Fitting not respecting the fitting pipeline

[hsorby]

This scenario did not have the outcome expected:

I did a manual alignment first then added a fit. Next, I added an additional Align step and manually moved the scaffold out of place (not something a sensible person will do). The scaffold moved to where I want but since it is a bad move, I decided to undo that step by removing the check next to the last Align step. The fitter reverted to the scaffold after the fit step again. So I clicked Done but in Data Embedder, the fitted scaffold I see is the one was manually moved in the Align step, instead of the fit step.