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In order to get a smaller executable for your program you now have to recompile the program completely with the configuration file containing pragmas Eliminate generated by gnatelim. If these pragmas are placed in gnat.adc file located in your current directory, just do:
$ gnatmake -f main_prog
(Use the -f option for gnatmake to
recompile everything
with the set of pragmas Eliminate that you have obtained with
gnatelim).
Be aware that the set of Eliminate pragmas is specific to each
program. It is not recommended to merge sets of Eliminate
pragmas created for different programs in one configuration file.