Fixed by:

commit fb30f07866d7b48e036dd0333be32b9460e22273
Author: Jan Schmidt <jan@centricular.com>
Date:   Fri Jan 29 04:50:42 2016 +1100

    pkg-config: Don't generate and install pkg-config with relative paths
    
    Don't put relative paths in pkg-config files, including uninstalled
    ones. For those, use @abs_topbuilddir@ and @abs_topsrcdir@ as we
    do elsewhere.
    
    Remove libraries= directives, which doesn't seem to be a pkg-config
    variable that actually exists, but has been in all our pkg-config
    files for as long as they've existed.

and additionally (to prevent it happening again):

commit 6dc67b6d294d1f9628e3b126b67bf71f6d4b82d5
Author: Jan Schmidt <jan@centricular.com>
Date:   Fri Jan 29 05:00:39 2016 +1100

    pkgconfig: Complain loudly about relative include paths
    
    If an pkgconfig file provides a relative path for includes,
    complain loudly and abort. Include paths should be absolute.