Another tip, make more subs, give them good names, give variables good names, ... maybe BeeWork( $indexStore, $filingsStore, $filingsFile, $startyear, $endyear, $startqtr, $endqtr  ); ??? :D

If you make subs your loops can shrink

## yearloop
{
## quarterloop
    {
        ...
        BeeIO( $infile, $outfile , \@FormGetRes );
 
#~         my $downloads = path( $filingsStore, $yr );
        my $dlyear = path( $direct, $yr);

        my @aonly = BeeAonly( $dlyear,  $outfile );
        BeeFtpGet( \@aonly , $dlyear );
    }
}
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Why subs? If there is a problem in BeeAOnly, you only have to debug BeeAOnly, you don't have to debug all of BeeWork