During installation of an extension from the configure script, the extension archive can be download and extracted twice, once by EXTEND.pm and again by tools/extender.pl if the archive contains an installer script. During the second extraction, the files created by EXTEND.pm are moved to names ending in ".bak" to preserve them before being replaced by identical copies.
A possible fix would be for EXTEND.pm to download the archive to the TWiki root directory, and only extract the installer script (if it has one). When the installer script is called, tools/extender.pl would use the previously downloaded archive and would complete the installation without creating unnecessary .bak files. For archives that don't contain an installer script, the current behavior will have to be retained.