* Install headers into 'hmmer3' subdir and not into global includedir
* Respect AR

--- a/easel/Makefile.in
+++ b/easel/Makefile.in
@@ -465,11 +465,12 @@
 	${INSTALL} -d ${DESTDIR}${bindir}
 	${INSTALL} -d ${DESTDIR}${libdir}
 	${INSTALL} -d ${DESTDIR}${includedir}
+	${INSTALL} -d ${DESTDIR}${includedir}/hmmer3
 	${INSTALL} -m 0644 libeasel.a ${DESTDIR}${libdir}/
 	for file in ${HDRS}; do\
-	   ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/ ;\
+	   ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/hmmer3/ ;\
 	done
-	${INSTALL} -m 0644 esl_config.h ${DESTDIR}${includedir}/
+	${INSTALL} -m 0644 esl_config.h ${DESTDIR}${includedir}/hmmer3/
 	${QUIET_SUBDIR0}miniapps      ${QUIET_SUBDIR1} install
 
 # "make uninstall" reverses the steps of "make install"
--- a/libdivsufsort/Makefile.in
+++ b/libdivsufsort/Makefile.in
@@ -16,7 +16,7 @@
 CFLAGS    = @CFLAGS@ @PTHREAD_CFLAGS@ @PIC_FLAGS@
 CPPFLAGS  = @CPPFLAGS@
 MPILIBS   = @MPILIBS@
-AR        = @AR@ rc
+AR        = @AR@
 RANLIB    = @RANLIB@
 INSTALL   = @INSTALL@
 
@@ -43,7 +43,7 @@
 
 
 libdivsufsort.a: $(OBJS)
-	${QUIET_AR}${AR} libdivsufsort.a $(OBJS)
+	${QUIET_AR}${AR} rc libdivsufsort.a $(OBJS)
 	@${RANLIB} libdivsufsort.a
 	@chmod 644 libdivsufsort.a
 
--- a/Makefile.in
+++ b/Makefile.in
@@ -143,6 +143,7 @@
 	${INSTALL} -d ${DESTDIR}${bindir}
 	${INSTALL} -d ${DESTDIR}${libdir}
 	${INSTALL} -d ${DESTDIR}${includedir}
+	${INSTALL} -d ${DESTDIR}${includedir}/hmmer3
 	${INSTALL} -d ${DESTDIR}${man1dir}
 	${INSTALL} -d ${DESTDIR}${pdfdir}
 	${QUIET_SUBDIR0}src           ${QUIET_SUBDIR1} install
--- a/src/impl_dummy/Makefile.in
+++ b/src/impl_dummy/Makefile.in
@@ -152,8 +152,9 @@
 	${CC} ${CFLAGS} ${SIMDFLAGS} ${CPPFLAGS} ${LDFLAGS} ${DEFS} ${MYLIBDIRS} ${MYINCDIRS} -D$${DFLAG} -o $@ $${DFILE} ${LIBS}
 
 install:
+	${INSTALL} -d ${DESTDIR}${includedir}/hmmer3
 	for file in ${HDRS}; do \
-	   ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/ ;\
+	   ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/hmmer3/ ;\
 	done
 
 uninstall:
--- a/src/impl_sse/Makefile.in
+++ b/src/impl_sse/Makefile.in
@@ -155,8 +155,9 @@
 
 
 install:
+	${INSTALL} -d ${DESTDIR}${includedir}/hmmer3
 	for file in ${HDRS}; do \
-	   ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/ ;\
+	   ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/hmmer3/ ;\
 	done
 
 uninstall:
--- a/src/impl_vmx/Makefile.in
+++ b/src/impl_vmx/Makefile.in
@@ -152,8 +152,9 @@
 	${CC} ${CFLAGS} ${SIMDFLAGS} ${CPPFLAGS} ${LDFLAGS} ${DEFS} ${MYLIBDIRS} ${MYINCDIRS} -D$${DFLAG} -o $@ $${DFILE} ${LIBS}
 
 install:
+	${INSTALL} -d ${DESTDIR}${includedir}/hmmer3
 	for file in ${HDRS}; do \
-	   ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/ ;\
+	   ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/hmmer3/ ;\
 	done
 
 uninstall:
--- a/src/Makefile.in
+++ b/src/Makefile.in
@@ -322,15 +322,16 @@
 	${CC} ${CFLAGS} ${SIMDFLAGS} ${CPPFLAGS} ${LDFLAGS} ${DEFS} ${MYLIBDIRS} ${MYINCDIRS} -D$${DFLAG} -o $@ $${DFILE} ${LIBS}
 
 install:
+	${INSTALL} -d ${DESTDIR}${includedir}/hmmer3
 	${QUIET_SUBDIR0}${IMPLDIR} ${QUIET_SUBDIR1} install
 	for file in ${PROGS}; do \
 	   ${INSTALL} -m 0755 $$file ${DESTDIR}${bindir}/ ;\
 	done
 	${INSTALL} -m 0755 libhmmer.a ${DESTDIR}${libdir}/
 	for file in ${HDRS}; do \
-	   ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/ ;\
+	   ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/hmmer3/ ;\
 	done
-	${INSTALL} -m 0644 p7_config.h ${DESTDIR}${includedir}/ ;\
+	${INSTALL} -m 0644 p7_config.h ${DESTDIR}${includedir}/hmmer3/ ;\
 
 uninstall:
 	${QUIET_SUBDIR0}${IMPLDIR} ${QUIET_SUBDIR1} uninstall