Zotfile does not work with Zotero 6. However, Zotero 6 has many of the same functionalities as Zotfile ( see e.g. Zotero 6 compatibility by dstillman · Pull Request #573 · jlegewie/zotfile · GitHub).
I followed the workflow above until section 3.2 and here is my version of 3.2:
Extraction of Notes
When you have added your notes to a paper in Zotero 6 using their annotator, you can create a note with all annotations in the PDF by right-clicking on the parent item in the items list and select Add Note from Annotations. (see pdf_reader [Zotero Documentation])
Following this you can right-click on the parent item in the items list and select Mdnotes -> Create full export note to get the formatted output in Obsidian.
The Create full export note menu exports an item’s metadata and its Zotero notes as a single file. For that it uses the Mdnotes Default Template.md, which you should edit by adding your desired metadata placeholders like done in this tutorial. Zotero notes included in this export will use a new template you need to add to the same root directory as Mdnotes Default Template.md called Zotero Note Template.md. My Zotero Note Template.md only contains one line
{{noteContent}}
Formatting the extraction of notes
The customizing of annotations can be done using note templates in the Config Editor in Zotero, like in Section 3.1. A brief link on how the Config Editor customization works can be found here: note_templates [Zotero Documentation] . Now you need to change
extensions.zotero.annotations.noteTemplates.titleextensions.zotero.annotations.noteTemplates.noteextensions.zotero.annotations.noteTemplates.highlight
3.2.2 Changing the Note Title
In Zotero’s Config Editor, you need to change the setting extensions.zotero.annotations.noteTemplates.title to change the title of the Extracted note. The default is <h1>{{title}}<br/>({{date}})</h1> but as I am not interested in keeping the date, I changed it to <h3>{{title}}<br/></h3>.
3.2.3 Editing the Annotated Comments
I want to highlight my annotated comments from parts of the main text that are highlighted. However, Mdnotes does not yet support italics or bold (In the Changelog (https://argentinaos.com/zotero-mdnotes/changelog/) this feature is listed under “Unreleased”).
In Zotero’s Config Editor, you need to change the setting extensions.zotero.annotations.noteTemplates.note to change the behavior of Notes/Sticky Notes
So for now I have changed it to <p>[[Note]] {{highlight quotes='true'}} {{citation}}</p> <blockquote><p>{{comment}}</p></blockquote> {{if tags}} <blockquote><p><b>Tags:</b> #{{tags join=' #'}}</p></blockquote>{{endif}}
Line by line:
<p>[[Note]] {{highlight quotes='true'}} {{citation}}</p>This adds the link Note to this comment and tells me where in the document I added this sticky note.<blockquote><p>{{comment}}</p></blockquote>: This adds my own note as a blockquote to separate it from the rest of the main text.{{if tags}} <blockquote><p><b>Tags:</b> #{{tags join=' #'}}</p></blockquote>{{endif}}: This adds another blockquote with any tags given to this note.
3.2.4 Changing Underlines
This I could not find the setting for.
3.2.5 Highlight Colors
In Zotero’s Config Editor, you need to change the setting extensions.zotero.annotations.noteTemplates.highlight to change the behavior of the highlight.
This is a bit more limited than before as there as of now only are 5 colours in Zotero Annotator : yellow: ‘#ffd400’, red: ‘#ff6666’, green: ‘#5fb236’, blue: ‘#2ea8e5’, purple: ‘#a28ae5’.
My system currently is: yellow is a default highlight, red is notes I disagree with the authors, green marks interesting follow-up material, blue highlights things that confuse me, and purple are important conclusions.
For now I have changed it to this long bit
{{if comment}} {{if color == '#ffd400'}}<p>{{highlight quotes='true'}} {{citation}}</p><blockquote><p>{{comment}}</p></blockquote> {{elseif color == '#5fb236'}}<p>{{highlight quotes='true'}} {{citation}}</p><p> - [ ] {{comment}} #task</p> {{elseif color == '#ff6666'}}<p>[[Disagreement]]: {{highlight quotes='true'}} {{citation}}</p> <blockquote> <p>{{comment}}</p></blockquote> {{elseif color == '#2ea8e5'}}<p>[[Confusion]]: {{highlight quotes='true'}} {{citation}}</p> <blockquote><p>{{comment}}</p></blockquote> {{elseif color == '#a28ae5'}}<p>[[Important]]: {{highlight quotes='true'}} {{citation}}</p> <blockquote><p>{{comment}}</p></blockquote> {{else}}<p>{{highlight quotes='true'}} {{citation}}</p><blockquote><p>{{comment}}</p></blockquote>{{endif}} {{if tags}} <blockquote><p><b>Tags:</b> #{{tags join=' #'}}</p></blockquote>{{endif}} {{else}}<p>[[Highlight]]:{{highlight quotes='true'}} {{citation}}</p>{{endif}}
Again let us go through it line by line:
{{if comment}}: If a text comment was added to the highlight, do some of the following
-{{if color == '#ffd400'}}<p>{{highlight quotes='true'}} {{citation}}</p><blockquote><p>{{comment}}</p></blockquote>: If the color is yellow, just add a blockquote note.
-{{elseif color == '#5fb236'}}<p>{{highlight quotes='true'}} {{citation}}</p><p> - [ ] {{comment}} #task</p>: If the color is green, add a to-do item with the comment and tag the item with the label#task. This makes it possible to do the neat Dataview extraction in Obsidian as explained at the end of tutorial.
-{{elseif color == '#ff6666'}}<p>[[Disagreement]]: {{highlight quotes='true'}} {{citation}}</p> <blockquote> <p>{{comment}}</p></blockquote>: If the color is red, mark the comment as Disagreement and add the note in a blockquote.
-{{elseif color == '#2ea8e5'}}<p>[[Confusion]]: {{highlight quotes='true'}} {{citation}}</p> <blockquote><p>{{comment}}</p></blockquote>: If the color is blue, mark the comment as Confusion and add the note in a blockquote.
-{{elseif color == '#a28ae5'}}<p>[[Important]]: {{highlight quotes='true'}} {{citation}}</p> <blockquote><p>{{comment}}</p></blockquote>: If the color is purple, label the comment as Important and add the note in a blockquote.
-{{else}}<p>{{highlight quotes='true'}} {{citation}}</p><blockquote><p>{{comment}}</p></blockquote>{{endif}}: If the color is something else (not yet implemented), then just add the note in a blockquote.{{if tags}} <blockquote><p><b>Tags:</b> #{{tags join=' #'}}</p></blockquote>{{endif}}: All tags are added to a list
{{else}}<p>[[Highlight]]:{{highlight quotes='true'}} {{citation}}</p>{{endif}}If the highlight contains no notes, mark it asHighlight.
Workflow
So the workflow becomes:
Add notes and highlights to your paper,
Right-click paper and Add Note from Annotations
Right-click paper and Mdnotes -> Create full export note