I am assuming that by:
run flash files(.swf)
you mean that you want
Tomcat to serve .swf files correctly like it serves .gif, .jpg, etc etc files.
Tomcat configures assigning mime-types to files based on file type by means of entries in the default web.xml file located in the conf directory.
I see that Tomcat 5.5 has an entry for .swf as follows:
so Tomcat should be able to serve .swf files without modification.
Bill