"Include in Search" Checkbox

And with another of the options in that same menu, you can achieve a level of specific control over what is being searched, as opposed to purely categorical, with the “Search Binder Selection Only” setting. A simple demonstration of that would be to use Cmd-click and Shift-click to pick a few files out of the binder, constraining search to just those selected items.

However for a more persistent case (like a checkbox would provide), it’s useful to keep in mind that the Collections feature (§10.2, Using Collections, in the user manual PDF) is, among other things, a way of saving a selection for convenient future use.

  • After selecting the individual items you want to restrict your search to, use the Documents ▸ Add to Collection ▸ New Collection menu command.
  • In the future, when you want to search by this restricted list of items:

[*] Use the Navigate ▸ Collections ▸ submenu to select your restricted search collection.

  • In the sidebar, hit ⌘A to select all.
  • Run your search with the “Search Binder Selection Only” option enabled.
  • or– click the “hook arrow” button in the collection header bar to load the collection into a corkboard or outliner view, and in that view, hit ⌘F to filter the collected items by a search. (Though note if you intend to use that method, you can more directly get to the point of having the preselected items in your editor via the Navigate ▸ Go To ▸ Collections command, or from the right-click contextual menu in the editor header bar.)
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One more tip: try Snapshots for this kind of thing going forward (§15.8, Using Snapshots). One of the advantages of snapshots is that they are not considered proper binder items for the purposes of things like project search. Past revisions/notes of a text are stored exclusively within the sidebar of the chunk of text they pertain to, like metadata would be. Consequently searches only ever return one copy of a section, the most recent revision of that text.

And if you do periodically want to search through old versions you may still do so, with the Documents ▸ Snapshots ▸ Show Snapshots Manager menu command.