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my @array = qw(001.file.a 001.file.b 002.file.a 002.file.b) ;

...
for ( keys %groups ) {
    print "group $_ has files @{ $groups{$_} }\n"
}

group 002 has files 002.file.a 002.file.b
group 001 has files 001.file.a 001.file.b