Hi,
Just seen your project here. I think I could help you very fast bcouze I already have some base implementation of FIX protocol (based on QuickFIX/J) for FXCM FIX xml specification.
Briefly : I'm programming Java more than 15 years, last 5 years I've been working on projects related to trading algos (misc. FIX implementations like FXCM, Lime, IB).
In your case we could consider do not scan files in directory - I suspect it'd be bit slow, but use something fast communication protocol (for instance 0MQ) to notify connector about your order/action.
0MQ library has a lot of bindigs for different languages. What's your application where you doing calculations for your model/signals ?