Upgrade StorageFeature Request: Syncable folder/package attachments for Markdown files and assets
Hello Zotero team,
I would like to suggest support for syncable folder/package attachments in Zotero, especially for Markdown-based research notes that contain local asset folders.
Current problem
Many users write research notes in Markdown using editors such as Obsidian, Typora, VS Code, Zettlr, or other plain-text tools. In practice, a Markdown note is often not a single standalone file. It commonly has a structure like this:
note.md
assets/
image-001.png
image-002.jpg
figure-1.svg
The Markdown file then references images and other resources through relative paths:
This structure is portable, editor-independent, and very common in Markdown-based writing workflows.
Currently, Zotero can store and sync individual attachment files through Zotero Storage or WebDAV. Zotero can also link to external files. However, linked files are not synced by Zotero itself, and the Linked Attachment Base Directory only helps resolve paths for linked attachments. It does not make Zotero sync the associated assets/ folder together with the Markdown file.
As a result, when a user attaches only note.md to Zotero, the Markdown file may sync, but its local images and asset files do not remain attached as a coherent unit. If the user uses linked files, the folder structure can be preserved locally, but Zotero Sync does not sync that folder. If the user stores the Markdown file and images as separate attachments, Zotero no longer understands that they belong to the same Markdown note, and the relative path relationship is easily broken.
Why this is especially important in the AI era
I believe this feature is becoming especially important as AI tools become widely used in academic and research workflows.
Research notes are no longer only human-readable documents. Increasingly, they are also used as structured, machine-readable knowledge sources for AI assistants, local LLMs, RAG systems, literature review tools, writing agents, and personal research knowledge bases.
Markdown has become one of the most important formats in this context because it is:
plain text
portable
version-controllable
easy for AI systems to parse
easy to combine with citations, figures, screenshots, tables, code outputs, and diagrams
In AI-assisted research workflows, a Markdown note and its assets are not separate things. The images, screenshots, figures, diagrams, OCR targets, tables, and generated charts inside the assets/ folder are often part of the evidence and context that AI tools need to understand the note correctly.
For example, an AI assistant may need to process:
note.md
assets/
paper-figure-1.png
experiment-result-table.png
screenshot-of-annotation.jpg
model-architecture.svg
If Zotero can only sync the Markdown file but not its associated assets folder as a coherent unit, the note becomes incomplete. This limits Zotero’s usefulness in modern AI-assisted research workflows.
This is not just a convenience issue. It affects:
long-term preservation of research notes
reproducibility of AI-assisted literature reviews
multimodal research workflows involving text and images
local knowledge-base construction
citation-grounded AI writing
cross-device continuity of AI-readable research materials
As AI becomes more deeply integrated into research, Zotero has an opportunity to remain the central reference-management infrastructure not only for PDFs and metadata, but also for structured research materials that are designed to be read by both humans and AI systems.
Supporting syncable folder/package attachments would make Zotero more future-proof without requiring Zotero to become an AI tool or a Markdown editor.
What I am requesting
I am not requesting that Zotero become a Markdown editor.
Instead, I am suggesting that Zotero support a new kind of stored attachment, such as:
Package Attachment
Folder Attachment
Markdown Package Attachment
Stored Folder Attachment
The core idea is simple:
Zotero should be able to treat a folder as one stored, syncable attachment while preserving its internal directory structure.
For example, a Zotero item could have one attachment displayed in the UI:
Markdown Package: note.md
But internally, that attachment would preserve this structure:
note.md
assets/
image-001.png
image-002.jpg
figure-1.svg
Zotero Storage or WebDAV would then sync the whole package recursively, not just the entry Markdown file.
Expected behavior
A minimal implementation could work as follows:
The user adds a folder as a stored package attachment.
Zotero preserves the internal folder structure.
The user can specify one entry file, such as note.md.
In the Zotero item view, the package appears as a single attachment.
Double-clicking the attachment opens the entry file.
“Show File” or a new “Show Package Folder” action opens the package root folder.
Zotero Storage or WebDAV syncs all files inside the package folder.
Exporting the attachment preserves the original folder structure.
