rnmanhon,
The configuration folder you mentioned is not a user area, it is modified by eclipse – plugins may be expanded there, moved to different locations, etc. In all cases, this should not be a problem, – if eclipse expands the spring plugins to a new location, the corresponding classpath containers will still work as expected. Were you referencing some of these files directly?
I’m sorry to hear about your trouble with the -clean flag, but this is a long standing issue with Eclipse itself in certain circumstances. To force eclipse to start with a given workspace, can you try using the -data flag? You need to specify the workspace location, like so: -data “c:\workspaces\myworkspace” and that should force Eclipse to start with the given workspace.
Please let me know how this works or if you need further assistance.