It should be that you can have magic sync ignore certain folders, or only watch certain folders, on a per project basis. For example, I often want to track changes to the the theme folder and a custom plugin folder only, or ALWAYS ignore the uploads folder. For example, if a client is adding media to their site while I am working on some code changes, I don't want to ever accidentally delete that media. At present, every time I push files I have to repeat the process of deselecting folders / files I do not ever want to overwrite or sync, creating repetitive work that could be prone to an error... Each site connection should have an options area to configure what directories are going to be watched by magic sync.