diff --git a/Makefile.in b/Makefile.in
index df048988..197f11ab 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -537,8 +537,9 @@ EXTERNAL_DEPENDENCIES = 1
 # the dependency information will remain external, so it doesn't
 # pollute the git logs.
 #
-Makefile.dep: $(PERLREQ) $(tools)/mkdep.pl config.status
-	$(RUNPERL) $(tools)/mkdep.pl -M Makefile.in -- $(DEPDIRS)
+Makefile.dep: $(tools)/mkdep.pl config.status $(PERLREQ)
+	$(RUNPERL) $(tools)/mkdep.pl -s '$(top_srcdir)' \
+		-M $(srcdir)/Makefile.in -- $(DEPDIRS)
 
 dep: Makefile.dep
 
diff --git a/Mkfiles/msvc.mak b/Mkfiles/msvc.mak
index ae4a3470..da0bb09c 100644
--- a/Mkfiles/msvc.mak
+++ b/Mkfiles/msvc.mak
@@ -157,7 +157,7 @@ WARNSRCS  = $(patsubst %.obj,%.c,$(LIBOBJ_NW))
 # have Perl just to recompile NASM from the distribution.
 
 # Perl-generated source files
-PERLREQ = config\unconfig.h \
+PERLREQ_CLEANABLE = \
 	  x86\insnsb.c x86\insnsa.c x86\insnsd.c x86\insnsi.h x86\insnsn.c \
 	  x86\regs.c x86\regs.h x86\regflags.c x86\regdis.c x86\regdis.h \
 	  x86\regvals.c asm\tokhash.c asm\tokens.h asm\pptok.h asm\pptok.c \
@@ -168,10 +168,14 @@ PERLREQ = config\unconfig.h \
 	  misc\nasmtok.el \
 	  version.h version.mac version.mak nsis\version.nsh
 
+# Special hack to keep config\unconfig.h from getting deleted
+# by "make spotless"...
+PERLREQ = config\unconfig.h $(PERLREQ_CLEANABLE)
+
 INSDEP = x86\insns.dat x86\insns.pl x86\insns-iflags.ph x86\iflags.ph
 
-config\unconfig.h: config\config.h.in
-	$(RUNPERL) $(tools)\unconfig.pl \
+config\unconfig.h: config\config.h.in autoconf\unconfig.pl
+	$(RUNPERL) '$(srcdir)'\autoconf\unconfig.pl \
 		'$(srcdir)' config\config.h.in config\unconfig.h
 
 x86\iflag.c: $(INSDEP)
@@ -243,11 +247,12 @@ x86\regs.h: x86\regs.dat x86\regs.pl
 # reasonable, but doesn't update the time stamp if the files aren't
 # changed, to avoid rebuilding everything every time. Track the actual
 # dependency by the empty file asm\warnings.time.
-warnings:
-	$(RM_F) $(WARNFILES) $(WARNTIMES)
+.PHONY: warnings
+warnings: dirs
+	$(RM_F) $(WARNFILES) $(WARNTIMES) asm\warnings.time
 	$(MAKE) asm\warnings.time
 
-asm\warnings.time: $(WARNSRCS)
+asm\warnings.time: $(WARNSRCS) asm\warnings.pl
 	$(EMPTY) asm\warnings.time
 	$(MAKE) $(WARNTIMES)
 
diff --git a/Mkfiles/openwcom.mak b/Mkfiles/openwcom.mak
index 3d8dcf05..b0402be2 100644
--- a/Mkfiles/openwcom.mak
+++ b/Mkfiles/openwcom.mak
@@ -170,7 +170,7 @@ WARNSRCS  = $(LIBOBJ_NW:.obj=.c)
 # have Perl just to recompile NASM from the distribution.
 
 # Perl-generated source files
-PERLREQ = config\unconfig.h &
+PERLREQ_CLEANABLE = &
 	  x86\insnsb.c x86\insnsa.c x86\insnsd.c x86\insnsi.h x86\insnsn.c &
 	  x86\regs.c x86\regs.h x86\regflags.c x86\regdis.c x86\regdis.h &
 	  x86\regvals.c asm\tokhash.c asm\tokens.h asm\pptok.h asm\pptok.c &
@@ -181,10 +181,14 @@ PERLREQ = config\unconfig.h &
 	  misc\nasmtok.el &
 	  version.h version.mac version.mak nsis\version.nsh
 
+# Special hack to keep config\unconfig.h from getting deleted
+# by "make spotless"...
+PERLREQ = config\unconfig.h $(PERLREQ_CLEANABLE)
+
 INSDEP = x86\insns.dat x86\insns.pl x86\insns-iflags.ph x86\iflags.ph
 
