft.NETCore.App\1.1.2\System.Collections.Immutable.dll

After about an hour, I found out what the problem was. My .NET Core library referenced Microsoft.NETCore.App, which referenced System.Collections.Immutable. I looked at the dependencies for the former, but overlooked System.Collections.Immutable because that package references maybe 50 other packages. I ended up finding this out by creating a brand-new xUnit test project, and trying to see if ImmutableArray<> was present without installing anything. Sure enough, I could use it out of the box.

I had a similar issue with VS2017 and a different nuget package that wouldn't fully uninstall. I ultimately had to create a new project and cut and paste all my code into it. Kind of a sledge hammer approach, but faster than crawling through dependencies.

All projects referencing sub-project must install NuGet package Microsoft.Bcl.Build (C#/Windows Phone 7)?

I'm having a particularly difficult refactoring session involving a C# solution with multiple projects in Visual Studio 2012. I needed to pull out a bunch of code into their own assemblies so that code could be shared across several projects, all in the same solution. However, no matter what I try, I get warnings for the projects that reference the new shared projects that "All projects referencing {shared project name} must install nuget package Microsoft.Bcl.Build".
I have been over the dependent projects and the shared projects with a fine-tooth comb, verifying in detail that they all use the same version and exact same DLL for the Microsoft.Bcl version 1.0.1.19 and Microsoft.Bcl.Async version 1.0.16 packages:
System.Runtime
System.Threading.Tasks
Microsoft.Threading.Task
Microsoft.Threading.Tasks.Extensions
Microsoft.Threading.Tasks.Extensions.Phone
The DLL paths are all resolved and identical. The XAP file does build but I still get that warning telling me that Microsoft.Bcl.Build is not referenced in the dependent projects, despite the fact that I can see that it is.
If I try instead to uninstall and then reinstall those two packages using NuGet for each project involved, I get references with empty paths and the warning icon for the 5 DLL references involved. For some reason NuGet adds the references but can't find the DLLs. Also, if I do this, I find myself with the problem frequently of having projects where I get the "Can't add reference" error when trying to add a reference. Then I have close and re-open the solution, and that leads to a "project failed to load" error. So I have to edit the project file manually, remove the faulty package import statements, and reload the project.
How can I fix this problem and what is the general technique for avoiding this headache in the future? Letting NuGet manage missing packages didn't help at al.

In case anyone else comes across this and #Swell's solution made you go "wtf":
I recently went through an older MVC project and updated it (updated razor, asp, http, etc. nuget packages). The project, independent of itself, built fine, but when i went to publish it failed with the OP's errors.
It turns out it's because I didn't update the *.Tests project associated with it (should have figured, though not sure why Tests is that closely tied to the project). So, to fix:
Right-click the Solution and manage nuget packages.
Go through all the packages that were updated in the web project and apply them to the other projects as well (each "Update" will display a tree with the applicable projects, I was fine just OKAY-clicking through).
Rebuild.
You should now be good and it shouldn't bark at you. Hope that helps others.

I just came throught the same issue and a bug is opened here: http://nuget.codeplex.com/workitem/3268
What I've done is the following, I added to the solution level the package Microsoft.Bcl.Build
In my dev env if you don't have the package loaded, just right click the solution and select manage nuget packages, you see a yellow bar with a restore button, just click it and you will be fine.
In my build script before compiling the project I run this command:
.\myproject\.nuget\NuGet.exe install .\myproject\.nuget\packages.config -OutputDirectory .\myproject\packages
This will restore solution level packages and you will be fine.
This should be fixed by the end of this summer in version 2.7 according to the issue report