I hope this is somewhat on-point. I'm working on one application where the package Requires gcc, and the design spec Requires "-Wall -Werror".
I find I have to put some code before the call to AC_PROG_CC to remove -Werror or gcc will die (during, say, config.status --recheck) because "main() defaults to int type". This may have changed with 2.54, I don't know. However, with 2.54 I am now seeing message about how I should't be using CFLAGS (or a whole bunch of others), but should be using the AM_ versions instead. The automake documentation, however, does not always use the AM_ versions of the user variables. This last point is made somewhat worse because the autoconf documentation still uses the traditional "user" variables. So what's the preferred way to write software that uses automake and autoconf given that some of these variables need to be amended during the configure process? H
