includes are not stripped correctly (sometimes)

[Peter]

From email with Jari:

The problem is that in doxygen.config.in @abs_top_srcdir@ is used to strip the prefix of the path.

When I manually fix the documentation, I do cd tmp/pristine, which means that @abs_top_srcdir@ is /home/william/jari/tmp/pristine/yat-0.13.x while doxygen reads it as /scratch/bob/jari/tmp/pristine/yat-0.13.x. This is not a problem when cron is run as it does "correct" cd.

Not sure if fixing this is worth the effort? A possible solution is to use pwd -P because then symbolic links are skiped (ie phycisal path is showed). Another possibility is to get doxygen to behave correctly and not choose the physical path (as autotools does).

[Peter]

(In [3690]) fixes #851