Converts packages.config into PackageReference at *.csproj project file. Requires XSLT stylesheet available as second file in the gist.

Convert-ToPackageReference.ps1

Function Convert-ToPackageReference
{
    Param ( [Parameter( Mandatory, ValueFromPipeline )][String] $inputUri,
            [String] $stylesheetUri = "https://gist.githubusercontent.com/a4099181/074a6c3dd524ea0d343382137492399c/raw/cdd0fb31efd70c4c0f8c86ddb314de86ab8972e8/Convert-ToPackageReference.xsl",
            [String] $resultsFile   = [System.IO.Path]::GetTempFileName() )

    Process {
        $xslt = New-Object System.Xml.Xsl.XslCompiledTransform
        $xslt.Load( $stylesheetUri )
        $xslt.Transform( $inputUri, $resultsFile )
        Get-Content $resultsFile
    }
}

Function Update-ProjectFile
{
    Param ( [Parameter( Mandatory )][String] $projectFile,
            [Parameter( Mandatory, ValueFromPipeline )][String] $content )

    Begin   { $packageReference = '' }
    Process { $packageReference += $content }
    End     {
        $projXml = New-Object System.Xml.XmlDocument
        $projXml.Load( $projectFile )

        $nameSpc = New-Object System.Xml.XmlNamespaceManager $projXml.NameTable
        $nameSpc.AddNamespace("x", "http://schemas.microsoft.com/developer/msbuild/2003");

        $prefXml = New-Object System.Xml.XmlDocument
        $prefXml.LoadXml( $packageReference )

        $prefXml.SelectNodes( "/x:Project/x:ItemGroup/x:PackageReference", $nameSpc ) |
            % {
                $pkgNode = $projXml.ImportNode( $_, $true )
                $pkgName = $_.Include.Split('-')[0]
                $version = $_.Version

                $nodes   = $projXml.SelectNodes( "/x:Project/x:ItemGroup/x:Reference", $nameSpc ) |
                                ? Include -Like  "$pkgName*"

                if ( $nodes.Count -eq 0 )
                {
                    Write-Information "$projectFile $pkgName package outside the project file."
                    $itemGroup = $projXml.CreateElement( "ItemGroup", $nameSpc.LookupNamespace( "x" ) )
                    $itemGroup.AppendChild( $pkgNode )
                    $projXml.DocumentElement.AppendChild( $itemGroup )
                }
                else {
                    $nodes | % {
                        if ( $_.Include -Match "$version" )
                        {
                            Write-Information "$projectFile $pkgName valid reference."
                            $_.ParentNode.AppendChild( $pkgNode )
                            $_.ParentNode.RemoveChild( $_ )
                        }
                        else
                        {
                            Write-Warning "$projectFile $pkgName version mismatched."
                            $_.ParentNode.InsertBefore( $pkgNode, $_ )
                        }
                    }
                }
            }

        $projXml.SelectNodes( "/x:Project/x:ItemGroup/x:*[@Include='packages.config']", $nameSpc ) |
            % { $_.ParentNode.RemoveChild( $_ ) }

        $projXml.Save( $projectFile )
    }
}

Get-ChildItem . -Recurse -File -Filter packages.config |
    select @{ Name="ProjectFile";    Expression={ "$($_.Directory)\$($_.Directory.BaseName).csproj" } },
           @{ Name="PackagesConfig"; Expression={ $_.FullName } } |
    ? { Test-Path $_.ProjectFile } |
    % {
        $_.PackagesConfig | Convert-ToPackageReference | Update-ProjectFile $_.ProjectFile -InformationAction Continue
        Remove-Item $_.PackagesConfig
    }

Convert-ToPackageReference.xsl

<?xml version="1.0" encoding="utf-8" ?>
<xsl:stylesheet version="1.0"
                xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
                xmlns="http://schemas.microsoft.com/developer/msbuild/2003">

  <xsl:output omit-xml-declaration="yes" method="xml" indent="no"/>

  <xsl:template match="/">
    <xsl:element name="Project">
        <xsl:element name="ItemGroup">
            <xsl:apply-templates/>
        </xsl:element>
    </xsl:element>
  </xsl:template>

  <xsl:template match="package">
    <xsl:element name="PackageReference">
        <xsl:attribute name="Include">
            <xsl:value-of select="@id" />
        </xsl:attribute>
        <xsl:attribute name="Version">
            <xsl:value-of select="@version" />        
      </xsl:attribute>
    </xsl:element>
  </xsl:template>

</xsl:stylesheet>

@a4099181, thank you for this script, but unfortunately it doesn't work for me.
I can see that your "usage tip" doesn't include downloading xslt file too. I've downloaded it manually but it still doesn't work - I execute ./Convert-ToPackageReference.ps1 and get no any response (so it silently executes), no changes are done (as I can see with git).

UPD. It seems it cannot locate project files in my case, as their names don't match the folder names.

UPD. Ok, I was able to rewrite bottom part of this script to make it usable for case when .csproj file name doesn't match the folder name:

Get-ChildItem . -Recurse -File -Filter packages.config |
    select @{ Name="ProjectFile";    Expression={ (Get-ChildItem -Path "$($_.Directory)\*.csproj").FullName } },
           @{ Name="PackagesConfig"; Expression={ $_.FullName } } |
    ? { $_.ProjectFile } |
    % {
        Write-Host "Found: " $_.ProjectFile
        $_.PackagesConfig | Convert-ToPackageReference | Update-ProjectFile $_.ProjectFile -InformationAction Continue
        Remove-Item $_.PackagesConfig
    }

My fork https://gist.github.com/aienabled/0bce5e4b17118122f2772e7c9218bf9c

@aienabled Fine, well done. I'm very glad that you've got it worked out and my script is useful anyway. Yes, "usage tip" does not include downloading xslt file. It is not required while

$xslt.Load( $stylesheetUri )

is able to handle xslt file from web.

The script saved my night! Thanks!