-config\unconfig.h: config\config.h.in
-	$(RUNPERL) $(tools)\unconfig.pl &
+config\unconfig.h: config\config.h.in autoconf\unconfig.pl
+	$(RUNPERL) '$(srcdir)'\autoconf\unconfig.pl &
 		'$(srcdir)' config\config.h.in config\unconfig.h
 
 x86\iflag.c: $(INSDEP)
@@ -256,11 +260,12 @@ x86\regs.h: x86\regs.dat x86\regs.pl
 # reasonable, but doesn't update the time stamp if the files aren't
 # changed, to avoid rebuilding everything every time. Track the actual
 # dependency by the empty file asm\warnings.time.
-warnings:
-	$(RM_F) $(WARNFILES) $(WARNTIMES)
+.PHONY: warnings
+warnings: dirs
+	$(RM_F) $(WARNFILES) $(WARNTIMES) asm\warnings.time
 	$(MAKE) asm\warnings.time
 
-asm\warnings.time: $(WARNSRCS)
+asm\warnings.time: $(WARNSRCS) asm\warnings.pl
 	$(EMPTY) asm\warnings.time
 	$(MAKE) $(WARNTIMES)
 
diff --git a/tools/mkdep.pl b/tools/mkdep.pl
index f7cc349f..65dac8b6 100755
--- a/tools/mkdep.pl
+++ b/tools/mkdep.pl
@@ -36,34 +36,52 @@
 # Script to create Makefile-style dependencies.
 #
 # Usage:
-#   perl mkdep.pl [-s path-separator][-o obj-ext] dir... > deps
 #   perl mkdep.pl [-i][-e][-m makefile]...[-M makefile... --] dir...
 #
 
+use strict;
+use integer;
+
 use File::Spec;
 use File::Basename;
 use File::Copy;
 use File::Temp;
 use Fcntl;
 
-$barrier = "#-- Everything below is generated by mkdep.pl - do not edit --#\n";
+my $barrier =
+    "#-- Everything below is generated by mkdep.pl - do not edit --#\n";
 
 # This converts from filenames to full pathnames for our dependencies
-%dep_path = ();
+my %dep_path = ();
 
 # List of files that cannot be found; these *must* be excluded
-@must_exclude = ();
+my @must_exclude = ();
+
+#
+# Variables derived from the command line
+#
+my %deps;
+my %excludes;
+my @files;
+my @mkfiles;
+my $mkmode = 0;
+my @searchdirs = (File::Spec->curdir());
+my %searchdirs = (File::Spec->curdir() => 1);
+my $force_inline = 0;
+my $externalize = 0;
+my $debug = 0;
 
 #
 # Scan files for dependencies
 #
-sub scandeps($) {
-    my($file) = @_;
+sub scandeps {
+    # path is the filesystem path, file what the output should call it
+    my($path, $file) = @_;
     my $line;
     my %xdeps;
     my %mdeps;
 
-    open(my $fh, '<', $file)
+    open(my $fh, '<', $path)
 	or return;		# If not openable, assume generated
 
     while ( defined($line = <$fh>) ) {
@@ -128,8 +146,8 @@ sub convert_file($$) {
 #
 # Insert dependencies into a Makefile
 #
-sub _insert_deps($$) {
-    my($file, $out) = @_;
+sub insert_deps($) {
+    my($file) = @_;
 
     open(my $in, '<', $file)
 	or die "$0: Cannot open input: $file\n";
@@ -192,8 +210,13 @@ sub _insert_deps($$) {
     $is_external = $is_external && defined($external);
     undef $external if ( !$is_external );
 
+    my $out;
+    my $outpath;
     if ( !$is_external || $externalize ) {
+	$out = File::Temp->new(DIR => dirname($outpath = $file));
 	print $out @outfile;
+    } else {
+	$out = File::Temp->new(DIR => dirname($outpath = $external));
     }
 
     print $out $barrier;
@@ -204,78 +227,60 @@ sub _insert_deps($$) {
 	    print $out "$include_command $external\n";
 	}
 	unlink($external);
-	return undef;
-    }
+    } else {
 
-    my $e;
+	my $e;
 
-    foreach my $dfile ($external, sort(keys(%deps)) ) {
-	my $ofile;
-	my @deps;
+	foreach my $dfile ($external, sort(keys(%deps)) ) {
+	    my $ofile;
+	    my @deps;
 
-	next unless (defined($dfile));
+	    next unless (defined($dfile));
 
-	if ( $selfrule && $dfile eq $external ) {
-	    $ofile = convert_file($dfile, $sep).':';
-	    @deps = sort(keys(%deps));
-	} elsif ( $dfile =~ /^(.*)\.[Cc]$/ ) {
-	    $ofile = convert_file($1, $sep).$obj.':';
-	    @deps = ($dfile,alldeps($dfile,1));
-	}
+	    if ( $selfrule && $dfile eq $external ) {
+		$ofile = convert_file($dfile, $sep).':';
+		@deps = sort(keys(%deps));
+	    } elsif ( $dfile =~ /^(.*)\.[Cc]$/ ) {
+		$ofile = convert_file($1, $sep).$obj.':';
+		@deps = ($dfile,alldeps($dfile,1));
+	    }
 
