I have a legacy WPF application - which has been upgraded to a SDK style project, and to .Net 6 (from 4.7.2)

Note - I am running the Publish from Visual Studio.

Everything is fine with the application, until I try to publish. The publish folder used to look like this:

Now it looks like this (basically the whole bin directory is additionally in the root folder as well as the Application Files\1_0_0_0)

This is how the .pubxml looks:

<?xml version="1.0" encoding="utf-8"?>
<!--
https://go.microsoft.com/fwlink/?LinkID=208121.
-->
<Project>
  <PropertyGroup>
    <ApplicationRevision>0</ApplicationRevision>
    <ApplicationVersion>1.0.0.0</ApplicationVersion>
    <BootstrapperEnabled>True</BootstrapperEnabled>
    <Configuration>Release</Configuration>
    <CreateWebPageOnPublish>False</CreateWebPageOnPublish>
    <Install>True</Install>
    <IsRevisionIncremented>False</IsRevisionIncremented>
    <IsWebBootstrapper>False</IsWebBootstrapper>
    <ManifestCertificateThumbprint>06EF1B2FBCB3164AC4AA984B4790B18FF909C9C4</ManifestCertificateThumbprint>
    <ManifestKeyFile>TemporaryKey.pfx</ManifestKeyFile>
    <MapFileExtensions>True</MapFileExtensions>
    <OpenBrowserOnPublish>False</OpenBrowserOnPublish>
    <Platform>win-x64</Platform>
    <ProductName>Orders</ProductName>
    <PublishDir>C:\Temp\PublishTest\Orders2\</PublishDir>
    <PublisherName>xxxxxx</PublisherName>
    <PublishProtocol>ClickOnce</PublishProtocol>
    <PublishReadyToRun>False</PublishReadyToRun>
    <PublishSingleFile>False</PublishSingleFile>
    <SelfContained>False</SelfContained>
    <SignatureAlgorithm>sha256RSA</SignatureAlgorithm>
    <SignManifests>True</SignManifests>
    <SuiteName>xxxxxx Platform</SuiteName>
    <TargetFramework>net6.0-windows10.0.17763.0</TargetFramework>
    <UpdateEnabled>True</UpdateEnabled>
    <UpdateMode>Foreground</UpdateMode>
    <UpdateRequired>True</UpdateRequired>
  </PropertyGroup>
  <ItemGroup>
    <BootstrapperPackage Include="Microsoft.NetCore.DesktopRuntime.6.0.x64">
      <Install>True</Install>
      <ProductName>.NET Desktop Runtime 6.0.1 (x64)</ProductName>
    </BootstrapperPackage>
  </ItemGroup>
</Project>

I feel like it is a tooling error, but I cannot find anything online about why this would be happening. Any help would use useful.