Use archive mode for cp

- This will help ensure the file copies in to the Flatpak perserve as
  much metadata and intended filesystem layout as possible

{{ cookiecutter.format }}/manifest.yml

@@ -20,11 +20,11 @@ modules:
     buildsystem: simple
     build-commands:
       - mkdir -p /app/bin
-      - cp -r support/python/bin/* /app/bin
+      - cp --archive support/python/bin/* /app/bin
       - mkdir -p /app/include
-      - cp -r support/python/include/* /app/include
+      - cp --archive support/python/include/* /app/include
       - mkdir -p /app/lib
-      - cp -r support/python/lib/* /app/lib
+      - cp --archive support/python/lib/* /app/lib
       # Update installation prefix for pip package builds
       - sed --follow-symlinks -i 's/prefix="\/install"/prefix="\/app"/g' /app/bin/python3-config
       - sed --follow-symlinks -i 's/prefix=\/install/prefix=\/app/g' /app/lib/pkgconfig/python3.pc /app/lib/pkgconfig/python3-embed.pc
@@ -45,7 +45,7 @@ modules:
     buildsystem: simple
     build-commands:
       - install -D {{ cookiecutter.bundle_identifier }}.desktop /app/share/applications/{{ cookiecutter.bundle_identifier }}.desktop
-      - cp -r icons /app/share/icons
+      - cp --archive icons /app/share/icons
     sources:
       - type: file
         path: {{ cookiecutter.bundle_identifier }}.desktop
@@ -86,7 +86,7 @@ modules:
       no-debuginfo: true
     build-commands:
       - mkdir -p /app/briefcase
-      - cp -r src/app/ /app/briefcase/app
+      - cp --archive src/app/ /app/briefcase/app
     sources:
       - type: dir
         path: src/app/