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/cgilib/makefile src/hg/cgilib/makefile
index 5701fa1dda1..057b3c63e04 100644
--- src/hg/cgilib/makefile
+++ src/hg/cgilib/makefile
@@ -29,31 +29,31 @@
   search.o sessionThumbnail.o sgdClone.o sgdDescription.o simpleNucDiff.o simpleRepeat.o snp125.o \
   snp125CodingCoordless.o snp125Ui.o snp132Ext.o snpMap.o snpUi.o softPromoter.o softberryHom.o stsInfo.o \
   stsInfoMouse.o stsInfoMouseNew.o stsInfoRat.o stsMapMouse.o stsMapMouseNew.o stsMapRat.o suggest.o \
   switchDbTss.o synteny100000.o tRNAs.o targetDb.o tfbsConsFactors.o tfbsConsMap.o tfbsConsSites.o \
   trackLayout.o trackTable.o transMapGene.o transMapInfo.o transMapSrc.o transMapStuff.o transRegCode.o \
   transRegCodeProbe.o ucscRetroInfo.o ucscRetroOrtho.o userRegions.o variant.o variome.o vegaInfoZfish.o \
   visiGene.o vntr.o wabAli.o wgRna.o yaleGencodeAssoc.o zdobnovSynt.o
 
 ifeq (${GBROWSE}, 1)
   GBROWSE_D=-DGBROWSE
 else
   GBROWSE_D=
 endif
 
 %.o: %.c
-	${CC} ${COPT} ${CFLAGS} ${GBROWSE_D} ${LOWELAB_DEFS} ${HG_DEFS} ${HG_WARN} ${HG_INC} ${XINC} -o $@ -c $<
+	${CC} ${COPT} ${CFLAGS} ${GBROWSE_D} ${LOWELAB_DEFS} ${HG_DEFS} ${HG_WARN} ${HG_INC} ${XINC} ${DEPGEN} -o $@ -c $<
 
 ../../lib/$(MACHTYPE)/jkhgapcgi.a: $(O)
 	ar rcus ../../lib/$(MACHTYPE)/jkhgapcgi.a $(O)
 
 clean:
 	rm -f $(O);
 	rm -f ../../lib/$(MACHTYPE)/jkhgapcgi.a;
 
 ctags:
 	ctags *.c *.h ../inc/*.h ../lib/*.c ../../inc/*.h ../../lib/*.c ../inc/encode/*.h ../lib/encode/*.c
 
 tags:
 	etags *.c *.h ../inc/*.h ../lib/*.c ../../inc/*.h ../../lib/*.c ../inc/encode/*.h ../lib/encode/*.c
 
 test: