Well, I have good news on my end in regards to this. The last few days I have spent re-installing the OS, and testing some commands in regards to this. I am happy to report that I found a process that removes everything from the C:\Program Files\WindowsApps folder, except for one directory called Deleted (which, btw is empty).
Also, when I launch powershell, and execute the "Get-AppxPackage -AllUsers" I only get 8 applications back. These are the ones that you cannot remove, and have a source other then C:\Program Files\WindowsApps.
Windows PowerShell
Copyright (C) 2013 Microsoft Corporation. All rights reserved.
PS C:\Windows\system32> Get-AppxPackage -AllUsers
Name : CheckPoint.VPN
Publisher : CN=Microsoft Windows, O=Microsoft Corporation, L=Redmond, S=Washington, C=US
Architecture : Neutral
ResourceId : neutral
Version : 1.0.0.1
PackageFullName : CheckPoint.VPN_1.0.0.1_neutral_neutral_cw5n1h2txyewy
InstallLocation : C:\Windows\vpnplugins\checkpoint
IsFramework : False
PackageFamilyName : CheckPoint.VPN_cw5n1h2txyewy
PublisherId : cw5n1h2txyewy
PackageUserInformation : {S-1-5-21-3712613860-3856576307-2993473897-1001 [Brian A. Plencner]: Installed,
S-1-5-21-3712613860-3856576307-2993473897-500 [Administrator]: Installed}
IsResourcePackage : False
IsBundle : False
IsDevelopmentMode : False
Name : f5.vpn.client
Publisher : CN=Microsoft Windows, O=Microsoft Corporation, L=Redmond, S=Washington, C=US
Architecture : Neutral
ResourceId : neutral
Version : 1.0.0.11
PackageFullName : f5.vpn.client_1.0.0.11_neutral_neutral_cw5n1h2txyewy
InstallLocation : C:\Windows\vpnplugins\f5
IsFramework : False
PackageFamilyName : f5.vpn.client_cw5n1h2txyewy
PublisherId : cw5n1h2txyewy
PackageUserInformation : {S-1-5-21-3712613860-3856576307-2993473897-1001 [Brian A. Plencner]: Installed,
S-1-5-21-3712613860-3856576307-2993473897-500 [Administrator]: Installed}
IsResourcePackage : False
IsBundle : False
IsDevelopmentMode : False
Name : FileManager
Publisher : CN=Microsoft Windows, O=Microsoft Corporation, L=Redmond, S=Washington, C=US
Architecture : Neutral
ResourceId : neutral
Version : 6.3.9600.16384
PackageFullName : FileManager_6.3.9600.16384_neutral_neutral_cw5n1h2txyewy
InstallLocation : C:\Windows\FileManager
IsFramework : False
PackageFamilyName : FileManager_cw5n1h2txyewy
PublisherId : cw5n1h2txyewy
PackageUserInformation : {S-1-5-21-3712613860-3856576307-2993473897-1001 [Brian A. Plencner]: Installed,
S-1-5-21-3712613860-3856576307-2993473897-500 [Administrator]: Installed}
IsResourcePackage : False
IsBundle : False
IsDevelopmentMode : False
Name : JuniperNetworks.JunosPulseVpn
Publisher : CN=Microsoft Windows, O=Microsoft Corporation, L=Redmond, S=Washington, C=US
Architecture : Neutral
ResourceId : neutral
Version : 1.0.0.206
PackageFullName : JuniperNetworks.JunosPulseVpn_1.0.0.206_neutral_neutral_cw5n1h2txyewy
InstallLocation : C:\Windows\vpnplugins\juniper
IsFramework : False
PackageFamilyName : JuniperNetworks.JunosPulseVpn_cw5n1h2txyewy
PublisherId : cw5n1h2txyewy
PackageUserInformation : {S-1-5-21-3712613860-3856576307-2993473897-1001 [Brian A. Plencner]: Installed,
S-1-5-21-3712613860-3856576307-2993473897-500 [Administrator]: Installed}
IsResourcePackage : False
IsBundle : False
IsDevelopmentMode : False
Name : Microsoft.MoCamera
Publisher : CN=Microsoft Windows, O=Microsoft Corporation, L=Redmond, S=Washington, C=US
Architecture : Neutral
ResourceId : neutral
Version : 6.3.9600.16384
PackageFullName : Microsoft.MoCamera_6.3.9600.16384_neutral_neutral_cw5n1h2txyewy
InstallLocation : C:\Windows\Camera
IsFramework : False
PackageFamilyName : Microsoft.MoCamera_cw5n1h2txyewy
PublisherId : cw5n1h2txyewy
PackageUserInformation : {S-1-5-21-3712613860-3856576307-2993473897-1001 [Brian A. Plencner]: Installed,
S-1-5-21-3712613860-3856576307-2993473897-500 [Administrator]: Installed}
IsResourcePackage : False
IsBundle : False
IsDevelopmentMode : False
Name : SonicWALL.MobileConnect
Publisher : CN=Microsoft Windows, O=Microsoft Corporation, L=Redmond, S=Washington, C=US
Architecture : Neutral
ResourceId : neutral
Version : 1.0.0.8
PackageFullName : SonicWALL.MobileConnect_1.0.0.8_neutral_neutral_cw5n1h2txyewy
InstallLocation : C:\Windows\vpnplugins\sonicwall
IsFramework : False
