This powershell script that could generate the .wxs file based on the source directories and build the .msi file using Wix (Windows Install by XML). To use this script, please modify the definition of variables in each function.

HeatTransform.xslt

<?xml version="1.0" encoding="UTF-8"?>
<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
    xmlns:wix="http://schemas.microsoft.com/wix/2006/wi"
    xmlns="http://schemas.microsoft.com/wix/2006/wi"
  exclude-result-prefixes="wix">

  <xsl:output method="xml" encoding="UTF-8" indent="yes" />

  <xsl:template match="wix:Wix">
    <xsl:copy>
      <!-- The following enters the directive for adding the config.wxi include file to the dynamically generated file -->
      <!--xsl:processing-instruction name="include">$(sys.CURRENTDIR)wix\config.wxi</xsl:processing-instruction-->
      <xsl:apply-templates select="@*" />
      <xsl:apply-templates />
    </xsl:copy>
  </xsl:template>

  <!-- ### Adding the Win64-attribute to all Components -->
  <xsl:template match="wix:Component">

    <xsl:copy>
      <xsl:apply-templates select="@*" />
        <!-- Adding the Win64-attribute as we have a x64 application -->
        <xsl:attribute name="Win64">yes</xsl:attribute>

        <!-- Now take the rest of the inner tag -->
        <xsl:apply-templates select="node()" />
    </xsl:copy>

  </xsl:template>

  <xsl:template match="@*|node()">
    <xsl:copy>
      <xsl:apply-templates select="@*|node()" />
    </xsl:copy>
  </xsl:template>

</xsl:stylesheet>

Makefile_win.ps1

$gWorkingDir = Convert-Path .
$gSourceDirName = "dist"
$gSourceDirPath = Join-Path -Path $gWorkingDir -ChildPath $gSourceDirName
$gXmlFileName = 'wix_template_auto'
$gWxsFilePath = Join-Path -Path $gWorkingDir -ChildPath "$gXmlFileName.wxs"
$gWixObjFilePath = Join-Path -Path $gWorkingDir -ChildPath "$gXmlFileName.wixobj"
$gProductCode = [guid]::NewGuid().GUID.ToUpper()
$gUpgradeCode = [guid]::NewGuid().GUID.ToUpper()
$gProductVersion = "1.0.0.0"
$gNamespace = "http://schemas.microsoft.com/wix/2006/wi"
$gCompanyName = "COMPANY_NAME"
$gProductName = "PRODUCT_NAME"
$gFinalProductName = "PRODUCT_NAME"
$gExeFileName = "EXE_FILE_NAME"
$gWixDirPath = "C:\Program Files (x86)\WiX Toolset v3.11\bin"

Function AddGlobalSettingNode($xmlFilePath) {
    $productAttributes = @{Id= "*"; UpgradeCode= $gUpgradeCode; Name= $gProductName; Language="1033"; Version= $gProductVersion; Manufacturer= $gCompanyName; Codepage= "1252";}

    $mediaAttributes = @{Id= "1"; Cabinet= "CABINET.cab"; EmbedCab="yes"}  
    $packageAttributes = @{Description= "Description shows here"; Comments= "Comments shows here"; InstallerVersion= "200"; Platform= "x64"; Compressed= "yes"}
    $globalSettings = @{nodeType = "Package"; nodeContent= $packageAttributes}, 
                      @{nodeType = "Media"; nodeContent= $mediaAttributes}

    $xmlDoc = [System.Xml.XmlDocument](Get-Content $xmlFilePath)
    ## Add product Node
    $productNode = $xmlDoc.CreateElement("Product", $gNamespace)
    $xmlDoc.SelectSingleNode("//wixns:Wix", $nsmgr).AppendChild($productNode)
    foreach($key in $productAttributes.keys) {
        $productNode.SetAttribute($key, $productAttributes[$key])
    }

