On Mon, 28 May 2012, the CTAN team tried to explain our policy regarding uploads in TDS format:
https://lists.dante.de/pipermail/ctan-ann/2012-May/006327.html
It seems that this message was not sufficiently clear. Hence this addendum.
As we wrote before, the CTAN team has decided that packages on the archive shall remain in a browsing-friendly layout. Submissions for the main tree, that are arranged in TDS format, will be rejected, and the submitter will receive a mail to explain the reason for the rejection.
In parallel, CTAN offers the install/ subtree for TDS-structured ZIP files (not: tar files). Such a file will only be accepted as an addition to an upload, not as a replacement.
The CTAN Team (What is left of it)