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Syncthing works great, if you want a web based file browser you can install one of the many available on a server with syncthing.
it does! I use it to sync my music, but I feel like it's not the right tool for the job here.
I don't want to "have the folders connected", I want to have the ability to sync files easily, while excluding specific folders and files.
Ahh gotcha, selective sync or virtual file system are the common terms for that. Nextcloud supports it, Owncloud does too and I think Owncloud Infinite Scale does but it's not 100% clear.
When you say Owncloud couldn't keep files local without uploading, was that with VFS enabled on the client?
I tried with both, but I didn't figure out how if such an option exists. I did manage to do the opposite (keeping files uploaded but not having them locally), both with and without VFS (with VFS it's in a context menu in nautilus, without it's in the desktop app).