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Ok, so this seems like a great thread to ask this question.

I want a research tool with the following features:

  - Collaborative
  - Cloud based with offline mode (changes can be synced back up)
  - History  
  - Separate workspaces/projects
  - The repository would be "taggable", meaning that after I set all the notes in a project as "v1" I can interact with the research with that snapshot, further when I create a "v2" I can see everything that has changed since "v1".  
  - Media files (images) can be added
Secondary concerns

  - The ability to "comment" in a collaborative manner.  
  - an API to extract the data
  - Native apps
  - Dead simple end user workflow, (ex, don't have to run git commands)
  - Simple user permissions (ex. read only, contributor, admin)


If your team is okay with using markdown and git (can be GUI), I think Github wikis would fit the bill rather well. Through the web interface, you can upload images by drag & dropping them.


I'm imagining whatever product would use git as a base, but Github wiki's itself doesn't offer anything that would benefit someone doing research, from UX to creating relationships between documents.




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