    ## Add other global setting Nodes
    foreach($globalSetting in $globalsettings) {
        $nodeType = $globalSetting["nodeType"]
        $nodeContent = $globalSetting["nodeContent"]
        $globalSettingNode = $xmlDoc.CreateElement($nodeType, $gNamespace)
        $xmlDoc.SelectSingleNode("//wixns:Wix/wixns:Product", $nsmgr).AppendChild($globalSettingNode)

        foreach($key in $nodeContent.keys) {
            $globalSettingNode.SetAttribute($key, $nodeContent[$key])
        }
    }
    $xmlDoc.Save($xmlFilePath) 
}

Function AddDirectoryNode($xmlFilePath) {
    $directoryIndex = 0
    $directories = @(
        @(@{Id= "ProgramFiles64Folder"; Name="PFiles"}, @{Id= "ProgramFilesFolderHp"; Name=$gCompanyName}, @{Id= "INSTALLDIR"; Name=$gProductName}),
        @(@{Id= "ProgramMenuFolder"}, @{Id= "ProgramMenuDirHP"; Name=$gCompanyName},@{Id= "ProgramMenuDirHpProduct"; Name=$gProductName})
    )

    $xmlDoc = [System.Xml.XmlDocument](Get-Content $xmlFilePath);
    $directoryNode = $xmlDoc.CreateElement("Directory", $gNamespace)
    $xmlDoc.SelectSingleNode("//wixns:Wix/wixns:Product", $nsmgr).AppendChild($directoryNode)
    $directoryNode.SetAttribute("Id", "TARGETDIR")
    $directoryNode.SetAttribute("Name", "SourceDir")

    foreach($directory in $directories) {
        foreach($subDirectory in $directory) {
            $subDirectoryDst = "//wixns:Wix/wixns:Product"
            $subDirectoryLevel = $directory.IndexOf($subDirectory)
            for ($i = 0; $i -lt $subDirectoryLevel + 1; $i++) {
                if ($i -eq 1) {
                    $subDirectoryDst += "/wixns:Directory[$($directoryIndex + 1)]"
                }
                else {
                    $subDirectoryDst += "/wixns:Directory"
                }
            }

            $subDirectoryNode = $xmlDoc.CreateElement("Directory", $gNamespace)
            $xmlDoc.SelectSingleNode($subDirectoryDst, $nsmgr).AppendChild($subDirectoryNode)
            foreach($key in $subDirectory.keys) {
                $subDirectoryNode.SetAttribute($key, $subDirectory[$key])
            }
        }

        $directoryIndex++
    }

    $xmlDoc.Save($xmlFilePath)
}

Function AddDirectoryRefNode($xmlFilePath) {
    $features = New-Object System.Collections.ArrayList
    $directoryRefIndex = 0
    $directoryRefDatas = 
        @{
            Id= "INSTALLDIR";
            components= @{nodeType= "RemoveFolder"; Id= "componentINSTALLDIR"; Directory= "INSTALLDIR"; On= "uninstall"}},
        @{
            Id= "ProgramMenuDirHpProduct";
            components= @{nodeType="Shortcut"; Id= "SHORTCUT"; Name= $gProductName; Target= "[INSTALLDIR]$gExeFileName"; WorkingDirectory= "INSTALLDIR"},
                        # @{nodeType="Shortcut"; Id= "UninstallProductShortCut"; Name= "Uninstall $gProductName"; Target= "[SystemFolder]msiexec.exe"; Arguments="/x [ProductCode]";},
                        @{nodeType="RemoveFolder"; Id= "removeProgramMenuDirHP"; Directory= "ProgramMenuDirHP"; On= "uninstall"},
                        @{nodeType="RemoveFolder"; Id= "removeProgramMenuDirHpProduct"; Directory= "ProgramMenuDirHpProduct"; On= "uninstall"},
                        @{nodeType="RegistryValue"; Root= "HKCU"; Name= "installed"; Key= "Software\$gCompanyName\$gProductName"; Type= "integer"; Value= "1"; KeyPath= "yes"}}
    