Relative paths inside the Markdown file remain valid across devices after sync.
Why this matters
This would make Zotero much more compatible with modern plain-text and AI-assisted research workflows.
Markdown notes are often used for:
literature notes
reading summaries
research diaries
figures and screenshots
draft fragments
reproducible research notes
AI-readable knowledge bases
RAG source documents
thesis and paper-writing materials
For these workflows, the note and its assets are logically one unit. Syncing only the .md file is not enough, because the images and other local resources are part of the note.
At the same time, this feature would not require Zotero to implement a full Markdown editor, Markdown previewer, AI assistant, or Obsidian-like knowledge management system. Zotero would only need to manage the attachment as a stored package and keep its internal file structure intact.
Possible minimal viable version
The first version could be intentionally simple:
Stored Package Attachment
root folder
entry file
preserved internal directory structure
recursive Zotero Storage/WebDAV sync
open entry file
reveal package folder
export package folder
Markdown-specific features such as previewing, image insertion, broken-link checking, manifest files, or AI integration could be added later or handled by third-party plugins.
The most important part is the underlying attachment model:
a syncable folder/package attachment that preserves internal relative paths.
Why separate files are not enough
Storing note.md, image-001.png, and image-002.jpg as separate Zotero attachments does not solve the problem, because Zotero does not know that these files form one Markdown workspace. The relative path relationship between the Markdown file and its assets/ folder is part of the document structure.
Similarly, linked attachments can preserve the local folder structure, but they do not use Zotero’s file sync. This means users still need a separate sync tool for the Markdown workspace, which defeats the purpose for users who want Zotero Storage or WebDAV to manage their research attachments.
Summary
I would like to propose native support for syncable stored folder/package attachments.
This would allow Zotero to store and sync a folder such as:
note.md
assets/
image-001.png
image-002.jpg
as one coherent attachment under a Zotero item.
This would be valuable in the AI era, where notes increasingly serve as human- and AI-readable knowledge sources.
It would help Zotero remain a central part of future academic workflows while keeping Zotero’s role focused on reference and attachment management, rather than turning it into a Markdown editor or AI application.
Thank you for considering this feature request.
I would like to suggest support for syncable folder/package attachments in Zotero, especially for Markdown-based research notes that contain local asset folders.
Current problem
Many users write research notes in Markdown using editors such as Obsidian, Typora, VS Code, Zettlr, or other plain-text tools. In practice, a Markdown note is often not a single standalone file. It commonly has a structure like this:
note.md
assets/
image-001.png
image-002.jpg
figure-1.svg
The Markdown file then references images and other resources through relative paths:
This structure is portable, editor-independent, and very common in Markdown-based writing workflows.
Currently, Zotero can store and sync individual attachment files through Zotero Storage or WebDAV. Zotero can also link to external files. However, linked files are not synced by Zotero itself, and the Linked Attachment Base Directory only helps resolve paths for linked attachments. It does not make Zotero sync the associated assets/ folder together with the Markdown file.
As a result, when a user attaches only note.md to Zotero, the Markdown file may sync, but its local images and asset files do not remain attached as a coherent unit. If the user uses linked files, the folder structure can be preserved locally, but Zotero Sync does not sync that folder. If the user stores the Markdown file and images as separate attachments, Zotero no longer understands that they belong to the same Markdown note, and the relative path relationship is easily broken.
Why this is especially important in the AI era
I believe this feature is becoming especially important as AI tools become widely used in academic and research workflows.
Research notes are no longer only human-readable documents. Increasingly, they are also used as structured, machine-readable knowledge sources for AI assistants, local LLMs, RAG systems, literature review tools, writing agents, and personal research knowledge bases.
Markdown has become one of the most important formats in this context because it is:
plain text
portable
version-controllable
easy for AI systems to parse
easy to combine with citations, figures, screenshots, tables, code outputs, and diagrams
In AI-assisted research workflows, a Markdown note and its assets are not separate things. The images, screenshots, figures, diagrams, OCR targets, tables, and generated charts inside the assets/ folder are often part of the evidence and context that AI tools need to understand the note correctly.
