The problem is in these lines. On each iteration, the code clobbers whatever's in the hash already:

foreach $filename1 (@sourcesorted) {
    %hashsource = ($filename1,$filename1);
}
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To fix it, I'd probably do something like this:

my %hashsource;
@hashsource{@sourcesorted} = @sourcesorted;
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That does what you intend, by assigning a list of keys to a list of values.

There are other things to correct in the code, but that will fix the issue you described.