5f47cb8c328b76c41a9a21599477bfacf4d91a37
braney
  Sun Sep 6 16:57:16 2026 -0700
makefiles: let the compiler write the header dependencies

The tree had 72 hand-written "foo.o: bar.h" lines across 15 makefiles, so
almost every object was rebuilt only when its own .c file changed.  Editing a
header left every other object that included it holding the old layout, and the
crash landed somewhere the change never touched.

The %.o: %.c rule in inc/common.mk now passes -MMD -MP.  The compiler writes
foo.d beside foo.o listing the headers that compile really read, and an
-include reads them back.  Nine makefiles keep a compile rule of their own,
because they add -DGBROWSE, -DGFSERVER_HUGE or -DCGI_BIN=; each got ${DEPGEN}
too.  lib and hg/lib are the only two that build objects into a subdirectory,
and each reads its own subdirectory .d files at the foot of its own file.

Touching hg/hgTracks/wigCommon.h used to rebuild 2 objects.  It now rebuilds
11, which is every .c file in that directory that includes the header.

A .d file holds rules, and make takes its default goal from the first rule it
reads, included files and all.  common.mk is read before a makefile's own
rules, so the include has to save $(.DEFAULT_GOAL) and set it back afterwards;
without that, make in lib built adjacency.o and stopped.

Fifteen link rules in directories the build enters named a library on the
command line without depending on it.  Each now lists it.  hg/hgPhyloPlace,
hg/visiGene/hgVisiGene and hg/orthoMap were the three whose target is a real
file and could go stale.

make clean still leaves the .d files.  A shared clean:: rule in common.mk would
first mean converting about 320 single-colon clean: rules, since make refuses
to mix the two forms on one target.  A leftover .d cannot break a build: -MP
writes an empty target for each header, so a deleted or renamed one does not
leave make asking for a file no rule can build.

refs #36621

diff --git src/hg/mouseStuff/whyConserved/makefile src/hg/mouseStuff/whyConserved/makefile
index f941e5c7d26..a40aceb23c7 100644
--- src/hg/mouseStuff/whyConserved/makefile
+++ src/hg/mouseStuff/whyConserved/makefile
@@ -1,21 +1,21 @@
 kentSrc = ../../..
 include ../../../inc/common.mk
 
 L += -lm $(MYSQLLIBS)
 MYLIBDIR = ../../../lib/$(MACHTYPE)
 MYLIBS =  $(MYLIBDIR)/jkhgap.a $(MYLIBDIR)/jkweb.a
 
 O = whyConserved.o 
 
 all: whyConserved trackOverlap
 
 whyConserved: $O $(MYLIBS)
 	${CC} ${COPT} ${CFLAGS} -o ${DESTDIR}${BINDIR}/whyConserved $O $(MYLIBS) $L
 	${STRIP} ${DESTDIR}${BINDIR}/whyConserved${EXE}
 
-trackOverlap: trackOverlap.o
+trackOverlap: trackOverlap.o $(MYLIBS)
 	${CC} ${COPT} ${CFLAGS} -o ${DESTDIR}${BINDIR}/trackOverlap trackOverlap.o $(MYLIBS) $L
 	${STRIP} ${DESTDIR}${BINDIR}/trackOverlap${EXE}
 
 clean::
 	rm -f ${O}