build: Move Makefile-*.am.inc up one level

This takes them out of the directory that is "owned" by the subproject,
which will not be ignoring our Flatpak-specific generated files in
its .gitignore, and puts them in a directory that is "owned" by Flatpak,
which can ignore them.

Signed-off-by: Simon McVittie <smcv@collabora.com>