Policy Decision On Correct Alignment Behaviour When References Superceded

[ConorFWild]

When a reference dataset for an alignment is updated, what is the desired behaviour? I.e. B was aligned to A, but now the updated A' is offset by 10A. Alignment is still possible, and new datasets aligned to A' are no longer aligned to previous alignments.

This has become relevant now with the updated version of Ryan's dataset (upload_2).

Options include:

1. Generate new alignments to the reference dataset
2. Keep the old version of A for the purposes of alignment, and align the new version, A', to the old version
3. Don't do anything

Also important: what if an update means that it is no longer possible to align to datasets? I.e. A was aligned to C via B, but now B has changed, so A can no longer be aligned to B. If A is also updated, we presumably need to generate A', which can no longer be aligned to B.

Options include:

1. Break the original site into child sites and regenerate alignments to each.
2. Keep the old site and keep the old version of B for the purposes of performing alignments
3. Don't do anything

@phraenquex Need your executive decision on this before continuing work

[phraenquex]

@ConorFWild I think you've fixed this already? If not, please move back to "ASAP Critical" swimlane.

[Waztom]

Linked to #1280

[phraenquex]

Moving to won'tfix.