The problem with keeping the generated files in the code management
system is that the timestamps mess up you can have a bigger mess to
clean up.

You should also knmow what versions of the auto* tools you require, and
use AC_PREREQ() in configure.ac and AUTOMAKE_OPTIONS in your Makefile.am
files.

ntp (for example) uses

 AC_PREREQ(2.53)

and

 AUTOMAKE_OPTIONS = ... 1.5

as those versions or later are known to work.

I actually use autoconf 2.59 and automake 1.9.6.

H


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