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