Notes folder (Obsidian and others)

Set up the notes folder

1. Open the setting:
   • Mac · iPadSettings › Sync & Backup › Notes folder.
   • WindowsSettings › Sync › Notes folder.
   • AndroidSettings › Sync & Backup › Notes folder.
2. Choose Choose folder… and pick a folder, for example one inside your Obsidian vault.
3. When you choose the folder, Rectoly makes a note for every paper that has annotations. After that it brings a note up to date when you open its paper and whenever its annotations change. Last written: … shows the latest one.

• Only papers that have no note yet get one. A note already in the folder is not rewritten. Rectoly does the same once each time it starts.
• Zotero editionA paper you have not opened on this device gets a note too, if you annotated it in Zotero (during the trial and after purchase). Otherwise the papers annotated on this device get notes.
• Mendeley editionThe papers that get notes are the ones annotated on this device.

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.

From a note back to the place in the paper

Each annotation in a note ends with ↗. Press it in Obsidian or another app and Rectoly opens the paper on the page of that annotation.

• The link is there when the paper is in your Mendeley or Zotero library. Notes of a PDF that is not in the library have none.
• If the paper is not in the library on that device, Rectoly says it could not open it.
• The link is written the same way on every device, so sharing one folder between a Mac and a PC does not rewrite the lines.
• A note attached to a highlight (the indented line) has no ↗ of its own. Use the highlight's.

Research themes in the same folder

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

• Mac · iPad · AndroidWithout 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.