The synchronization uses a repeated three-way merge algorithm, very similar to Git's merge when merging branches. It is triggered by recursive filesystem watching, which is also used to accelerate filesystem rescans. It maintains a virtual most-recent-ancestor and uses the two synchronization endpoints as the "branches" being merged. Much like Git has "-X ours" and "-X theirs" options, Mutagen also has automated conflict resolution[0] modes that can be specified. You can find the reconciliation algorithm here[1] (and there are an exhaustive set of test cases in the corresponding _test.go file).

To avoid a large class of race conditions (at least to the extent possible allowed by POSIX and Windows), Mutagen will use `*at` style system calls for all filesystem traversal on POSIX systems, with a similar strategy on Windows.

Also, to avoid race conditions due to filesystem changes between scan time and change-application time, Mutagen will perform just-in-time checks that filesystem contents haven't changed from what was fed into the reconciliation algorithm.

[0]: https://mutagen.io/documentation/synchronization#modes [1]: https://github.com/mutagen-io/mutagen/blob/master/pkg/synchr...