Use a hash-of-arrays to group the paths by filename.

my %sourcesAndPaths;
foreach (@classedSources) {
    my ( $dir, $file ) = m{ ^ (.+) / ([^/]+?) $ }x or do {
        warn "Can't parse '$_'";
        next;
    };
    push @{ $sourcesAndPaths{$file} }, $dir;
}


foreach my $file ( sort keys %sourcesAndPaths ) {
    my @dirs = @{ $sourcesAndPaths{$file} };

    next if @dirs == 1;

    print "\n$file\n";
    print "\t$_\n" for @dirs;
}
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