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The ArcGIS 9.3.1 MXD Editor does not delete temporary files when the application closes unexpectedly. These files and directories stay in the workspace and accumulate over time.
The MXD Editor cleans up all the temporary files when it is closed properly. When the MXD Editor is closed unexpectedly, the exit procedure is not completed; therefore, the temporary files are left behind and do not get deleted from the workspace.
Delete the arcgis_workspace folder.