Comment 8 for bug 728326

Synapse by design does not store any usage information itself, it relies on system-wide usage as logged by Zeitgeist. That way Synapse just works immediately without the need to teach it something yourself. Of course this brings some drawbacks, but the system-wide integration outweighs those imo.

Bottom line, what you want it to do should work since version 0.2.2 (maybe 0.2.4) if you have Zeitgeist installed. If not, please open a new bug, this one will keep track of sorting folders based on their usage.