Comment by xenoscopic

One option I often recommend is setting up multiple synchronization sessions targeting different parts of a particular codebase with different synchronization configurations (kept mutually exclusive via ignore specifications). Quite often people want unidirectional replicas for a certain folder (e.g. a build directory) with more standard bidirectional synchronization for the rest of the code. It can be a little more complex to orchestrate, but you can use Mutagen's project functionality or a shell script to automate the setup a bit.