Hi Dave
I don't think that this will be developed by Juan (or me) in the shot/mid term. AFAIK, we both are more of "divide and conquer" guys than "do it all".
Having said that, almost everything is currently working as separate processes. So, a script to automate everything should not be too hard to create. Of course, there is the problem of working with large arrays of data, with "unknown" format, and one wants to have everything inside the same code. So, it should be well organized.
On a parallel note, I'll be writing a process module that performs some of this tasks, in a much more simpler way. I have to calibrate and align microscopic image for a project I'm working on the university. I may release the code of the "preprocessing" steps, in a month or two. The workflow shares some steps, but then it diverges and needs other steps not applicable to astronomy. Anyway, if anybody wants to write something from the scratch, this may help a bit.