diff --git a/Recipe b/Recipe
index 0cd8a402..03b6970b 100644
--- a/Recipe
+++ b/Recipe
@@ -19,7 +19,7 @@
 !makefile lcc windows/Makefile.lcc
 !makefile gtk unix/Makefile.gtk
 !makefile unix unix/Makefile.ux
-!makefile am unix/Makefile.am
+!makefile am Makefile.am
 !makefile osx macosx/Makefile
 !makefile devcppproj windows/DEVCPP
 !makefile vstudio10 windows/VS2010
@@ -247,8 +247,8 @@ CFLAGS += -DMACOSX
 
 # List the man pages for the automake makefile.
 !begin am
-man1_MANS = ../doc/plink.1 ../doc/pscp.1 ../doc/psftp.1 ../doc/pterm.1 \
-            ../doc/putty.1 ../doc/puttygen.1 ../doc/puttytel.1
+man1_MANS = doc/plink.1 doc/pscp.1 doc/psftp.1 doc/pterm.1 \
+            doc/putty.1 doc/puttygen.1 doc/puttytel.1
 !end
 
 # In automake, chgrp/chmod pterm after installation, if configured to.
diff --git a/configure b/configure
deleted file mode 100755
index d56f50a3..00000000
--- a/configure
+++ /dev/null
@@ -1,3 +0,0 @@
-#!/bin/sh
-
-$(echo "$0" | sed '$s!configure$!unix/configure!') "$@"
diff --git a/unix/configure.ac b/configure.ac
similarity index 100%
rename from unix/configure.ac
rename to configure.ac
diff --git a/mkauto.sh b/mkauto.sh
index 4a467a51..9759438f 100755
--- a/mkauto.sh
+++ b/mkauto.sh
@@ -8,4 +8,4 @@
 test -f unix.h && cd ..
 
 # Run autoconf on our real configure.in.
-(cd unix && autoreconf -i && rm -rf autom4te.cache)
+autoreconf -i && rm -rf autom4te.cache
diff --git a/mkfiles.pl b/mkfiles.pl
index 9ec915a0..bb767c16 100755
--- a/mkfiles.pl
+++ b/mkfiles.pl
@@ -1472,7 +1472,8 @@ if (defined $makefiles{'unix'}) {
 }
 
 if (defined $makefiles{'am'}) {
-    $dirpfx = "\$(srcdir)/" . &dirpfx($makefiles{'am'}, "/");
+    die "Makefile.am in a subdirectory is not supported\n"
+        if &dirpfx($makefiles{'am'}, "/") ne "";
 
     ##-- Unix/autoconf Makefile.am
     open OUT, ">$makefiles{'am'}"; select OUT;
@@ -1485,8 +1486,7 @@ if (defined $makefiles{'am'}) {
     # auto-generated parts of this makefile, but Recipe might like to
     # have it available as a variable so that mandatory-rebuild things
     # (version.o) can conveniently be made to depend on it.
-    @sources = ("allsources", "=",
-                map {"${dirpfx}$_"} sort keys %allsourcefiles);
+    @sources = ("allsources", "=", sort keys %allsourcefiles);
     print &splitline(join " ", @sources), "\n\n";
 
     @cliprogs = ("bin_PROGRAMS", "=");
@@ -1506,12 +1506,12 @@ if (defined $makefiles{'am'}) {
     print "endif\n\n";
 
     %objtosrc = ();
-    foreach $d (&deps("X", undef, $dirpfx, "/", "am")) {
+    foreach $d (&deps("X", undef, "", "/", "am")) {
       $objtosrc{$d->{obj}} = $d->{deps}->[0];
     }
 
     print &splitline(join " ", "AM_CPPFLAGS", "=",
-                     map {"-I$dirpfx$_"} @srcdirs), "\n";
+                     map {"-I\$(srcdir)/$_"} @srcdirs), "\n";
 
     @amcflags = ("\$(COMPAT)", "\$(XFLAGS)", "\$(WARNINGOPTS)");
     print "if HAVE_GTK\n";
@@ -1909,7 +1909,7 @@ if ($do_unix) {
     system "./mkauto.sh";
     die "mkfiles.pl: mkauto.sh returned $?\n" if $? > 0;
     if ($do_unix == 1) {
-        chdir ($targetdir = dirname($makefiles{"am"}))
+        chdir ($targetdir = "unix")
             or die "$targetdir: chdir: $!\n";
     }
     system "./configure", @confargs;
diff --git a/mkunxarc.sh b/mkunxarc.sh
index b15e2f45..8b17dc51 100755
--- a/mkunxarc.sh
+++ b/mkunxarc.sh
@@ -70,7 +70,7 @@ if test "x$ver" != "x"; then
    md5sum `find . -name '*.[ch]' -print` > manifest;
    echo "$ver" > version.def)
 fi
-sed "s/^AC_INIT(putty,.*/AC_INIT(putty, $autoconfver)/" unix/configure.ac > uxarc/$arcname/unix/configure.ac
+sed "s/^AC_INIT(putty,.*/AC_INIT(putty, $autoconfver)/" configure.ac > uxarc/$arcname/configure.ac
 (cd uxarc/$arcname && sh mkauto.sh) 2>errors || { cat errors >&2; exit 1; }
 
 tar -C uxarc -chzof $arcname.tar.gz $arcname
diff --git a/unix/configure b/unix/configure
new file mode 100755
index 00000000..b2b033d8
--- /dev/null
+++ b/unix/configure
@@ -0,0 +1,3 @@
+#!/bin/sh
+
+$(echo "$0" | sed '$s!configure$!../configure!') "$@"