Moved the pipeline logic into a dedicated function

Makes it easier to call from other places if/when needed.
Call dataModified on the aligned data
Python scripts for image series alignment
Made the dialog a little wider to see full script
Generalize the reaction class for multiple scripts

Generalize the reconstruct reaction class to act for different
scripts, and use it for several new scripts we want in the menu.
Move classes to more sensible name

Now they have been generalized.