This issue is in response to this comment (also here).
The basic idea is to add a extensible settings page for contextual links (e.g., modifiable via hook_form_FORM_ID_alter()) that provide a place to turn on/off and/or modify different aspects of Contextual Links.
A suggested place would be admin/config/administration/contextual-links, which seems to fit, and would also help provide a reason for admin/config/administration to have a submenu (currently there's only one submenu item, admin/config/administration/admin-bar).
An example use case—which also creates the setting page—is PR https://github.com/backdrop/backdrop/pull/3790, which creates layout and theme-related contextual links, in response to https://github.com/backdrop/backdrop-issues/issues/2626. (At this point, it's looking like a different PR that doesn't create contextual links will solve that issue, but this is an example of the type of setting that would belong there.)
It would also be a good home for the settings in Layout Contextual Links module (which is the contrib version of PR https://github.com/backdrop/backdrop/pull/3790).
Other possible use cases that have been mentioned in discussions include finer-grained controls on which contextual links to display, to allow site-builders to turn on/off contextual links selectively, or to optionally add additional information to contextual links (e.g., the title of the thing being linked to).
At this point (assuming that PR https://github.com/backdrop/backdrop/pull/3790 doesn't go forward), there's not yet a specific proposal for something to include in this settings page, but adding the issue here (per @BWPanda's comment) so that it doesn't get lost, and perhaps future proposals of modifications to contextual links that need their own settings can extend or link to this issue and resurrect the concept.
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