Using FeynmanLM with Reference Managers

FeynmanLM is designed to work alongside your existing reference manager, not replace it. Keep organizing and citing papers in Zotero, Mendeley, or Endnote — FeynmanLM reads your library in the background and makes papers available as sources for AI-assisted learning.

Key principles:

• Your reference manager remains the source of truth for paper organization and citations.
• FeynmanLM reads your library read-only — it never modifies your data.
• Papers with attached PDFs are immediately available as sources.
• Deduplication works across all sources: a paper in Zotero and added via URL only appears once.
• Libraries are scanned on each Studio launch and auto-refreshed every few minutes.

Zotero (automatic sync)

FeynmanLM reads your local Zotero database directly. Papers appear in Studio automatically — titles, authors, DOIs, tags, and attached PDFs are all imported.

Setup

1. Go to Settings → Reference Managers.
2. The Zotero Library toggle is on by default.
3. If you use the default data directory (~/Zotero), no further setup is needed. If you moved your Zotero data directory, enter the custom path.
4. A green checkmark confirms the database was found.

How it works

• Scans zotero.sqlite read-only on each Studio launch (safe to run while Zotero is open).
• Papers with PDFs in Zotero storage are linked directly — no copying or downloading needed.
• Zotero tags are preserved and mapped to FeynmanLM tags.
• Both imported PDFs (stored in Zotero's storage/ folder) and linked files (absolute paths) are resolved.

Supported item types

Journal articles, theses, documents, preprints, conference papers, reports, and book sections.

Custom data directory

If you changed Zotero's data directory (in Zotero → Settings → Advanced → Files and Folders), enter the same path in FeynmanLM's settings. The default is ~/Zotero.

Mendeley (automatic sync)

FeynmanLM auto-detects and reads your local Mendeley database. Both Mendeley Desktop (classic) and Mendeley Reference Manager (newer) are supported.

Setup

1. Go to Settings → Reference Managers.
2. The Mendeley Library toggle is on by default.
3. FeynmanLM auto-detects the database location. If you use a custom data directory, enter it in the text field.
4. A green checkmark confirms the database was found.

Where Mendeley stores data

Version	Default location
Mendeley Desktop	~/Library/Application Support/Mendeley Ltd./Mendeley Desktop/
Mendeley Reference Manager	~/Library/Application Support/Mendeley Reference Manager/

Mendeley Desktop names its database file <your-email>@www.mendeley.com.sqlite. FeynmanLM finds it automatically.

How it works

• Scans the Mendeley SQLite database read-only.
• Imports titles, authors, DOIs, URLs, abstracts, and tags.
• For Mendeley Desktop: resolves attached PDF paths (both absolute and relative to the data directory).
• For Mendeley Reference Manager: imports metadata; PDFs may need to be in your FeynmanLM Papers folder if they aren't stored locally.

Tip: Mendeley Desktop file organizer

If you use Mendeley Desktop's File Organizer (Tools → Options → File Organizer), your PDFs are already in a predictable local folder. FeynmanLM reads them directly from there — no need to copy anything.

Endnote (automatic sync)

FeynmanLM scans for Endnote library packages (.enlp) in your Documents folder and reads the embedded SQLite database.

Setup

1. Go to Settings → Reference Managers.
2. The Endnote Library toggle is on by default.
3. If your .enlp library is in ~/Documents/, FeynmanLM finds it automatically. Otherwise, enter the path to your library package.
4. A green checkmark confirms the library was found.

Where Endnote stores data

Endnote 20+ uses .enlp packages (which are folders). Inside:

MyLibrary.enlp/
  MyLibrary.Data/
    sdb/
      sdb.eni          ← SQLite database
    PDF/
      1234 - Author - 2024 - Title.pdf

FeynmanLM reads sdb.eni and resolves PDFs from the PDF/ folder.

How it works

• Scans ~/Documents/*.enlp for library packages (or uses a custom path).
• Reads the SQLite database read-only (safe while Endnote is open).
• Imports titles, authors, DOIs, URLs, abstracts, years, and keywords.
• Resolves PDF attachments from the library's PDF folder using Endnote's naming convention.

Supported fields

Title, author(s), DOI, URL, abstract, year, and keywords. The exact fields depend on your Endnote version's database schema — FeynmanLM adapts to the columns available.

Paperpile (via Google Drive)

Paperpile stores PDFs in Google Drive. To use them with FeynmanLM:

1. With Google Drive desktop app: Your PDFs are already synced locally at ~/Google Drive/Paperpile/. Copy (or symlink) them to your FeynmanLM Papers folder.
2. Without desktop app: In Google Drive, right-click the Paperpile folder → Download to get a .zip file. Unzip and copy the PDFs.

# Copy from Google Drive sync
cp ~/Google\ Drive/Paperpile/*.pdf \
  ~/Library/Mobile\ Documents/com~apple~CloudDocs/Documents/FeynmanLM/Papers/

Paperpile names PDFs using the paper title, so FeynmanLM picks up clean titles automatically.

Other reference managers (BibTeX / RIS export)

Any reference manager that can export PDFs works with FeynmanLM:

1. Export your PDFs — most managers have an "Export with files" or "Download all PDFs" option.
2. Copy the PDFs to your FeynmanLM Papers folder:

   iCloud Drive → Documents → FeynmanLM → Papers

3. Open FeynmanLM — papers are discovered automatically.

The Papers folder in iCloud is the universal import target. Get your PDFs there by any means, and FeynmanLM handles the rest.

How FeynmanLM complements your reference manager

Task	Reference manager	FeynmanLM
Organize papers	Collections, tags, folders	Reads your organization
Store PDFs	Your library's storage	Links to your existing PDFs
Citations	BibTeX, formatted references	Not applicable
Read & annotate	Built-in PDF viewer	Studio Reader panel
Learn the content	Not applicable	AI-assisted learning via MCP
Test understanding	Not applicable	Feynman technique review via AI assistant

The workflow: collect and organize in your reference manager, learn and retain using FeynmanLM + your AI assistant. Both tools stay in sync automatically.

Troubleshooting

"No database found"

• Zotero: Make sure Zotero is installed and has been opened at least once (to create the database). Check if you moved the data directory.
• Mendeley: Make sure Mendeley Desktop or Reference Manager has been opened and synced at least once.
• Endnote: Make sure your .enlp library file is in ~/Documents/. If it's elsewhere, enter the path manually.

Papers appear but PDFs aren't linked

• The reference manager may store PDFs in a cloud-only location. Make sure the PDFs are downloaded locally.
• For Zotero: check that your storage folder contains the actual PDF files (not just metadata).
• For Mendeley Desktop: enable the File Organizer to keep local copies.

Duplicate papers

FeynmanLM deduplicates by DOI, URL, and filename. If duplicates still appear, they likely have different DOIs or the URL normalization didn't match. You can skip duplicates from the context menu in Studio.

Database locked errors

FeynmanLM opens all databases in read-only mode, so this shouldn't happen. If it does, try closing and reopening FeynmanLM after the reference manager finishes syncing.