Deployment remote server exclude folders from uploading only

We work on a development server so the entire team can see each others website easily. Working from home opening that project in PhpStorm is quite slow. So I clone the project locally, add a deployment and upload on save to the development server. 

This works great but recently we started using Statamic. Here you make changed on the website itself and then files on the server are changed (these files need to be commited and included in the project).

The problem here is that if PhpStorm syncs with the development server it overwrites the changed files (the ones that changed via the website) thus I don't commit the changes.

 

Does anyone know a good way to do this? Can I exclude directories from uploading but have them auto download onto the project?

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No, there's no such option as IDE can't detect the changes in remote files automatically, unfortunately: https://youtrack.jetbrains.com/issue/WI-1284.

To be honest, I'm not getting why "if PhpStorm syncs with the development server it overwrites the changed files". How exactly are you calling sync?
If you open the remote host tool window you can click "Sync with local" - that would present you an option to download remote changes over the local copy of a project.

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