Running Clean Project will remove the following files in the project:
 
.*.rpt
.*.rpt.htm
.*.rpt.htm_files
.*.msf
.*.smsg
.*.summary
.jdi
.pin
.pof
.sof
.done
(all revision files in the db, incremental_db, and persona directories)

For more information, please refer to the command in the URL link below.
 http://quartushelp.altera.com/13.0/mergedProjects/tafs/tafs/tcl_pkg_project_ver_6.0_cmd_project_clean.htm