During deploy artifacts to SVN an instance of ScmWagon is initialized and artifact metadata is downloaded to a local folder. After that maven tries to upload the jar file. ScmWagon.put(File,String) is called which internally overwrites the checkoutDirectory field and checks out the repo again to another temporary folder. The original folder is forgotten.
Maven uploads jars, poms, checksums and for each file ScmWagon checks out a new directory.
In the end the closeConnection() method is called which removes the last used folder.
UPD: this causes false positive in testWagonPutDirectoryWhenDirectoryAlreadyExists(): the test deletes the test checkout dir before calling get(), but the wagon checkout dir remains and the file is retrieved from there.