Follow-up Comment #1, bug #19893 (project freeciv):

There's more. The situation cannot be fixed by running autogen.sh in target
system even if it has required tools (which would not be needed for
./configure && make).

1) aclocal is used to collect old macros from m4/ before libtoolize is used
(see 2) to put new macros there
2) as macro files are already present (from tarball) and libtoolize is not
forced to overwrite them, old macros remain in m4/

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