Yes, commands available to be executed include: start, stop, isRunning (checks whether the engine is running or not), dispose, size (number of flow charts on the engine), expedite, resume, pause, interrupt, remove, recover and export.

For instance to start a Flux engine you could use the command:

java -cp .;flux.jar flux.Main server start 

To see the number of flow charts on your Flux engine you could use the command:

java -cp .;flux.jar flux.Main client -host myHost size "/" 

To export a flow chart to your Flux engine you could use the command:

 
java -cp .;flux.jar flux.Main client export "path/to/flowChart.ffc"

For a full list of available commands type:

java -cp .;flux.jar flux.Main help