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Setting a Project Root that is Different than your web root

I'm trying to create a project from existing files on sftp.

What I would like to do is set a project root that is different than the web root. For instance, my bootstrap file and web assets folder are under the web root on ftp at /html, but my application files are below the /html directory in a separate directory named /app/

I may be missing something simple, but I can't seem to setup a project so that I can relate the web root to a folder inside of the project root instead of the project root itself.

Thanks for any help,

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