3ba0a1c2f2cb0b220a2989225ff9512d2531070b
max
  Fri Dec 19 07:33:10 2014 -0800
changes after code review, refs #14545
diff --git src/makefile src/makefile
index 4d41ed1..27e984a 100644
--- src/makefile
+++ src/makefile
@@ -14,36 +14,39 @@
 	${MAKE} clean
 
 topLibs:
 	@MACHTYPE=${MACHTYPE} ./machTest.sh
 	cd lib && ${MAKE}
 	cd jkOwnLib && ${MAKE}
 	cd parasol/lib && ${MAKE}
 
 hgLib:
 	@./hg/sqlEnvTest.sh
 	cd hg/lib && ${MAKE}
 
 libs: topLibs hgLib
 
 cgi: libs
+	cd utils && ${MAKE} cgi
 	cd hg && ${MAKE} cgi
 
 cgi-alpha: libs
+	cd utils && ${MAKE} alpha
 	cd hg && ${MAKE} alpha
 
 cgi-beta: check-beta libs
+	cd utils && ${MAKE} beta
 	cd hg && ${MAKE} beta
 
 check-beta:
 	# this will fail if we are not in a beta checkout:
 	git branch | egrep 'v[0-9]+_branch' > /dev/null	
 
 blatSuite: topLibs hgLib
 	cd blat && ${MAKE}
 	cd gfClient && ${MAKE}
 	cd gfServer && ${MAKE}
 	cd webBlat && ${MAKE}
 	cd hg/pslPretty && ${MAKE}
 	cd hg/pslReps && ${MAKE}
 	cd hg/pslSort && ${MAKE}
 	cd utils/nibFrag && ${MAKE}
@@ -95,32 +98,35 @@
 	rm -f tags TAGS
 
 testDirs = lib utils blat gfServer hg
 test:: $(testDirs:%=%.test)
 %.test:
 	cd $* && ${MAKE} test
 
 LIB_TAGS_IN = lib/*.[hc] */lib/*.[hc] */*/lib/*.[hc] */*/*/lib/*.[hc] jkOwnLib/*.c inc/*.h hg/inc/*.h hg/encode3/encodeDataWarehouse/lib/*.c hg/encode3/encodeDataWarehouse/inc/*.h hg/encode3/eap/inc/*.h
 
 # build tags for libraries
 .PHONY: tags
 tags:
 	ctags ${LIB_TAGS_IN}
 
 cscope: 
-	find `pwd` -name '*.c' -o -name '*.h' > sourceFiles
-	cscope -Rb `cat sourceFiles`
+	find `pwd` -name '*.c' -o -name '*.h' > cscope.files
+	cscope -qRb `cat cscope.files`
+search:
+	cscope -d
+
 # build emacs tags for libraries
 .PHONY: etags
 etags:
 	etags ${LIB_TAGS_IN}
 
 # build tags for all files
 .PHONY: tags-all
 tags-all:
 	find . -name '*.[ch]' | ctags -L -
 
 # build emacs tags for all files
 .PHONY: etags-all
 etags-all:
 	find . -name '*.[ch]' | etags -