This way, warnings from headers that come from another package (in
particular linux-headers) won't show up when they get included.
To make sure we still track dependencies, use -MD instead of -MMD.
Since xdg-shell-unstable-5-protocol.c and xdg-shell-protocol.c
define conflicting symbols, this commit updates swc, netsurf, mupdf,
and st all at once.
