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CTAN is concerned about an "as flat as possible" directory structure of the "unpacked" archive, to ease browsing of the directory tree.
As a general rule, when a directory contains nothing but another directory, one of the two is clearly superfluous.
Unfortunately, the current directory cannot be flatten because the "AutoLaTeX" directory is a part (the root) of the namespace in the Perl source code. It is mandatory to enable the Perl interpreter to find the modules of AutoLaTeX (the pm files).
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