* TDS layout on CTAN: the problem.
CTAN was developed as a means of unifying access to TeX-related material; in pre-CTAN days, packages to use with TeX were dotted on ftp sites around the net, according to the whim of the sites' maintainers. To find a file, you prowled the mailing lists and news groups until someone mentioned the file.
CTAN, therefore, provides uniform access to a range of files, and those files may be found at the same place on any conforming CTAN site or mirror. The structure of the directory tree on a CTAN site is designed to ease browsing: packages form the leaf nodes of the tree (either as single files or as directories containing several files). The big distributions can be viewed, in this sense, as packages. Above all, the interested user can browse the tree to find out what CTAN offers.
Methods of access have changed, too; CTAN sites originally offered no more than FTP access. Today's archives offer web access as well (and rsync access for mirrors), and the CTAN team and its helpers provide many other related services, including a catalogue, an index of packages by topic (i.e., by subject and usage areas).
However, CTAN remains careful not to lose sight of a vital part of its original brief: an archive that users may browse.
Separately from the development of CTAN, a TUG working group defined the TeX Directory Structure (TDS), which makes possible TeX systems that offer efficient access to huge numbers of TeX-related files, in an efficient way. Most (if not all) modern TeX distributions lay out files in TDS-compiant way; but constructing a TDS-compliant form of a package is not trivial. How, then, is the user to decide where to put files of a new package?
An obvious solution is to provide packages on the archive laid out according to TDS format. Unfortunately, this conflicts with the requirement that people may browse CTAN; TDS layout could have been designed to discourage people from browsing -- it is typically dominated by directories whose only contents are links to other directories.
* The CTAN team's solution
The CTAN team have decided that packages on the archive shall remain in a browsing-friendly layout. In parallel, a new install tree has been created. The install tree's structure parallels those of the main trees: for any package
foo/bar/baz/...
on the main tree foo, a TDS-structured ZIP file would be found at
install/foo/bar/baz.tds.zip
which may be used to update a TeX system.
The CTAN team will check that baz.tds.zip correctly covers the package material, when each version of baz is uploaded. The check is not guaranteed to spot every problem, but it detects gross errors (such as updating a file zot.tex in the main tree, but not updating the copy in baz.tds.zip)
Note that, in most cases, the usefulness of the .tds.zip is transitory: most modern distributions provide most (free) packages, so that after a day or so, a new (version of a) package will be available via the distribution's update mechanism.
* Anomalies.
Overall, banishing TDS-format layouts remains our aim, but we can't possibly claim that the policy has always been applied as we would like. All over the archive there are packages that are variously wrong (by our reckoning above). We shall not be correcting these packages, unless new versions are uploaded, or some other imperative arises.
Another (inevitable) anomaly is the TeX distributions. CTAN archives provide a repository from which users load a distribution, and which supplies updates as parts of the distribution are upgraded. We do not expect to improve the distributions' layout (that is, any change will come from the distribution managers).
The CTAN Team (What is left of it)