diff --git a/.github/workflows/flathub.yml b/.github/workflows/flathub.yml
index a0f6c21b..c8c33f66 100644
--- a/.github/workflows/flathub.yml
+++ b/.github/workflows/flathub.yml
@@ -16,6 +16,13 @@ jobs:
       - name: Checkout app repo
         uses: actions/checkout@v4
 
+      - name: Checkout Flathub repo
+        uses: actions/checkout@v4
+        with:
+          repository: flathub/app.yaak.Yaak
+          token: ${{ secrets.FLATHUB_TOKEN }}
+          path: flathub-repo
+
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
@@ -32,22 +39,7 @@ jobs:
           git clone --depth 1 https://github.com/flatpak/flatpak-builder-tools flatpak/flatpak-builder-tools
 
       - name: Run update-manifest.sh
-        run: bash flatpak/update-manifest.sh "${{ github.event.release.tag_name }}"
-
-      - name: Checkout Flathub repo
-        uses: actions/checkout@v4
-        with:
-          repository: flathub/app.yaak.Yaak
-          token: ${{ secrets.FLATHUB_TOKEN }}
-          path: flathub-repo
-
-      - name: Copy updated files to Flathub repo
-        run: |
-          cp flatpak/app.yaak.Yaak.yml flathub-repo/
-          cp flatpak/cargo-sources.json flathub-repo/
-          cp flatpak/node-sources.json flathub-repo/
-          cp LICENSE flathub-repo/
-          sed -i 's|path: \.\./LICENSE|path: LICENSE|' flathub-repo/app.yaak.Yaak.yml
+        run: bash flatpak/update-manifest.sh "${{ github.event.release.tag_name }}" flathub-repo
 
       - name: Commit and push to Flathub
         working-directory: flathub-repo
diff --git a/flatpak/generate-sources.sh b/flatpak/generate-sources.sh
index f656d0aa..216d0a4d 100755
--- a/flatpak/generate-sources.sh
+++ b/flatpak/generate-sources.sh
@@ -7,20 +7,25 @@
 #   Clone https://github.com/flatpak/flatpak-builder-tools (for cargo generator)
 #
 # Usage:
-#   ./flatpak/generate-sources.sh
+#   ./flatpak/generate-sources.sh <flathub-repo-path>
+#   ./flatpak/generate-sources.sh ../flathub-repo
 
 set -euo pipefail
 
 SCRIPT_DIR="$(cd "$(dirname "$0")" && pwd)"
 REPO_ROOT="$(cd "$SCRIPT_DIR/.." && pwd)"
 
-# Generate cargo-sources.json
-python3 "$SCRIPT_DIR/flatpak-builder-tools/cargo/flatpak-cargo-generator.py" \
-  -o "$SCRIPT_DIR/cargo-sources.json" "$REPO_ROOT/Cargo.lock"
+if [ $# -lt 1 ]; then
+    echo "Usage: $0 <flathub-repo-path>"
+    echo "Example: $0 ../flathub-repo"
+    exit 1
+fi
+
+FLATHUB_REPO="$(cd "$1" && pwd)"
+
+python3 "$SCRIPT_DIR/flatpak-builder-tools/cargo/flatpak-cargo-generator.py" \
+  -o "$FLATHUB_REPO/cargo-sources.json" "$REPO_ROOT/Cargo.lock"
 
-# Generate node-sources.json from a patched copy of the lockfile.
-# npm omits resolved/integrity for some workspace deps, and
-# flatpak-node-generator can't handle workspace link entries.
 TMPDIR=$(mktemp -d)
 trap 'rm -rf "$TMPDIR"' EXIT
 
@@ -40,4 +45,4 @@ node -e "
 " "$TMPDIR/package-lock.json"
 
