It is deployed to the same site because you pass DeployIisAppPath on the command line.
You can create a publishing profile in each web application with the same name (for example, Stage.pubxml ), each of which contains a differen DeployIisAppPath . When deploying, you can specify /p:PublishProfile=Stage , and it will use the settings for this profile for each specific project.
If you want to specify properties such as SkipExtraFilesOnServer and MsDeployServiceUrl on the command line, just remove them from your publications.
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