-	if (defined($ofile)) {
-	    my $len = length($ofile);
-	    print $out $ofile;
-	    foreach my $dep (@deps) {
-		unless ($excludes{$dep}) {
-		    my $str = convert_file($dep, $sep);
-		    my $sl = length($str)+1;
-		    if ( $len+$sl > $maxline-2 ) {
-			print $out ' ', $cont, "\n ", $str;
-			$len = $sl;
-		    } else {
-			print $out ' ', $str;
-			$len += $sl;
+	    if (defined($ofile)) {
+		my $len = length($ofile);
+		print $out $ofile;
+		foreach my $dep (@deps) {
+		    unless ($excludes{$dep}) {
+			my $str = convert_file($dep, $sep);
+			my $sl = length($str)+1;
+			if ( $len+$sl > $maxline-2 ) {
+			    print $out ' ', $cont, "\n ", $str;
+			    $len = $sl;
+			} else {
+			    print $out ' ', $str;
+			    $len += $sl;
+			}
 		    }
 		}
+		print $out "\n";
 	    }
-	    print $out "\n";
 	}
     }
 
-    return $external;
-}
-
-sub insert_deps($)
-{
-    my($mkfile) = @_;
-    my $tmp = File::Temp->new(DIR => dirname($mkfile));
-    my $tmpname = $tmp->filename;
-
-    my $newname = _insert_deps($mkfile, $tmp);
-    close($tmp);
-
-    $newname = $mkfile unless(defined($newname));
-
-    move($tmpname, $newname);
+    close($out);
+    move($out->filename, $outpath);
 }
 
 #
 # Main program
 #
 
-my %deps = ();
-my @files = ();
-my @mkfiles = ();
-my $mkmode = 0;
-$force_inline = 0;
-$externalize = 0;
-$debug = 0;
-
 while ( defined(my $arg = shift(@ARGV)) ) {
     if ( $arg eq '-m' ) {
 	$arg = shift(@ARGV);
 	push(@mkfiles, $arg);
+    } elsif ( $arg eq '-s' ) {
+	$arg = shift(@ARGV);
+	push(@searchdirs, $arg);
     } elsif ( $arg eq '-i' ) {
 	$force_inline = 1;
     } elsif ( $arg eq '-e' ) {
@@ -297,27 +302,66 @@ while ( defined(my $arg = shift(@ARGV)) ) {
     }
 }
 
-my @cfiles = ();
-
-foreach my $dir ( @files ) {
-    opendir(DIR, $dir) or die "$0: Cannot open directory: $dir";
-
-    while ( my $file = readdir(DIR) ) {
-	$path = ($dir eq File::Spec->curdir())
-	    ? $file : File::Spec->catfile($dir,$file);
-	if ( $file =~ /\.[Cc]$/ ) {
-	    push(@cfiles, $path);
-	} elsif ( $file =~ /\.[Hh]$/ ) {
-	    print STDERR "Filesystem: $file -> $path\n" if ( $debug );
-	    $dep_path{$file} = $path; # Allow the blank filename
-	    $dep_path{$path} = $path; # Also allow the full pathname
-	}
-    }
-    closedir(DIR);
+sub mycatdir($$) {
+    my($a,$b) = @_;
+    return $b if ($a eq File::Spec->curdir());
+    return $a if ($b eq File::Spec->curdir());
+    return File::Spec->catdir($a,$b);
 }
 
+sub mycatfile($$) {
+    my($d,$f) = @_;
+    return $f if ($d eq File::Spec->curdir());
+    return File::Spec->catfile($d,$f);
+}
+
+my @cfiles = ();
+
+my $err = 0;
+my %scanned;
+
+foreach my $fdir ( @files ) {
+    my $found = 0;
+
+    foreach my $sdir ( @searchdirs ) {
+	my $dir = mycatdir($sdir, $fdir);
+	if ($scanned{$dir}) {
+	    # Have already been here
+	    $found = 1;
+	    next;
+	}
+
+	opendir(DIR, $dir) or next;
+	$scanned{$dir}++;
+	$found++;
+
+	while ( my $file = readdir(DIR) ) {
+	    # $fdir is correct here, because we expect VPATH to do
+	    # its job, and the output filename depends on that, not
+	    # on the full source dir path.
+	    my $path = mycatfile($fdir, $file);
+	    my $fullpath = mycatfile($dir, $file);
+	    if ( $file =~ /\.[Cc]$/ ) {
+		push(@cfiles, [$fullpath, $path]);
+	    } elsif ( $file =~ /\.[Hh]$/ ) {
+		print STDERR "Filesystem: $file -> $path\n" if ( $debug );
+		$dep_path{$file} = $path; # Allow the blank filename
+		$dep_path{$path} = $path; # Also allow the full pathname
+	    }
+	}
+	closedir(DIR);
+    }
+
+    if (!$found) {
+	print STDERR "$0: cannot find directory: $fdir\n";
+	$err++;
+    }
+}
+
+exit(1) if ($err);
+
 foreach my $cfile ( @cfiles ) {
-    scandeps($cfile);
+    scandeps(@$cfile);
 }
 
 foreach my $mkfile ( @mkfiles ) {