If you have to use flat files then you might want to load the second file in advance and place the company name and subdir into hashes, i.e.:
$company{'company_A'} = '/home/company/etc';

The company name will be the key and the subdirectory will be the value. If more than one subdir will be needed per company name, then load them into an anonymous array:

$company{'company_A'}[0] = '/home/company/etc';
$company{'company_A'}[1] = '/dev/null';
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You can then access these values as you traverse the values in your first file.