PackageFamilyName : SonicWALL.MobileConnect_cw5n1h2txyewy
PublisherId : cw5n1h2txyewy
PackageUserInformation : {S-1-5-21-3712613860-3856576307-2993473897-1001 [Brian A. Plencner]: Installed,
S-1-5-21-3712613860-3856576307-2993473897-500 [Administrator]: Installed}
IsResourcePackage : False
IsBundle : False
IsDevelopmentMode : False
Name : windows.immersivecontrolpanel
Publisher : CN=Microsoft Windows, O=Microsoft Corporation, L=Redmond, S=Washington, C=US
Architecture : Neutral
ResourceId : neutral
Version : 6.2.0.0
PackageFullName : windows.immersivecontrolpanel_6.2.0.0_neutral_neutral_cw5n1h2txyewy
InstallLocation : C:\Windows\ImmersiveControlPanel
IsFramework : False
PackageFamilyName : windows.immersivecontrolpanel_cw5n1h2txyewy
PublisherId : cw5n1h2txyewy
PackageUserInformation : {S-1-5-21-3712613860-3856576307-2993473897-1001 [Brian A. Plencner]: Installed,
S-1-5-21-3712613860-3856576307-2993473897-500 [Administrator]: Installed}
IsResourcePackage : False
IsBundle : False
IsDevelopmentMode : False
Name : winstore
Publisher : CN=Microsoft Windows, O=Microsoft Corporation, L=Redmond, S=Washington, C=US
Architecture : Neutral
ResourceId : neutral
Version : 1.0.0.0
PackageFullName : winstore_1.0.0.0_neutral_neutral_cw5n1h2txyewy
InstallLocation : C:\Windows\WinStore
IsFramework : False
PackageFamilyName : winstore_cw5n1h2txyewy
PublisherId : cw5n1h2txyewy
PackageUserInformation : {S-1-5-21-3712613860-3856576307-2993473897-1001 [Brian A. Plencner]: Installed,
S-1-5-21-3712613860-3856576307-2993473897-500 [Administrator]: Installed}
IsResourcePackage : False
IsBundle : False
IsDevelopmentMode : False
PS C:\Windows\system32>
I found a new command that was able to remove all of the packages that had the
PackageUserInformation equal to this value: "{S-1-15-18 [Unknown user]: Staged}
That command is run from an elevated command prompt (ie right-click on the shortcut for your command prompt, and select "run as administrator")
psexec -s powershell -c "get-appxpackage | remove-appxpackage"
By the way, what is psexec? Here is what Microsoft has to say about it.
quote:
PsExec is part of a growing kit of Sysinternals command-line tools that aid in the adminstration of local and remote systems named PsTools.
You can download PStools.zip, which contains the psexec.exe, from this link
http://technet.microsoft.com/en-us/sysinternals/bb897553.aspx
So, my first step here would be to download pstools.zip, and extract out the psexec.exe file. Then, from whatever directory you put it in, run that command from there (again, using an elevated command prompt).
When that is done, launch Windows Powershell by right-clicking on the shortcut and selecting "Run as administrator". Then, run this command
Get-AppxPackage -AllUsers
Once that is done, take the full output and post it to this message the same way that I did (using code tags). The powershell window is just like the command prompt window, where you can click on the little icon in the top corner, and get a menu where you can click on "edit" and then "select all" to highlight all of the text

Then, click the little icon again, and select "edit", and then "copy". You can then paste that into notepad to save, or paste it right into a post inside of code tags (which is what I did).
I would like to see fully what is left, and then help you get the rest of the items removed.
As I said, it is possible to do and you should be able to do it at this point. I did mine with a fresh install of the OS (I actually re-installed windows 4 times in the last 3 days to make sure my install steps worked). However, I would think you would be able to run specific powershell commands from specific users (or one that is for all users) to fully remove everything.
One last thing, and it is this comment you made in your last post
quote:
What Microsoft programmer thought that a dark red font on a dark blue background was a good idea? I'm about to go blind trying to read that.
I totally agree with that. Those color choices are totally AWFUL to look at inside of windows powershell. Red text on a black background, and not to mention that other one that shows up when the commands run (I think it was yellow text, on some kind of odd color background, with the black window). So very very hard to read.
--Brian