You know I always stress the point that it’s not autoconf (and automake) to be bad per-se, but rather the fact that it’s poorly documented and most people get the worst examples on how to do stuff.
One thing that I find totally misdesigned in autoconf though is the AC_CHECK_LIB macro. This macro is supposedly designed to look for certain functions in a library, to make sure that it’s linked upon if needed. The most simple case for this is using
AC_CHECK_LIB([dl], [dlopen])
to gather if the dlopen() function is in libdl or would be available directly from the C library. (Actually you usually use something more complex than this, but that’s another story).
What is the problem of this macro? Well, the problem comes when you check non-generic functions, because it has a side effect: if the function is found on the library, it is added to the LIBS variable, that is appended to every link line, causing the library to be linked in every target. This is fine when you only have one target, but it’s nasty in every other case.
This is one of the main cause of extra libraries being linked in on other libraries and executables, which are worked around with --as-needed (at least ELF side, as --as-needed does not help with libtool archives at all). It should really be avoided.
The easy way to avoid this is to reset the LIBS variable after AC_CHECK_LIB to the value it had before, it also helps if you set a new variable with the library you just detected, to use just where needed. A better way to handle this is to push on using pkg-config, which might not be the solution to all problems, but makes this problem quite easier to handle.
I know most people doing this mistake won’t be reading this, but at least I have it documented somewhere so that I can just point people at this post without repeating the reasoning. And yes, it’s problem like these that makes neon link against pam for no good reason.