 flatpak-node-generator --no-requests-cache \
-  -o "$SCRIPT_DIR/node-sources.json" npm "$TMPDIR/package-lock.json"
+  -o "$FLATHUB_REPO/node-sources.json" npm "$TMPDIR/package-lock.json"
diff --git a/flatpak/patch-lockfile.cjs b/flatpak/patch-lockfile.cjs
deleted file mode 100644
index 222f1b64..00000000
--- a/flatpak/patch-lockfile.cjs
+++ /dev/null
@@ -1,20 +0,0 @@
-// Adds missing `resolved` URLs to package-lock.json for nested workspace deps.
-// npm omits these fields for some packages (see https://github.com/npm/cli/issues/4460),
-// which breaks offline installs. This script constructs the URL from the package
-// name and version without requiring network access.
-
-const fs = require("fs");
-
-const p = process.argv[2] || "package-lock.json";
-const d = JSON.parse(fs.readFileSync(p, "utf-8"));
-
-for (const [name, info] of Object.entries(d.packages || {})) {
-  if (!name || info.link || info.resolved) continue;
-  if (!name.includes("node_modules/") || !info.version) continue;
-  const pkg = name.split("node_modules/").pop();
-  const base = pkg.split("/").pop();
-  info.resolved =
-    "https://registry.npmjs.org/" + pkg + "/-/" + base + "-" + info.version + ".tgz";
-}
-
-fs.writeFileSync(p, JSON.stringify(d, null, 2));
diff --git a/flatpak/update-manifest.sh b/flatpak/update-manifest.sh
index 1676365c..8ad59f70 100755
--- a/flatpak/update-manifest.sh
+++ b/flatpak/update-manifest.sh
@@ -1,30 +1,27 @@
 #!/usr/bin/env bash
 #
-# Update the Flatpak manifest for a new release.
+# Update the Flathub repo for a new release.
 #
 # Usage:
-#   ./flatpak/update-manifest.sh v2026.2.0
-#
-# This script:
-#   1. Updates the git tag and commit in the manifest
-#   2. Regenerates cargo-sources.json and node-sources.json from the tagged lockfiles
-#   3. Adds a new <release> entry to the metainfo
+#   ./flatpak/update-manifest.sh <version-tag> <flathub-repo-path>
+#   ./flatpak/update-manifest.sh v2026.2.0 ../flathub-repo
 
 set -euo pipefail
 
 SCRIPT_DIR="$(cd "$(dirname "$0")" && pwd)"
 REPO_ROOT="$(cd "$SCRIPT_DIR/.." && pwd)"
-MANIFEST="$SCRIPT_DIR/app.yaak.Yaak.yml"
-METAINFO="$SCRIPT_DIR/app.yaak.Yaak.metainfo.xml"
 
-if [ $# -lt 1 ]; then
-    echo "Usage: $0 <version-tag>"
-    echo "Example: $0 v2026.2.0"
+if [ $# -lt 2 ]; then
+    echo "Usage: $0 <version-tag> <flathub-repo-path>"
+    echo "Example: $0 v2026.2.0 ../flathub-repo"
     exit 1
 fi
 
 VERSION_TAG="$1"
 VERSION="${VERSION_TAG#v}"
+FLATHUB_REPO="$(cd "$2" && pwd)"
+MANIFEST="$FLATHUB_REPO/app.yaak.Yaak.yml"
+METAINFO="$SCRIPT_DIR/app.yaak.Yaak.metainfo.xml"
 
 if [[ "$VERSION" == *-* ]]; then
     echo "Skipping pre-release version '$VERSION_TAG' (only stable releases are published to Flathub)"
@@ -58,7 +55,7 @@ curl -fsSL "https://raw.githubusercontent.com/$REPO/$VERSION_TAG/package.json" -
 
 echo "Generating cargo-sources.json..."
 python3 "$SCRIPT_DIR/flatpak-builder-tools/cargo/flatpak-cargo-generator.py" \
-  -o "$SCRIPT_DIR/cargo-sources.json" "$TMPDIR/Cargo.lock"
+  -o "$FLATHUB_REPO/cargo-sources.json" "$TMPDIR/Cargo.lock"
 
 echo "Generating node-sources.json..."
 node "$SCRIPT_DIR/fix-lockfile.mjs" "$TMPDIR/package-lock.json"
@@ -74,7 +71,7 @@ node -e "
 " "$TMPDIR/package-lock.json"
 
 flatpak-node-generator --no-requests-cache \
-  -o "$SCRIPT_DIR/node-sources.json" npm "$TMPDIR/package-lock.json"
+  -o "$FLATHUB_REPO/node-sources.json" npm "$TMPDIR/package-lock.json"
 
 # Update metainfo with new release
 TODAY=$(date +%Y-%m-%d)
@@ -85,5 +82,5 @@ echo ""
 echo "Done! Review the changes:"
 echo "  $MANIFEST"
 echo "  $METAINFO"
-echo "  $SCRIPT_DIR/cargo-sources.json"
-echo "  $SCRIPT_DIR/node-sources.json"
+echo "  $FLATHUB_REPO/cargo-sources.json"
+echo "  $FLATHUB_REPO/node-sources.json"
diff --git a/flatpak/yaak.desktop b/flatpak/yaak.desktop
deleted file mode 100644
index 0b7f0736..00000000
--- a/flatpak/yaak.desktop
+++ /dev/null
@@ -1,9 +0,0 @@
-[Desktop Entry]
-Categories=Development;
-Comment=The API client for modern developers
-Exec=yaak-app
-Icon=yaak-app
-Name=Yaak
-StartupWMClass=yaak
-Terminal=false
-Type=Application