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Obsidian (Flatpak) — known issues and fixes

Obsidian is installed from Flathub (md.obsidian.Obsidian). The Flatpak sandbox introduces two quirks that don't exist with the AppImage build.

1. Zoom level / UI scale resets between launches

Symptom. Ctrl+= / Ctrl+- changes the zoom, but the new value is forgotten the next time Obsidian starts.

Cause. Under XWayland, Electron can't persist per-window scale state reliably. Native Wayland fixes it.

Fix. Grant the sandbox the Wayland socket and hint Electron to pick Wayland:

flatpak override --user \
    --socket=wayland \
    --env=ELECTRON_OZONE_PLATFORM_HINT=auto \
    md.obsidian.Obsidian

Already wired into setup.sh (see commit f539785).

2. obsidian CLI can't find Obsidian

Symptom.

$ obsidian daily
The CLI is unable to find Obsidian. Please make sure Obsidian is running and try again.

…even though Obsidian is running and the built-in CLI is enabled ("cli": true in ~/.var/app/md.obsidian.Obsidian/config/obsidian/obsidian.json).

Cause. Obsidian's CLI talks to the running app through a Unix socket at $XDG_RUNTIME_DIR/.obsidian-cli.sock. Inside the Flatpak sandbox, XDG_RUNTIME_DIR is remapped, so the plugin creates the socket at:

/run/user/$UID/.flatpak/md.obsidian.Obsidian/xdg-run/.obsidian-cli.sock

A CLI invoked on the host looks in /run/user/$UID/ and sees nothing.

Fix. Wrap the CLI so it looks inside the sandbox's runtime dir. The Flatpak already ships the obsidian-cli binary at a stable path, so no manual extraction is needed.

Drop this into ~/.local/bin/obsidian (must come before any other obsidian shim in $PATH):

#!/usr/bin/env bash
set -eu
export XDG_RUNTIME_DIR="/run/user/$(id -u)/.flatpak/md.obsidian.Obsidian/xdg-run"
exec "$HOME/.local/share/flatpak/app/md.obsidian.Obsidian/current/active/files/obsidian-cli" "$@"

Make it executable (chmod +x ~/.local/bin/obsidian) and confirm:

obsidian daily     # should open today's daily note

Verify the socket exists first if the wrapper still fails:

ls /run/user/$(id -u)/.flatpak/md.obsidian.Obsidian/xdg-run/.obsidian-cli.sock

Missing socket means Obsidian isn't running, or the in-app CLI toggle is off — turn it on under Settings → General → Command-line interface.

Alternative without a wrapper

If you don't want a wrapper, invoke the CLI via flatpak run each time (≈90 ms startup overhead):

flatpak run --command=/app/obsidian-cli md.obsidian.Obsidian daily