For example, an AI assistant may need to process:
note.md
assets/
paper-figure-1.png
experiment-result-table.png
screenshot-of-annotation.jpg
model-architecture.svg
If Zotero can only sync the Markdown file but not its associated assets folder as a coherent unit, the note becomes incomplete. This limits Zotero’s usefulness in modern AI-assisted research workflows.
This is not just a convenience issue. It affects:
long-term preservation of research notes
reproducibility of AI-assisted literature reviews
multimodal research workflows involving text and images
local knowledge-base construction
citation-grounded AI writing
cross-device continuity of AI-readable research materials
As AI becomes more deeply integrated into research, Zotero has an opportunity to remain the central reference-management infrastructure not only for PDFs and metadata, but also for structured research materials that are designed to be read by both humans and AI systems.
Supporting syncable folder/package attachments would make Zotero more future-proof without requiring Zotero to become an AI tool or a Markdown editor.
What I am requesting
I am not requesting that Zotero become a Markdown editor.
Instead, I am suggesting that Zotero support a new kind of stored attachment, such as:
Package Attachment
Folder Attachment
Markdown Package Attachment
Stored Folder Attachment
The core idea is simple:
Zotero should be able to treat a folder as one stored, syncable attachment while preserving its internal directory structure.
For example, a Zotero item could have one attachment displayed in the UI:
Markdown Package: note.md
But internally, that attachment would preserve this structure:
note.md
assets/
image-001.png
image-002.jpg
figure-1.svg
Zotero Storage or WebDAV would then sync the whole package recursively, not just the entry Markdown file.
Expected behavior
A minimal implementation could work as follows:
The user adds a folder as a stored package attachment.
Zotero preserves the internal folder structure.
The user can specify one entry file, such as note.md.
In the Zotero item view, the package appears as a single attachment.
Double-clicking the attachment opens the entry file.
“Show File” or a new “Show Package Folder” action opens the package root folder.
Zotero Storage or WebDAV syncs all files inside the package folder.
Exporting the attachment preserves the original folder structure.
Relative paths inside the Markdown file remain valid across devices after sync.
Why this matters
This would make Zotero much more compatible with modern plain-text and AI-assisted research workflows.
Markdown notes are often used for:
literature notes
reading summaries
research diaries
figures and screenshots
draft fragments
reproducible research notes
AI-readable knowledge bases
RAG source documents
thesis and paper-writing materials
For these workflows, the note and its assets are logically one unit. Syncing only the .md file is not enough, because the images and other local resources are part of the note.
At the same time, this feature would not require Zotero to implement a full Markdown editor, Markdown previewer, AI assistant, or Obsidian-like knowledge management system. Zotero would only need to manage the attachment as a stored package and keep its internal file structure intact.
Possible minimal viable version
The first version could be intentionally simple:
Stored Package Attachment
root folder
entry file
preserved internal directory structure
recursive Zotero Storage/WebDAV sync
open entry file
reveal package folder
export package folder
Markdown-specific features such as previewing, image insertion, broken-link checking, manifest files, or AI integration could be added later or handled by third-party plugins.
The most important part is the underlying attachment model:
a syncable folder/package attachment that preserves internal relative paths.
Why separate files are not enough
Storing note.md, image-001.png, and image-002.jpg as separate Zotero attachments does not solve the problem, because Zotero does not know that these files form one Markdown workspace. The relative path relationship between the Markdown file and its assets/ folder is part of the document structure.
Similarly, linked attachments can preserve the local folder structure, but they do not use Zotero’s file sync. This means users still need a separate sync tool for the Markdown workspace, which defeats the purpose for users who want Zotero Storage or WebDAV to manage their research attachments.
Summary
I would like to propose native support for syncable stored folder/package attachments.
This would allow Zotero to store and sync a folder such as:
note.md
assets/
image-001.png
image-002.jpg
as one coherent attachment under a Zotero item.
This would be valuable in the AI era, where notes increasingly serve as human- and AI-readable knowledge sources.
It would help Zotero remain a central part of future academic workflows while keeping Zotero’s role focused on reference and attachment management, rather than turning it into a Markdown editor or AI application.
Thank you for considering this feature request.
