Because there's a lot of work done and reading all the posts above is a waste of time I want to give a status report of the differences between the "master" and "pixelshift" (Pentax multi-frame file support) branches:

Improvements related to Pentax multi-frame raw files in general:
You can process each of the frames using the demosaicer of your choice for pixel-shift files and for 3-in-1 raw HDR files.
Improvements related to Pentax pixel-shift files:
You can combine the 4 frames of a pixel-shift raw with and without motion correction using the "pixelshift' demosaic method. I know it's not a demosaic method but I didn't find a better place for it in GUI
You can adjust the motion correction in several ways, though the default settings in adaptive mode are quite good.
The regions with motion are taken from the AMaZE-demosaiced frame of your choice.
Adaptive mode considers the ISO you took the shot for detecting regions of motion.
"Show motion" mode shows the regions with motion in the color the motions are detected in.
"Show mask only" mode shows the regions with motion in a grey mask which can be saved for further processing.
Currently supported pre-processing steps (applied to all frames before pixel-shift):
Raw CA correction.
Raw white level adjustments.
LCP vignetting correction.
Green equilibration.
Interpolate bad pixels provided by .badpixels file or by dark frames.
Currently unsupported pre-processing steps
Auto hot/dead pixel detection (currently the selected frame is used for that).
Line noise filter works only on the selected frame (I don't think we need that for Pentax files at all).
Flat Field correction
Dark Frame subtraction
TODO
GUI currently has too many controls because we are still testing motion correction methods.
GUI currently has some bad controls (Pixel-shift motion correction is a slider though a combobox would be better).