I am trying to deploy Orchard using WebDeploy.
Orchard has the following folder structure, Orchard.Web is the root of my web application
When i do a WebDeploy all bin folders that sit outside the root are not included in the package. Is there a way to include them?
Here are my deployment settings used by MSBuild
By design: you do not want these folders. They are rigorously useless and just an artifact of VS compilation.
You can turn off dynamic compilation if you rename Config\Sample.HostComponents.config to HostComponents.config in your Orchard.Web directory. This would allow you to compile your solution statically and you may be able to get away with not having your source on the server. In my experience though, Orchard doesn't really like running in static compilation mode, and this can have undesired side-effects.
You can WebDeploy an Orchard solution when you are in Release, from Visual Studio. If you look at the project file you will find some custom steps which enable it, like copying all Themes and Modules to the right location.