In the /downloader/pearlib directory is a shell script called Ã¢â¬ÅcleanÃ¢â¬Â.
If you execute this, the following directories and files will be removed:
rm -rf cache/* data/* docs/* download/* temp/* tests/* php/.channels php/.depdb php/.depdblock php/.filemap php/.lock php/.registry
The problem is, that after a cleanup with this script, the installed package list in your Magento Connect Manager will be empty.
To avoid this, only cleanup therese directories:
rm -rf cache/* data/* docs/* download/* temp/* tests/*