We are currently managing about 500+ workbenches, some in the filesystem some on FME Server. We try to name them based on the datasets they are working on and the source and destination systems/databases.
We do not know if it´s the best way to keep up with finding them again, but up to this scale it works.
A best-practice HowTo or tutorials about workbench documentation and management at larger scale would be great, maybe there are better ways than we do.


