This patch includes the patch 'manpages_are_no_binaries'
[1](Prevent upstream Makefile from handling manpages as binaries)
by Andreas Tille <tille@debian.org>
It [2]enables 'make' to use the $pkgdir-variable,
[3]adjusts the directory for manpages and
[4]comments out CFLAGS, so the ones set in /etc/makepkg.conf are used.
[2],[3] and [4] by boenki <boenki at gmx dot de>
--- Makefile	2010-10-07 00:28:17.000000000 +0200
+++ Makefile	2010-11-27 04:58:59.000000000 +0100
@@ -1,7 +1,7 @@
-PREFIX = /usr/local
+PREFIX = ${PKGDIR}/usr
 LIBDIR = $(PREFIX)/lib/mafft
 BINDIR = $(PREFIX)/bin
-MANDIR = $(PREFIX)/man/man1
+MANDIR = $(PREFIX)/share/man/man1
 
 #MNO_CYGWIN = -mno-cygwin
 
@@ -11,7 +11,7 @@
 CC = gcc
 
 #CFLAGS =  -O0  -pedantic -Wall -std=c99 -g -pg -DMALLOC_CHECK_=3 $(ENABLE_MULTITHREAD)
-CFLAGS = -O3 $(MNO_CYGWIN) $(ENABLE_MULTITHREAD)
+#CFLAGS = -O3 $(MNO_CYGWIN) $(ENABLE_MULTITHREAD)
 #CFLAGS =  -mno-cygwin -O3 # for cygwin
 #CFLAGS =  -fast -static      # for icc on Intel
 #CFLAGS =  -O3 -ipo -static   # for icc on AMD
@@ -114,7 +114,7 @@
 all : $(PROGS) $(SCRIPTS)
 	cp $(SCRIPTS) ../scripts
 	chmod 755 ../scripts/*
-	cp $(PROGS) $(MANPAGES) ../binaries
+	cp $(PROGS) ../binaries
 	chmod 755 ../binaries/*
 	@echo done.
 
@@ -491,7 +491,7 @@
 	chmod 755 $(SCRIPTS)
 	$(INSTALL) $(SCRIPTS)  $(BINDIR)
 	chmod 755 $(PROGS)
-	$(INSTALL) $(PROGS) $(MANPAGES) $(LIBDIR)
+	$(INSTALL) $(PROGS) $(LIBDIR)
 	( cd $(BINDIR); \
 rm -f linsi ginsi einsi fftns fftnsi nwns nwnsi xinsi qinsi; \
 rm -f mafft-linsi mafft-ginsi mafft-einsi mafft-fftns mafft-fftnsi mafft-nwns mafft-nwnsi mafft-xinsi mafft-qinsi; \
@@ -506,4 +506,4 @@
 
 	mkdir -p $(MANDIR)
 	chmod 755 $(MANDIR)
-	$(INSTALL) $(MANPAGES) $(MANDIR)
+	$(INSTALL) --mode=644 $(MANPAGES) $(MANDIR)
