Obsidian

Install the app

Download from obsidian.md. Run the installer.

Clone BibFlow as your starting vault

In Terminal:

cd ~/Documents/Masterarbeit
git clone https://github.com/Leon-Muehlenbruch/BibFlow.git 02_Notes

A fresh copy of the BibFlow scaffolding lands at 02_Notes/.

Open the vault

Obsidian → Open vault → Open folder as vault → pick 02_Notes/.

The folder pane shows 0 Meta/, 1 Literature/, 2 Wiki/, 9 Orga/, etc., pre-populated with templates and scripts.

Verify community plugins are enabled

Settings → Community plugins. These ship with the vault and should already be enabled:

Templater
Dataview
Obsidian Git
Zotero Integration
Juggl (optional, for inline graph view)

If any are missing or disabled, enable them.

Enable the custom CSS snippet

Settings → Appearance → CSS snippets. Toggle on zotero-highlights (ships at .obsidian/snippets/zotero-highlights.css).

Without this, your imported Zotero highlights still render — just in a flat browser-default colour rather than matching the Zotero palette.

Optional: PDF TOC extraction

Most commands work immediately. One — Refresh TOC, which reads a PDF’s bookmark outline into the note — needs a small Python dependency (pypdf). Templater’s User script files folder is already pointed at 9 Orga/Templater Scripts/, so all you add is a self-contained venv. From the vault root in Terminal:

cd "9 Orga/Templater Scripts"
python3 -m venv .venv
.venv/bin/pip install pypdf

The helper auto-detects this venv and falls back to a system python3 if it is missing. The .venv/ is git-ignored, so set it up once per machine. Full notes live in 9 Orga/Templater Scripts/README.md. Skip this if you do not use the TOC feature — everything else still works.