For me autodoc generation depends on a script that is only available in the source tree, not in the installed tree.
Most specifically the last parts: Converting the xml files to HTML.
Another large problem with the 'complex' module system is that it hardcodes paths to the pike 'smartlink' and system libgcc.
If you install a new version of pike, your external modules will still use the old one unless you re-run autoconf (note: Not configure, autoconf).
The same goes for gcc updates, the old libgcc will still be used (granted, that seldom hurts things badly, but still).
I don't subscribe to the 'rebuild everything' theory of software updates.
I don't mind if the module system provides default targets for documentation extraction (and default autoconf macros for setting gcc etc).
But I do mind that it currently enforces the exact same environment that was used to build the pike binary.
I have never had problems mixing the sun CC and gcc compilers, actually (unless one counts building things with gcc and then not linking libgcc, or doing cuthuloid level unthinkables (using gnu LD on Solaris))
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