    $xmlDoc = [System.Xml.XmlDocument](Get-Content $xmlFilePath)

    foreach($directoryRefData in $directoryRefDatas) {
        $directoryRefId = $directoryRefData["Id"]
        $directoryRefNode = $xmlDoc.CreateElement("DirectoryRef", $gNamespace)
        $xmlDoc.SelectSingleNode("//wixns:Wix/wixns:Product", $nsmgr).AppendChild($directoryRefNode)
        $directoryRefNode.SetAttribute("Id", $directoryRefId)

        $componentId = "component$directoryRefId"
        $componentNode = $xmlDoc.CreateElement("Component", $gNamespace) 
        $xmlDoc.SelectSingleNode("//wixns:Wix/wixns:Product/wixns:DirectoryRef[$($directoryRefIndex + 1)]", $nsmgr).AppendChild($componentNode)
        $componentNode.SetAttribute("Id", $componentId)
        $componentNode.SetAttribute("Guid", [guid]::NewGuid().GUID.ToUpper())
        $componentNode.SetAttribute("Win64", "yes")
        $directoryRefData.Item("components")

        foreach($component in $directoryRefData["components"]) {
            $subNodeType = $component["nodeType"]
            $subNode = $xmlDoc.CreateElement($subNodeType, $gNamespace) 
            $xmlDoc.SelectSingleNode("//wixns:Wix/wixns:Product/wixns:DirectoryRef[$($directoryRefIndex + 1)]/wixns:Component", $nsmgr).AppendChild($subNode)
            foreach($key in $component.keys) {
                if ($key -ne "nodeType") {
                    $subNode.SetAttribute($key, $component[$key])
                }
            }
        }
        $features.Add($componentId)

        $directoryRefIndex++
    }

    $xmlDoc.Save($xmlFilePath)  

    return $features
}

Function AddFeatureNode($features, $xmlFilePath) {
    $featureAttributes = @{Id= "FEATURE"; Description= "Description shows here"; Display= "expand"; Level="1"; ConfigurableDirectory="INSTALLDIR"; InstallDefault="local"; AllowAdvertise= "no"} 

    $xmlDoc = [System.Xml.XmlDocument](Get-Content $xmlFilePath)

    $featureNode = $xmlDoc.CreateElement("Feature", $gNamespace)
    $xmlDoc.SelectSingleNode("//wixns:Wix/wixns:Product", $nsmgr).AppendChild($featureNode)
    foreach($key in $featureAttributes.keys) {
        $featureNode.SetAttribute($key, $featureAttributes[$key])
    }

    foreach($feature in $features) {
        if ($feature -is [String]) {
            $componentRefNode = $xmlDoc.CreateElement("ComponentRef", $gNamespace)
            $xmlDoc.SelectSingleNode("//wixns:Wix/wixns:Product/wixns:Feature", $nsmgr).AppendChild($componentRefNode)
            $componentRefNode.SetAttribute("Id", $feature)
        }
    }

    $componentGroupRefNode = $xmlDoc.CreateElement("ComponentGroupRef", $gNamespace)
    $xmlDoc.SelectSingleNode("//wixns:Wix/wixns:Product/wixns:Feature", $nsmgr).AppendChild($componentGroupRefNode)
    $componentGroupRefNode.SetAttribute("Id", "HarvestedComponentId")    

    $xmlDoc.Save($xmlFilePath)    
}

Function AddUIRelatedNodes($xmlFilePath) {
    $publishIndex = 1
    $uiPublishDatas = @{Dialog = "WelcomeDlg"; Control = "Next"; Event = "NewDialog"; Value = "InstallDirDlg"},
                      @{Dialog = "InstallDirDlg"; Control = "Back"; Event = "NewDialog"; Value = "WelcomeDlg"; Order = 2}

