The underscores are ugly and the .pl extension is an implementation detail that shouldn't be visible to the outside.
Also, get rid of the *.in files. It's not really necessary to generate them. And I was always modifying the wrong file.
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AC_CONFIG_FILES([src/script/hydra_build.pl], [chmod +x src/script/hydra_build.pl])
AC_CONFIG_FILES([src/script/hydra_create.pl], [chmod +x src/script/hydra_create.pl])
AC_CONFIG_FILES([src/script/hydra_evaluator.pl], [chmod +x src/script/hydra_evaluator.pl])
AC_CONFIG_FILES([src/script/hydra_queue_runner.pl], [chmod +x src/script/hydra_queue_runner.pl])
AC_CONFIG_FILES([src/script/hydra_server.pl], [chmod +x src/script/hydra_server.pl])
AC_CONFIG_FILES([src/script/hydra_update_gc_roots.pl], [chmod +x src/script/hydra_update_gc_roots.pl])
AC_CONFIG_FILES([tests/query-all-tables.pl], [chmod +x tests/query-all-tables.pl])
AC_CONFIG_FILES([tests/evaluation-tests.pl], [chmod +x tests/evaluation-tests.pl])