All of the libtool stuff has been sent back upstream to the libtool project
a long time ago, and we see the results of this sometimes, when other
upstream authors update the libtool that they are using.  This includes
the 10.1 fix that you mention (-flat_namespace -undefined_suppress).

I don't think a permanent fix has been found for the "convenience bug",
though.  There was a fink guy who had a fix, I'm not sure of the status.

Another common issue is getting the order correct for flags given to the
linker.  GNU ld is more tolerant than Apple's ld, so sometimes packages
need modification to run on OS X.

What you are talking about, really, is getting patches "way upstream."
That's been done, but we have to wait for the stream to flow a bit,
as it were.

  -- Dave

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