    $xmlDoc = [System.Xml.XmlDocument](Get-Content $xmlFilePath)
    $uiPropertyNode = $xmlDoc.CreateElement("Property", $gNamespace)
    $xmlDoc.SelectSingleNode("//wixns:Wix/wixns:Product", $nsmgr).AppendChild($uiPropertyNode)
    $uiPropertyNode.SetAttribute("Id", "WIXUI_INSTALLDIR")
    $uiPropertyNode.SetAttribute("Value", "INSTALLDIR")

    $uiRefNode = $xmlDoc.CreateElement("UIRef", $gNamespace)
    $xmlDoc.SelectSingleNode("//wixns:Wix/wixns:Product", $nsmgr).AppendChild($uiRefNode)
    $uiRefNode.SetAttribute("Id", "WixUI_InstallDir")

    $uiNode = $xmlDoc.CreateElement("UI", $gNamespace)
    $xmlDoc.SelectSingleNode("//wixns:Wix/wixns:Product", $nsmgr).AppendChild($uiNode)

    foreach($uiPublishData in $uiPublishDatas) {
        $uiPublishNode = $xmlDoc.CreateElement("Publish", $gNamespace)
        $uiPublishElement = $xmlDoc.SelectSingleNode("//wixns:Wix/wixns:Product/wixns:UI", $nsmgr).AppendChild($uiPublishNode)
        $uiPublishElement.AppendChild($xmlDoc.CreateTextNode($publishIndex))

        foreach($key in $uiPublishData.keys) {       
            $uiPublishNode.SetAttribute($key, $uiPublishData[$key])
        }
        $publishIndex++
    }

    $xmlDoc.Save($xmlFilePath)
}

Function AddUpgradeNodes($xmlFilePath) {
    $upgradeVersions = @{OnlyDetect= "yes"; Minimum= $gMsiVersion; Property= "NEWERVERSIONDETECTED"; IncludeMinimum= "no"},
                       @{OnlyDetect= "no"; Maximum= $gMsiVersion; Property= "OLDERVERSIONBEINGUPGRADED"; IncludeMaximum= "no"},
                       @{OnlyDetect= "yes"; Minimum= $gMsiVersion; Maximum= $gMsiVersion; IncludeMinimum= "yes"; IncludeMaximum="yes"; Property="ANOTHERBUILDINSTALLED"}

    $xmlDoc = [System.Xml.XmlDocument](Get-Content $xmlFilePath)

    $upgradeNode = $xmlDoc.CreateElement("Upgrade", $gNamespace)
    $xmlDoc.SelectSingleNode("//wixns:Wix/wixns:Product", $nsmgr).AppendChild($upgradeNode)
    $upgradeNode.SetAttribute("Id", $gUpgradeCode)

    foreach($upgradeVersion in $upgradeVersions) {
        $upgradeVersionNode = $xmlDoc.CreateElement("UpgradeVersion", $gNamespace)
        $xmlDoc.SelectSingleNode("//wixns:Wix/wixns:Product/wixns:Upgrade", $nsmgr).AppendChild($upgradeVersionNode)
        foreach($key in $upgradeVersion.keys) {
            $upgradeVersionNode.SetAttribute($key, $upgradeVersion[$key])
        }
    }

    $installExecuteSequenceNode = $xmlDoc.CreateElement("InstallExecuteSequence", $gNamespace)
    $xmlDoc.SelectSingleNode("//wixns:Wix/wixns:Product", $nsmgr).AppendChild($installExecuteSequenceNode)
    $removeExistingProductsNode = $xmlDoc.CreateElement("RemoveExistingProducts", $gNamespace)
    $xmlDoc.SelectSingleNode("//wixns:Wix/wixns:Product/wixns:InstallExecuteSequence", $nsmgr).AppendChild($removeExistingProductsNode)
    $removeExistingProductsNode.SetAttribute("After", "InstallInitialize")

