Some tools, I have come across to deal with the “copy of source material” issue.
Depending on your source material, you might be able to use things like Zotero and Obsidian to annotate and export them into text files, for PDFs and webpages even I think. Just coming out from helping someone setup the workflow.
But if it is more like code or video, I am not certain. For me Emacs org-mode has been a huge help. I can insert links to the source content like code either directly to files or GitHub permalinks and write down my notes, have code highlights and even in some cases run the code and have results inserted back into docs.
Depending on your source material, you might be able to use things like Zotero and Obsidian to annotate and export them into text files, for PDFs and webpages even I think. Just coming out from helping someone setup the workflow.
But if it is more like code or video, I am not certain. For me Emacs org-mode has been a huge help. I can insert links to the source content like code either directly to files or GitHub permalinks and write down my notes, have code highlights and even in some cases run the code and have results inserted back into docs.