I have been looking for the answer to this for a year. I would pay a thousand dollars, happily, for the perfect system that allowed me:
to use an open source encrypted program
data saved on my server/ personal cloud or even just able to sync with USB
Web clipper
HIGHLIGHT AND TAG text within a PDF that is embedded within the app/program (this is the piece I am not able to get)
able to then use tags and/or highlights to mind map
search function which searches all notes made and the complete text of pdf.
Basically a blend of MarginNote3/Remnote and Joplin. I JUST want to tag text in PDFs to build a personal data library and it seems the world does not want this to happen. lol I'm hoping and praying for you someday!
Other than that, there may be developed a plugin that would retrive "named destinations" links from a PDF. Those destination links could be used to navigate inside a PDF (url-to-file/file.pdf#nameddest=dest3) and additionally linked within the note structure of Joplin.
I'm not sure what's the linklist implied but in original post I meant that a user potentially can extract the text from a pdf, highlight it and link a separate note for each highlight.
Here's the example:
A note with pdf (let's call it NoteTOC) keeps text extract from the pdf. In mind map view NoteTOC represents a TOC of pdf highlights. Each highlight of text in NoteTOC has a child note (backlinked to NoteTOC).
mermaid src
graph TD
subgraph NotebookPDF
Highlights --> Child1(Child note1)
Highlights --> Child2(Child note2)
Highlights --> Child3(Child note3)
subgraph NoteTOC
Pdf --> Text(Text from Pdf) --- Highlights
end
end
This way each highlight in pdf can be linked anywhere within the note structure (well, sharing externally is also possible). Also, you get the opportunity to comment each highlight in its own note.