Good question, Marcel. I’m afraid there’s no simple answer here, so let’s break it down.
The first thing to keep in mind is that there can only be one Paperpile-generated bibliography in the document (the final one with all references); any others you include must remain in plain text in order to avoid unexpected behavior.
Your second idea might be the less complicated to implement. You can create a main “Thesis” folder with “Chapter” subfolders and gradually add the corresponding references. Once arranged, select all references in a folder and cite them (either from the menu above or with Ctrl + C) - this will copy plain text bibliographic entries to your clipboard in the chosen style, which you can then copy to your thesis under the corresponding chapter. Keep in mind you will still have to manually insert the in-text citations in the chapters for those to appear in the final bibliography.
Another thought I had was to format the chapters in separate documents.
For the chapters written in Google Docs: if they already have Paperpile citations and bibliography, you can simply copy/paste the text (excluding the bibliography) to the main thesis document. The citations will remain “live” and appear in the thesis bibliography once formatted. You can then use our optional sidebar add-on to create a clean copy of the chapter document and from there copy/paste that chapter’s bibliography to the thesis.
For the chapters coming from PDFs: I would suggest pasting the text onto a separate document first and replacing the in-text citations with “live” ones. This will enable you to follow the same steps outlined above and ensure all those citations end up in the thesis bibliography once you’ve included the chapter.
Keep in mind that further citations/edits would have to be manually included in these chapter bibliographies.
Any other thoughts/ideas on the subject are more than welcome!