Knowledge Base - Part 3 - Backup

This is Part 3 of building a local knowledge base on top of my Obsidian vault. Part 1 covered the setup, Part 2 covered building the knowledge graph with graphify. This part is the boring but important one: backing the whole thing up on GitHub, so a dead laptop does not take years of notes — or the graph — with it.

Why git?

An Obsidian vault is a folder of plain Markdown files, which is exactly what git was built for. GitHub gives us free private repositories, full version history of every note, and a restore path to any machine. The graph from Part 2 also lives in the vault folder (graphify-out/), so one repo can carry both.

Step 1: Clean the vault first

Before the first push, decide what belongs in the repo. Create or edit .gitignore in the vault root:

.DS_Store
.obsidian/workspace.json
graphify-out/

• .obsidian/workspace.json changes every time you open Obsidian and creates noisy diffs; the rest of .obsidian/ is fine to keep if you want your settings backed up.
• graphify-out/ is generated — see below for whether you want it in git at all.

The critical part: secrets. Vaults accumulate API keys, tokens and SSH keys as stray notes. These must never reach GitHub, even in a private repo. Check what is already tracked:

cd ~/Documents/obsidian-vault
git ls-files | grep -iE 'key|token|secret|\.env'

If anything sensitive shows up, stop tracking it (keeping the local file) and add it to .gitignore:

git rm --cached <file>
echo "<file>" >> .gitignore

If a secret was already pushed, consider it compromised and rotate it — history keeps it forever otherwise.

Step 2: Create a private repo and push

Keep the backup repo private. From the vault folder:

git init                          # skip if the vault is already a repo
git add -A
git commit -m "Vault backup"
gh repo create obsidian-vault --private --source=. --push

That last line creates the private repo on GitHub, adds it as origin, and pushes. Any existing history is preserved.

Step 3: Back up from inside Obsidian

The Obsidian Git community plugin automates the whole loop without touching a terminal:

1. Settings → Community plugins → Browse → install Obsidian Git, enable it.
2. In its settings, set Auto backup interval (e.g. 10 minutes) and Auto pull interval.
3. Optionally enable Push on backup so commits reach GitHub automatically.

Now every writing session becomes a commit, and the plugin’s File history view gives per-note versioning inside Obsidian.

Step 4: Decide about the graph

The graph is derived data — the vault is the source of truth. Two workable strategies:

• Regenerate on restore (recommended): keep graphify-out/ ignored. After cloning the vault on a new machine, reinstall Hermes (Part 1), run /graphify, and the graph comes back. Since extraction is cached only locally, a rebuild costs a few credits — the price of simplicity.
• Snapshot the graph: if you want the exact graph versioned, commit graphify-out/graph.json and GRAPH_REPORT.md but keep the HTML visualization ignored — it is large and rebuildable:

graphify-out/*
!graphify-out/graph.json
!graphify-out/GRAPH_REPORT.md

Step 5: Restore

On a new machine:

gh repo clone <you>/obsidian-vault ~/Documents/obsidian-vault

Then open the folder as a vault in Obsidian, reinstall Hermes with the GLM key from Part 1, and run /graphify --update (or a full /graphify if you kept the graph ignored). Between the git history and the graph cache of extracted concepts, nothing is lost but the machine.

Tips

• Push after meaningful writing sessions even with automation — the plugin backs up on a timer, but a manual Backup (command palette) before closing the laptop never hurts.
• Check the repo size occasionally with du -sh .git — a vault with years of pasted images can grow. Keep large binaries out of notes, or move old attachments to cold storage.
• A private repo protects against accidents, not subpoenas — for sensitive notes, consider encrypting before committing or keeping them out of the vault entirely.