Remove files and foldes on Azure before a new deploy from VSTS

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First, it’s better to include the files to the project that the web app needs, then just check Remove additional files at destination option (Check Publish using Web Deploy option first) to remove additional files.

Secondly, you can remove the files through Kudu API. 

DELETE /api/vfs/{path}    (Delete the file at path)

More information, you can refer to: Interacting with Azure Web Apps Virtual File System using PowerShell and the Kudu API

Update (Add Kudu sample):

  1. Add Azure PowerShell step/task
  2. Sepcify arguments, for example: -resourceGroupName XXX -webAppName XXX -kuduPath Global.asax

Script:

param(
    [string]$resourceGroupName,
    [string]$webAppName,
    [string]$slotName="", 
    [string]$kuduPath
)
function Get-AzureRmWebAppPublishingCredentials($resourceGroupName, $webAppName, $slotName = $null){
    if ([string]::IsNullOrWhiteSpace($slotName)){
        $resourceType = "Microsoft.Web/sites/config"
        $resourceName = "$webAppName/publishingcredentials"
    }
    else{
        $resourceType = "Microsoft.Web/sites/slots/config"
        $resourceName = "$webAppName/$slotName/publishingcredentials"
    }
    $publishingCredentials = Invoke-AzureRmResourceAction -ResourceGroupName $resourceGroupName -ResourceType $resourceType -ResourceName $resourceName -Action list -ApiVersion 2015-08-01 -Force
    Write-Host $publishingCredentials   
    return $publishingCredentials
}
function Get-KuduApiAuthorisationHeaderValue($resourceGroupName, $webAppName, $slotName = $null){
    $publishingCredentials = Get-AzureRmWebAppPublishingCredentials $resourceGroupName $webAppName $slotName
    Write-Host $publishingCredentials.Properties.PublishingUserName
    Write-Host $publishingCredentials.Properties.PublishingPassword
    return ("Basic {0}" -f [Convert]::ToBase64String([Text.Encoding]::ASCII.GetBytes(("{0}:{1}" -f $publishingCredentials.Properties.PublishingUserName, $publishingCredentials.Properties.PublishingPassword))))
}
function Delete-FileToWebApp($resourceGroupName, $webAppName, $slotName = "", $kuduPath){

    $kuduApiAuthorisationToken = Get-KuduApiAuthorisationHeaderValue $resourceGroupName $webAppName $slotName
    if ($slotName -eq ""){
        $kuduApiUrl = "https://$webAppName.scm.azurewebsites.net/api/vfs/site/wwwroot/$kuduPath"
    }
    else{
        $kuduApiUrl = "https://$webAppName`-$slotName.scm.azurewebsites.net/api/vfs/site/wwwroot/$kuduPath"
    }

    Write-Output $kuduApiUrl
    Write-Output $kuduApiAuthorisationToken
    Invoke-RestMethod -Uri $kuduApiUrl `
                        -Headers @{"Authorization"=$kuduApiAuthorisationToken;"If-Match"="*"} `
                        -Method DELETE
}

Delete-FileToWebApp $resourceGroupName $webAppName $slotName $kuduPath

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