I love the update that adds persistent folding and color groups!
The implementation of color groups gave me an idea of how persistent graph sculpting could be implemented.
There could be a distinct category in the graph menu - it could even be called Graph sculpting.
Color groups Graph sculpting
The section would allow you to add search conditions - similarly to how color groups works - to be permanently excluded from the graph.
For instance I have a tag called #people which connects all pages dedicated to various people. By selecting tag:#people in the graph sculpting menu, all notes containing the tag would not be displayed.
By default, all groups are visible and no eye icons appears. The “visible eye” icon for a group appears whenever the mouse hovers over any of the interface elements for that group. (That exposes the interface option to the user.) Clicking the eye marks the group as hidden and the faded “hidden eye” icon appears. That icon persists when the mouse leaves so that the user can always see which groups are hidden. Clicking any “hidden eye” icon marks that group as visible again.
Since groups are visible by default, marking a group as hidden will hide all members of that group even if they are also a member of a visible group. Alternately, the sort order of groups takes priority for determining visibility just as it does for determining node color. (If the latter, I would like it to be easier to sort groups.)
With that said, we may be deep into plugin territory here. Best to keep the out of the box application focused and simple.