Peter,

Your report contains a number of points:
- Joining tags when using +=, this is by design. The parser used to do the
reading for an update of the Doxyfile is the same as the parser reading the
Doxyfile when processing sources files. The parser joins all the items
belonging to one tag (e.g. the ALIASES tag), when writing out the new
Doxyfile it is not known if += have been used. Similar things happens with
include files (they are merged into Doxyfile upon update).
- Only showing the last user comment in case of using a += tag construct.
I've pushed a proposed patch to github (pull request 293)
- Moving user comments at the beginning of the file to the first tag. This
is conform the documentation, I've corrected this, so that this is
preserved now in the before mentioned proposed patch.

Albert

On Tue, Jan 20, 2015 at 10:58 PM, Barnes, Peter D. <barne...@llnl.gov>
wrote:

> Hello Folks,
>
> I upgraded by doxygen to 1.8.9.1 from the sources.  (Mac 10.8.5, gcc
> 4.2.1).
>
> Then I protected some of my comments in our doxygen.conf using '##', for
> example:
>
> > ## -*- sh -*-
> >
> > ...
> >
>
> > ALIASES                =
> >
> > ## Link to bug tracker
> > ALIASES               += bugid{1}="<a href=\"
> http://www.nsnam.org/bugzilla/show_bug.cgi?id=\1\";>Bug \1</a>"
> >
> > ## Set off \internal docs
> > ALIASES               += internal="\par \b Internal:"
> >
> > ## Typeset parameter name in docs as in the "Parameters:" list
> > ## Usage:     /** \param [in/out] tag If found, \pname{tag} is ... */
> > ALIASES               += pname{1}="<span class=\"params\"><span
> class=\"paramname\">\1</span></span>"
> >
> > ## Link to RFC's
> > ALIASES               += RFC{1}="<a href=\"
> http://datatracker.ietf.org/doc/rfc\1/\";>RFC \1</a>"
>
> Finally I asked doxygen to update the config file:
>
> $ doxygen -u doxygen.conf
>
> However it modified the two regions above in undesirable ways:
>
> - The emacs mode line got moved after the doxygen opening comments.  It
> has to be on the first line for emacs to recognize it.
>
> - The aliases got bunched into a single block, and only the last comment
> was preserved:
>
> > ## Link to RFC's
> >
> > ALIASES                = "bugid{1}=<a href=\"
> http://www.nsnam.org/bugzilla/show_bug.cgi?id=\1\";>Bug \1</a>" \
> >                          "internal=\par \b Internal:" \
> >                          "pname{1}=<span class=\"params\"><span
> class=\"paramname\">\1</span></span>" \
> >                          "RFC{1}=<a href=\"
> http://datatracker.ietf.org/doc/rfc\1/\";>RFC \1</a>"
>
>
> Thanks,
> Peter
> _______________________________________________________________________
> Dr. Peter D. Barnes, Jr.                Physics Division
> Lawrence Livermore National Laboratory  Physical and Life Sciences
> 7000 East Avenue, L-50                  email:  pdbar...@llnl.gov
> P. O. Box 808                           Voice:  (925) 422-3384
> Livermore, California 94550             Fax:    (925) 423-3371
>
>
>
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