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Logseq Auto-Push Setup (Flatpak)

We have a Flatpak-based Logseq installation and want to configure automated pushing to a self-hosted (e.g. Gitea) repo.

Repo is cloned to a dir ~/graph. The original Logseq's ~/.logseq/.git "infrastructure" is not used.

We also have self-signed certificates on our repo management webapp.

We create a post-commit hook under ~/graph/.git/hooks and enable auto-commit in Logseq (time based + on exit)

But - although we see commits in git log -p, automatic push does not work.

Preliminary Checks

  • Ensure the hook is executable: 
    chmod +x ~/graph/.git/hooks/post-commit
  • Verify the Flatpak has network access: e.g. use flatseal or 
    flatpak info --show-permissions com.logseq.Logseq

Add Debug Entries to the Hook

  • Use relative paths or paths inside the graph directory for the log file. It must be inside the Flatpak sandbox or a directory it has permission to access.
    • Note: Using absolute paths like ~/ may result in no output if the sandbox cannot write there.
  • Redirect both stdout and stderr to a file within the graph directory:
#!/bin/bash
echo "--- Hook triggered at $(date) ---" >> git_debug.log
git push origin main >> git_debug.log 2>&1
echo "Exit code: $?" >> git_debug.log

For extended output using the host's network stack and CA certificates:

#!/bin/bash

# Use flatpak-spawn to utilize the host's git and environment
TOKEN="your_auth_token_here"
REPO_URL="your.server.address/repo.git"

flatpak-spawn --host /usr/bin/git -C "$PWD" push https://$TOKEN@$REPO_URL main

Troubleshooting "ServiceUnknown" Error

If flatpak-spawn fails with

Portal call failed: org.freedesktop.DBus.Error.ServiceUnknown, enable the D-Bus interface:

enable permission:

flatpak override --user --talk-name=org.freedesktop.Flatpak com.logseq.Logseq

To disable permission (when no longer needed):

flatpak override --user --no-talk-name=org.freedesktop.Flatpak com.logseq.Logseq

Add Certificate in Flatpak Environment

If using a self-signed certificate, the Flatpak environment requires the CA bundle.

Option A: Pass host certificates to the sandbox

flatpak override --user --filesystem=xdg-run/keyring com.logseq.Logseq

Option B: Disable SSL verification for the specific repo (less secure)

git config http.sslVerify false

Option C: Add certificate to dugite

Retrieve your certificate (e.g. from your CA server).

Append the certificate to the Flatpak bundle:

sudo vim /var/lib/flatpak/app/com.logseq.Logseq/current/active/files/logseq/resources/app/node_modules/dugite/git/ssl/cacert.pem

Remote Authentication

Embed an Access Token in the remote URL to bypass credential manager prompts.

  1. Generate a Token:
    • In your Git server (e.g., Gitea/GitHub), go to Settings > Applications.
    • Generate a token with repo (write) scope.
  2. Update the Git configuration:
    • Edit .git/config within your graph directory: url = https://<TOKEN_HERE>@your.server.address/user/repo.git

Check Flatpak Permissions

  • Host Communication: flatpak override --user --talk-name=org.freedesktop.Flatpak com.logseq.Logseq
  • Filesystem Access: (If the hook writes to directories outside the standard sandbox) flatpak override --user --filesystem=/path/to/target/dir com.logseq.Logseq
  • Visual Audit: Use Flatseal to review and manage all active overrides.