The workspace files are used by Flex Builder to determine
which all projects reside within the workspace in addition to some
configuration data associated with them.
If you separate away the workspace files, you'll be able to
cleanly determine that All folders under xyz are flex projects
except for _workspace (or whatever you want) which is housekeeping
related to your projects. (Otherwise it would have been "except for
.metadata and configuration".)
The concept of a workspace is pretty powerful if you are
dealing with a lot of projects.