Fix citations by using a universal tracker of the indices

This MR fixes current issues with outputting the correct citations by using a dedicated dictionary citation_index that contains all the pipelines/skymaps and their indices to explicitly choose the index for each citation. This gives a lot of control to use a flexible system for all types of circulars, the downside being that the order must be pre-determined and set prior to creating the circular.

This MR also fixes various other minor issues with circulars at the same time.