There is no way to set this absolutely globally, short of patching the compiler itself. There is no firm policy for configuring this thing. The dpkg-buildflags approach is an attempt to unify this to some degree, bit it is still young. It should work for most packages, but if it doesn't, you'll have to patch the source package (and perhaps inform the package maintainer to sort this out).
Using different branches is one approach, and I can suggest edits for @mestia’s answer if it seems appropriate (but read on...).
Another approach is to keep different files side-by-side; see Solaar for an example of this.
But both of these approaches have a significant shortcoming: they’re unsuitable for packages in Debian or Ubuntu (or probably other derivatives). If you intend on getting your package in a distribution some day, you should package it in such a way that the same set of files produces the correct result in the various distributions.
For an example of this, have a look at the Debian packaging for Solaar (full disclosure: I did the packaging).
The general idea is to ask dpkg-vendor what the distribution is; so for Solaar, which has different dependencies in Debian and Ubuntu, debian/rules has
derives_from_ubuntu := $(shell (dpkg-vendor --derives-from Ubuntu && echo "yes") || echo "no")
and further down an override for dh_gencontrol to fill in “substvars” as appropriate:
override_dh_gencontrol:
ifeq ($(derives_from_ubuntu),yes)
dh_gencontrol -- '-Vsolaar:Desktop-Icon-Theme=gnome-icon-theme-full | oxygen-icon-theme-complete' -Vsolaar:Gnome-Icon-Theme=gnome-icon-theme-full
else
dh_gencontrol -- '-Vsolaar:Desktop-Icon-Theme=gnome-icon-theme | oxygen-icon-theme' -Vsolaar:Gnome-Icon-Theme=gnome-icon-theme
endif
This fills in the appropriate variables in debian/control:
Package: solaar
Architecture: all
Depends: ${misc:Depends}, ${debconf:Depends}, udev (>= 175), passwd | adduser,
${python:Depends}, python-pyudev (>= 0.13), python-gi (>= 3.2), gir1.2-gtk-3.0 (>= 3.4),
${solaar:Desktop-Icon-Theme}
and
Package: solaar-gnome3
Architecture: all
Section: gnome
Depends: ${misc:Depends}, solaar (= ${source:Version}),
gir1.2-appindicator3-0.1, gnome-shell (>= 3.4) | unity (>= 5.10),
${solaar:Gnome-Icon-Theme}
You can use the test in debian/rules to control any action you can do in a makefile, which means you can combine this with alternative files and, for example, link the appropriate files just before they’re used in the package build.
Best Answer
What worked for me was adding flags to
dh_auto_configureunder theoverride_dh_auto_configuretarget. I had to find this myself (and it seemed to work for me), but I don't know if this is the most robust/elegant solution.