1940e5051adfdd71d35c9a329cd8e3bc407421a1
max
  Wed Aug 16 05:22:45 2023 -0700
fixing kent-core problem where a lot of tools were missing, refs #30812

diff --git src/hg/makefile src/hg/makefile
index 066d406..9f7d1cb 100644
--- src/hg/makefile
+++ src/hg/makefile
@@ -42,30 +42,35 @@
 	hgBatch \
 	makeSeqs \
 	oneShot \
 	synMap \
 	encode \
 	wikiPlot
 
 # can not build this on Mac OSX - has functions not supported
 UNAME_S := $(shell uname -s) 
 ifeq ($(UNAME_S),Darwin)
   buildRefresh=
 else
   buildRefresh=encode3
 endif
 
+# in the kent-core version of the tree, there is no encode3 directory
+ifeq ($(wildcard encode3/*),)
+  buildRefresh=
+endif
+
 # List of directories to build for userApps
 UTILS_APPLIST = \
 	autoDtd \
 	autoSql \
 	autoXml \
 	bedSort \
 	liftUp \
 	liftOver \
 	bedIntersect \
 	bedItemOverlapCount \
 	bedToGenePred \
 	blastToPsl \
 	checkCoverageGaps \
 	checkHgFindSpec \
 	checkTableCoords \
@@ -229,36 +234,38 @@
 
 all::    cgi utils
 
 hgLib:
 	cd lib && ${MAKE}
 ifneq ($(wildcard cgilib/makefile),)
 	cd cgilib && ${MAKE}
 endif
 
 userApps: $(UTILS_APPLIST:%=%.userApp)
 	cd altSplice/lib && $(MAKE)
 	cd altSplice/altSplice && $(MAKE) bedToExons
 	cd mouseStuff && $(MAKE) userApps
 	cd ratStuff && $(MAKE) userApps
 
+# tolerate missing directories, as some were removed in kent-core
 %.userApp: hgLib
-	cd $* && echo $* && $(MAKE)
+	if test -d $* ; then cd $* && echo $* && $(MAKE) ; fi
 
 utils: $(APPS:%=%.utils)
+# tolerate missing directories, as some were removed in kent-core
 %.utils: hgLib
-	cd $* && echo $* && $(MAKE)
+	if test -d $* ; then cd $* && echo $* && $(MAKE) ; fi
 
 # Compile only, the cgi's for those builds without write access
 #	to apache cgi-bin directories  (this compiles and links executables)
 
 compile: ${BROWSER_BINS:%=%.compile} ${BROWSER_LOADERS:%=%.compile}
 %.compile: hgLib
 	cd $* && echo $* && $(MAKE) compile
 
 # Build cgi's
 #   cgi: Destination for the binaries is /usr/local/apache/cgi-bin-${USER}
 
 cgi: ${BROWSER_BINS:%=%.bins} ${BROWSER_LOADERS:%=%.cgi} ${ENCODE_FILES:%=%.cgi}
 %.bins: hgLib
 	cd $* && echo $* && $(MAKE)
 %.cgi: hgLib