Before Obsidian, i used Docear to manage my annotations in PDF.
Docear can scan and retrieve highlights and annotation like zotfile. It also can remember the annotation position in the PDF file. However, it can retrieve annotation of multiple files at once, and do it faster than zotfile.
Currently, @argentum written mdnotes to bridge between obsidian and zotero. However, i think it would be more efficient to be able to retrieve annotation straight from PDF into obsidian. Each PDF will have their own md file. Each block linking with their respective PDF file. (basically zotfile for obsidian)
Docear is open source, and they uploaded all their code to their website.
Additional request: It would be even better if this plugin also link with zotero (as we still need zotero to cite in MS docx)