flatpak: Writeback manifest changes to disk
When the user changes build preferences in the Builder UI, those changes should propagate back to the manifest file on the disk. This commit accomplishes that in a somewhat hack-ish way (by reading the file line-by-line and making changes where necessary) so that formatting, comments, etc. are preserved that would be lost if JsonBuilder and JsonGenerator were used instead. https://bugzilla.gnome.org/show_bug.cgi?id=777959
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