cluster know which cluster_values are to be marked as deprecated upon update

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@cvandeplas is already working on this.

Since Jun 26, 2024.

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Description

enhancement

One of the challenges in regards to updating a galaxy/cluster in an automated way is to know which cluster_values do not exist anymore in the original source.
If we just iterate over the source, and update our galaxy we will not know which ones were not updated and should therefore be marked as deprecated.

Brainstorm for methods :

  1. an internal variable listing the uuids of the entries that were touched (append()) since a certain moment. Flush it before using. Add a new function to deprecate the delta.
  2. Add a new function to mark all as deprecated at once, and whenever we append() we mark them as non-deprecated
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