    $xmlDoc.Save($xmlFilePath)
}

Function CreateWixSourceXML() {    
    # add the top layer of Wix
    $xmlFilePath = $gWxsFilePath

    $xmlWriter = New-Object System.XMl.XmlTextWriter($xmlFilePath, $Null)
    $xmlWriter.Formatting = 'Indented'
    $xmlWriter.Indentation = 1
    $XmlWriter.IndentChar = "`t"
    $xmlWriter.WriteStartDocument()
    $xmlWriter.WriteStartElement("Wix", $gNamespace)
    $xmlWriter.WriteEndElement()
    $xmlWriter.WriteEndDocument()
    $xmlWriter.Finalize
    $xmlWriter.Flush()
    $xmlWriter.Close()

    $xmlDoc = [System.Xml.XmlDocument](Get-Content $xmlFilePath);
    $nsmgr = new-object System.Xml.XmlNamespaceManager($xmlDoc.NameTable)
    $nsmgr.AddNamespace("wixns", $gNamespace)

    AddGlobalSettingNode $xmlFilePath
    AddDirectoryNode $xmlFilePath
    $features = AddDirectoryRefNode $xmlFilePath
    AddFeatureNode $features $xmlFilePath
    AddUIRelatedNodes $xmlFilePath
    AddUpgradeNodes $xmlFilePath
}

Function BuildWithWix () {
    $harvestFileName = "harvested_result"
    $harvestWsxFilePath = Join-Path -Path $gWorkingDir -ChildPath "$harvestFileName.wxs"
    $harvestWixObjFilePath = Join-Path -Path $gWorkingDir -ChildPath "$harvestFileName.wixobj"
    $harvestTemplateFilePath = Join-Path -Path $gWorkingDir -ChildPath "HeatTransform.xslt"
    $heatExePath = Join-Path $gWixDirPath -ChildPath "heat.exe"
    $candleExePath = Join-Path $gWixDirPath -ChildPath "candle.exe"
    $lightExePath = Join-Path $gWixDirPath -ChildPath "light.exe"
    $msiFilePath = Join-Path -Path $gWorkingDir -ChildPath "$gFinalProductName.msi".Replace(" ", "_")

    Write-Host "`"$heatExePath`" dir `"$gSourceDirPath`" -o `"$harvestWsxFilePath`" -t `"$harvestTemplateFilePath`" -cg HarvestedComponentId -dr INSTALLDIR -var var.Dist -scom -frag -srd -sreg -gg"
    Start-Process -Wait -NoNewWindow -FilePath "$heatExePath" -ArgumentList "dir `"$gSourceDirPath`"","-o `"$harvestWsxFilePath`"","-t `"$harvestTemplateFilePath`"","-cg HarvestedComponentId","-dr INSTALLDIR","-var var.Dist","-scom","-frag","-srd","-sreg","-gg"

    Write-Host "`"$candleExePath`" `"$harvestWsxFilePath`" -dDist=`"$gSourceDirPath`""
    Start-Process -Wait -NoNewWindow -FilePath "$candleExePath" -ArgumentList "`"$harvestWsxFilePath`"","-dDist=`"$gSourceDirPath`""

    Write-Host "`"$candleExePath`" `"$gWxsFilePath`""
    Start-Process -Wait -NoNewWindow -FilePath "$candleExePath" -ArgumentList "`"$gWxsFilePath`""

    Write-Host "`"$lightExePath`" `"$gWixObjFilePath`" `"$harvestWixObjFilePath`" -o `"$msiFilePath`" -ext WixUIExtension"
    Start-Process -Wait -NoNewWindow -FilePath "$lightExePath" -ArgumentList "`"$gWixObjFilePath`"", "`"$harvestWixObjFilePath`"", "-o `"$msiFilePath`"", "-ext WixUIExtension"
}

CreateWixSourceXML
BuildWithWix