|is there more run-time efficient way than my second suggestion in Perl?
Given the original statement of the problem, with or without the (rather disingenuous) extension to the original problem, I would have suggested that it would help matters noticeably if the input were sorted with respect to the column containing the file name.
The sorting would be really easy to do, either prior to passing the data to perl, or within the perl script (though there might be memory issues doing it in the script, if we're talking about millions of lines instead of dozens).
I hope the esteemed java programmer knows about the unix "sort" command (and the fact that it's ported to windows)...
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