Notes folder (Obsidian and others)

Keep a Markdown file for each paper, with its highlights and notes, in a folder you choose, ready for Obsidian and other note apps. Rectoly keeps the files up to date as you read.

Applies to Mendeley and Zotero editions Windows · Mac · iPad Free

Set up the notes folder

  1. Open the setting:
    • Mac · iPadSettings › Sync & Backup › Notes folder.
    • WindowsSettings › Sync › Notes folder.
  2. Choose Choose folder… and pick a folder, for example one inside your Obsidian vault.
  3. From now on, Rectoly writes a note when you open a paper and whenever its annotations change. Last written: … shows the latest one.

To use another folder, choose Change folder…. To stop, choose Stop; the files already written stay where they are.

What goes in the files

  • One Markdown file per paper, named by its citation key, such as devlin2019bert.md. See where the key comes from.
  • The file holds the paper's highlights and notes, with the citation key under the title in the format you chose. See Citation key format.
  • Rectoly rewrites only what is between its two marker lines. Anything you write outside them, above or below, stays as it is.

Research themes in the same folder

Your research themes are kept in the Themes folder inside the notes folder, on iPad, Mac and Windows alike.

  • Mac · iPadWithout a notes folder, themes are kept inside the app. When you choose a folder, they move into its Themes folder.
  • Mac · iPadShow the themes folder in the same setting opens it.

If the folder cannot be reached

  • If the folder is on a drive that is not connected, or cannot be reached for a moment, "The folder can't be reached right now" appears. Notes are written when it is back.
  • If a note could not be written, "The last note couldn't be written." appears. Check that the folder can still be written to, or choose it again.

Updated September 20, 2026