Overhauls how 'make install' works.

now we install only (18) programs and their man pages, + hmmer.man
page. We no longer install libhmmer.a, pdf, or .h headers.

hmmerfm-exactmatch and hmmc2 removed from installed ${PROGS}, moved to
an ${AUXPROGS} list that gets built but not installed.

`make install` is now always verbose about what it's doing; removed
quiet beautification.

Variable substitution in .tex and .man files is now done by
./configure from *.in files, not by outmoded sedition script.

Removed ifneq conditionals from Makefiles. We're aiming to have a
github master branch clone act identically to a release tarball, so
release procedure can have no file modifications or
removals. Supersedes need to check for existence of documentation/,
release-notes/.

removed LICENSE.sh, LICENSE.tag, also as part of simplifying release
procedure.

updated HISTORY with 3.x release dates.

updates config.sub, config.guess with new ones from gnu mothership.

updates LICENSE with some additional credits.

removes some empty or fragmented/unnecessary in-depths-of-time-anyway
release notes.

LICENSE

@@ -32,11 +32,17 @@ sources, including:
    Walt Shands  
    Travis Wheeler    
 
+HMMER also includes copyrighted and licensed code that has been
+incorporated from other sources, including:
+
+   Yuta Mori                       libdivsufsort-lite
    Apple Computer                  
    Free Software Foundation, Inc.  
    IBM TJ Watson Research Center   
    X Consortium                    
 
+
+
 HMMER uses the Easel software library, which has its own license and
 copyright information. See easel/COPYRIGHT and easel/LICENSE.
 

Makefile.in

@@ -6,11 +6,13 @@
 # Optionally, you can run a test suite:
 #     % make check
 #
-# And optionally, you can install everything more permanently:
+# Optionally, you can install programs and man pages more permanently:
 #     % make install
 #
-# For more information, see the Installation chapter of the HMMER
-# User's Guide.
+# Optionally, you can install some small tools ("miniapps") from our Easel library:
+#     % (cd easel; make install)
+#
+# For more information, see the Installation section in the User's Guide.
 #
 
 
@@ -76,25 +78,6 @@ ifndef V
 		        ${MAKE} -s -C $$subdir
 endif
 
-# Programs installed by HMMER (stable, documented)
-#
-PROGS = alimask\
-	hmmalign\
-	hmmbuild\
-	hmmconvert\
-	hmmemit\
-	hmmfetch\
-	hmmpress\
-	hmmscan\
-	hmmsearch\
-	hmmsim\
-	hmmstat\
-	jackhmmer\
-	phmmer\
-	nhmmer\
-	nhmmscan\
-	hmmpgmd
-
 .PHONY: all dev check pdf install uninstall clean distclean TAGS
 
 # all: Compile all documented executables.
@@ -134,25 +117,25 @@ check:
 pdf:
 	${QUIET_SUBDIR0}documentation ${QUIET_SUBDIR1} pdf
 
-# install: installs the binaries in ${bindir}/
-#          When man pages are done, will install man pages in MANDIR/man1/  (e.g. if MANSUFFIX is 1)
+# install: binaries in ${bindir}/, man pages in ${man1dir}/
 #          Creates these directories if they don't exist.
-#          Prefix those paths with ${DESTDIR} (rarely used, usually null;
-#          may be set on a make command line when building contrib RPMs).
+#
+#          Prefix paths with optional ${DESTDIR}, which
+#          downstream packagers may set on make command line when
+#          building packages.
+#
+#          Does not use quiet beautification magic; always verbose.
 install: 
 	${INSTALL} -d ${DESTDIR}${bindir}
-	${INSTALL} -d ${DESTDIR}${libdir}
-	${INSTALL} -d ${DESTDIR}${includedir}
 	${INSTALL} -d ${DESTDIR}${man1dir}
-	${INSTALL} -d ${DESTDIR}${pdfdir}
-	${QUIET_SUBDIR0}src           ${QUIET_SUBDIR1} install
-	${QUIET_SUBDIR0}documentation ${QUIET_SUBDIR1} install
+	${MAKE} -C src install
+	${MAKE} -C documentation install
 
-# uninstall: Reverses the steps of "make install".
+# uninstall: reverses the steps of "make install".
 #
 uninstall: 
-	${QUIET_SUBDIR0}src           ${QUIET_SUBDIR1} uninstall
-	${QUIET_SUBDIR0}documentation ${QUIET_SUBDIR1} uninstall
+	${MAKE} -C src uninstall
+	${MAKE} -C documentation uninstall
 
 # "make clean" removes almost everything except configuration files.
 #
@@ -179,11 +162,13 @@ distclean:
 	${QUIET_SUBDIR0}${SADIR}      ${QUIET_SUBDIR1} distclean
 	${QUIET}-rm config.log config.status
 	${QUIET}-rm -rf autom4te.cache
-	${QUIET}-rm -f release-notes/LICENSE.sh
 	${QUIET}-rm -f *.o *~ Makefile.bak core TAGS gmon.out
 	${QUIET}-rm -f cscope.po.out cscope.out cscope.in.out cscope.files
 	${QUIET}-rm -f src/impl
 	${QUIET}-rm Makefile
+ifndef V
+	@echo '     ' CLEAN hmmer
+endif
 
 TAGS:
 	./makeTAGS.sh