Handle deep/nested manifests

[lionirdeadman]

Example of test when I used it to build gnome-software :

---Testing---
AppID check.. failed!
gzip: /var/home/DaSH/.cache/flatpak-builder-builddir/contrib/org.gnome.SoftwareDevel/files/share/app-info/xmls/contrib/org.gnome.SoftwareDevel.xml.gz: No such file or directory
128x128 icon check.. failed!
Appstream check
/var/home/DaSH/.cache/flatpak-builder-builddir/contrib/org.gnome.SoftwareDevel/files/share/appdata/contrib/org.gnome.SoftwareDevel.appdata.xml: /var/home/DaSH/.cache/flatpak-builder-builddir/contrib/org.gnome.SoftwareDevel/files/share/appdata/contrib/org.gnome.SoftwareDevel.appdata.xml could not be read: Failed to open file “/var/home/DaSH/.cache/flatpak-builder-builddir/contrib/org.gnome.SoftwareDevel/files/share/appdata/contrib/org.gnome.SoftwareDevel.appdata.xml”: No such file or directory
---