runtimes: Don't include Flatpak metadata overlay in sysroot

It's rather out of place there.
Signed-off-by: Simon McVittie <smcv@collabora.com>

flatdeb/debos-runtimes.yaml

@@ -177,9 +177,8 @@ actions:
     command: 'echo; dpkg --purge --force-remove-essential --force-depends dpkg'
   {{ end }}
 
-  # This adds the Flatpak metadata and the final apt configuration
   - action: overlay
-    source: runtimes/{{ $runtime }}/overlay
+    source: runtimes/{{ $runtime }}/apt-overlay
 
   - action: run
     label: save final sources.list
@@ -243,6 +242,9 @@ actions:
     chroot: false
     command: 'echo; "$RECIPEDIR/usrmerge" "$ROOTDIR"'
 
+  - action: overlay
+    source: runtimes/{{ $runtime }}/flatpak-overlay
+
   - action: run
     label: symlink-alternatives
     chroot: true

run.py

@@ -1142,13 +1142,13 @@ class Builder:
                         argv.append(
                             'platform_post_script:platform_post_script')
 
-                overlay = os.path.join(scratch, 'runtimes', runtime, 'overlay')
+                overlay = os.path.join(
+                    scratch, 'runtimes', runtime, 'flatpak-overlay')
                 self.create_flatpak_manifest_overlay(
                     overlay, prefix, runtime, sdk=sdk)
-                self.configure_apt(
-                    os.path.join(scratch, 'runtimes', runtime, 'overlay'),
-                    self.final_apt_sources,
-                )
+                overlay = os.path.join(
+                    scratch, 'runtimes', runtime, 'apt-overlay')
+                self.configure_apt(overlay, self.final_apt_sources)
 
                 argv.append(dest_recipe)
                 subprocess.check_call(argv)