This is the second iteration for this MR which addresses only AGIPD changes for running dark and correct calibration processes for AGIPD's single module detector.
1- Create a temporary agipd_single_module_geometry function to plot a single AGIPD module using extra-geom
2- Removing skipping parts in dark notebook from previous MR.
3. Fix AGIPDCtrls by removing AGIPD1M and AGIPD500K assumptions when sorting the dark runs.
4. Differentiate between the list for modules and the list of module indices mod_indices. This needs a bigger change by using the new CALCAT metadata for the detector's module indices.
5. Other fixes while testing dark processing for proposal p900438 runs from 1 to 3 and correction for run 1
