Hi David,
This is easy enough to do in PJSR, but I think this presents a problem since each module is loaded at startup. They don't have visibility to each other.
Unfortunately this still isn't possible in version 1.7.0. We call this feature
intermodule communication (IMC). It is already implemented and working extremely well for file format modules (ImageCalibration, ImageIntegration, StarAlignment and many other tools are using it). However, I still haven't had the time to implement IMC for processes. I intended to implement it for 1.7.0 but the project functionality took me more time than expected, IMC is very complex, and achieving a stable 1.7.0 release before Summer was an absolutely priority. IMC for processes is one of the next priority tasks so It will be implemented during the 1.7 cycle, that is during Q4 2011.
For now, don't hesitate to reimplement things. If you need an auto STF, just copy and paste the relevant code from the IntensityTransformations module. Keep in mind that this is a temporary situation; once we have IMC for processes working we'll get the same flexibility in PCL that we have now in PJSR.
Alternatively I'd want modules to push their GUI components into a different window so you could effectively combine several modules into one without having to re-write the entire GUI for each module.
This is indeed very desirable and it will be implemented as part of IMC for processes, both in PJSR and PCL. I am sure that you can figure out the complexity involved in this feature. Keep in mind that these functionalities can compromise stability of the whole platform. A defective implementation can be a real nightmare instead of something useful. If you know me then you know that I won't release such a significant feature until I am 100% sure that my implementation works correctly and won't cause problems.