Thanks for the quick response!
So I tested the notes search in Skim. You are correct, when searching the PDF Skim does not search in the notes. To search the notes from the PDF you need to search in the Notes search panel and Skim will show notes with the search term but will not show notes details or highlight searched term.
But when I open a Skim Notes file (not the PDF) through EagleFiler it opens only the notes and there is a search field. The search results show the notes with the searched term but will not highlight any notes. Also the Skim Notes file appears to be stored not as plaintext, so highlighting the search outside the Skim interface might be tricky.
Given that the Skim notes viewer has a search field, would it be possible to pass on the search term when opening Skim notes, just like EageFiler currently passes on search term to opened Skim PDF? This way I can pinpoint to an annotation with my search term by first searching in EagleFiler and then just opening the Skim notes. (I saw a thread where some people did not want the functionality of passing search term to PDF. I actually think this feature is great and very thoughtful. I like it and it works well with my workflow. So, thanks for adding that!)
Oh wait, the way EagleFiler opens Skim notes from search results what I just suggested above would not work. This is actually a little confusing behavior. So I have a PDF and an attached Skim notes file. In the file viewer, EagleFiler shows both the Skim notes file and the pdf. When I open the Skim notes file, EagleFiler opens just the notes (not the pdf) with Skim viewer. But when I open the same Skim notes file when it appears in a search result, EagleFiler will open the associated PDF instead of opening the notes file. Is this the intended functionality? I am happy to share more details about this to reproduce this.