The file jdk/make/sun/jconsole/Makefile is missing a few lines:

diff -r 0e1d82bbcb2c make/sun/jconsole/Makefile
--- a/make/sun/jconsole/Makefile Wed Jun 25 16:44:55 2008 -0700
+++ b/make/sun/jconsole/Makefile Tue Jul 01 13:31:04 2008 -0700
@@ -87,4 +87,5 @@ build: $(FILES_png) $(FILES_gif) $(TEMPD
 
 clean clobber::
        $(RM) $(TEMPDIR)/manifest $(JARFILE)
+ $(RM) $(GENSRCDIR)/sun/tools/jconsole/Version.java
 
Without this change a 'gmake clean' in the jdk/make/sun/jconsole directory does not properly clean up the build results.