I have recently added the following feature request to JAC (https://jira.atlassian.com/browse/JRA-29307). However, since it will need votes to be considered and because I am not sure what I am missing here (maybe I am not understanding the way it works), I would like to discuss with the community.
When adding custom fields they can only be restricted to certain projects but there is no way to make them available for a scheme. Manually choosing the projects a custom field context applies to is not a good way because it is very error-prone (think about what happens when the customer adds projects at a later stage). Therefore most people end up using the global context but restricting the field to certain field configurations. However, the field is automatically added to all field configurations and per default SHOWN. This means you have to go through every single field configuration you don't want to use it for and HIDE it.
I can think of two possible solutions:
(1) Implement Custom Field Schemes
OR
(2) Implement another wizard page when adding a new custom field that allows to show / hide the custom field for certain field configurations (just like it is done with Screens)
I attached the diagram the Atlassian Support team referred me to and added annotations (in red) to visualize my understanding. They said everything works as designed and makes sense, but I think they are missing the custom fields situation here...
You should be using different screens and that might fix some of you problems. Eventhough the fields are automatically added to field configurations and "shown" by default, they are never added to all screens by default. The admin has to select the screens.
Having said that, contexts works for us. It might be error prone but hey, you have an option!
We are extensively making use of screens, but the custom fields still appear in the Search Navigator as well as the Issue Navigator and therefore confuse our users and clients (!).
Contexts are a workaround, but I believe they need improvements (as per my feature request) since we recently ran into a lot of problems where projects where not added to every custom field context and therefore resulted in different configurations (in specific, there were problems with missing fields and the inability to move issues, etc.).
As a reference and to explain why this is so important to us: We currently have 200+ custom fields and 500 projects.
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