There have been significant changes to the makefile and to the management
of external libraries.
I am surprised that the autotools build system was introduced for your software.
https://github.com/coccinelle/coccinelle/blob/feec80c30d140c69f5d894bd09b6071247d0fbaa/configure.ac
Would you like to add the macro call "AC_PREREQ" to your current build
specification?
http://www.freesoftwaremagazine.com/articles/configuring_a_project_with_autoconf
How do you think about to delete the script "configure" and any auxiliary files
from the source code repository because they can be regenerated automatically?
Regards,
Markus
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