diff --git a/aclocal.m4 b/aclocal.m4
index 8e047b55aa7..d5a35326131 100644
--- a/aclocal.m4
+++ b/aclocal.m4
@@ -225,24 +225,13 @@ wine_fn_has_flag ()
 
 wine_fn_depend_rules ()
 {
-    if wine_fn_has_flag config
-    then
-        wine_fn_append_rule \
-"$ac_dir/Makefile: $srcdir/$ac_dir/Makefile.in Makefile config.status \$(MAKEDEP)
-	@./config.status --file $ac_dir/Makefile && \$(MAKEDEP) -iMakefile $ac_dir
-depend: $ac_dir/depend
-.PHONY: $ac_dir/depend
-$ac_dir/depend: \$(MAKEDEP) dummy
-	@./config.status --file $ac_dir/Makefile && \$(MAKEDEP) -iMakefile $ac_dir"
-    else
-        wine_fn_append_rule \
+    wine_fn_append_rule \
 "$ac_dir/Makefile: $srcdir/$ac_dir/Makefile.in Makefile \$(MAKEDEP)
 	\$(MAKEDEP) $ac_dir
 depend: $ac_dir/depend
 .PHONY: $ac_dir/depend
 $ac_dir/depend: \$(MAKEDEP) dummy
 	\$(MAKEDEP) $ac_dir"
-    fi
 }
 
 wine_fn_pot_rules ()
diff --git a/configure b/configure
index 3903e4f4a65..3d6d5214922 100755
--- a/configure
+++ b/configure
@@ -7415,24 +7415,13 @@ wine_fn_has_flag ()
 
 wine_fn_depend_rules ()
 {
-    if wine_fn_has_flag config
-    then
-        wine_fn_append_rule \
-"$ac_dir/Makefile: $srcdir/$ac_dir/Makefile.in Makefile config.status \$(MAKEDEP)
-	@./config.status --file $ac_dir/Makefile && \$(MAKEDEP) -iMakefile $ac_dir
-depend: $ac_dir/depend
-.PHONY: $ac_dir/depend
-$ac_dir/depend: \$(MAKEDEP) dummy
-	@./config.status --file $ac_dir/Makefile && \$(MAKEDEP) -iMakefile $ac_dir"
-    else
-        wine_fn_append_rule \
+    wine_fn_append_rule \
 "$ac_dir/Makefile: $srcdir/$ac_dir/Makefile.in Makefile \$(MAKEDEP)
 	\$(MAKEDEP) $ac_dir
 depend: $ac_dir/depend
 .PHONY: $ac_dir/depend
 $ac_dir/depend: \$(MAKEDEP) dummy
 	\$(MAKEDEP) $ac_dir"
-    fi
 }
 
 wine_fn_pot_rules ()
diff --git a/tools/make_makefiles b/tools/make_makefiles
index e86c95bdda3..78b6deaef7b 100755
--- a/tools/make_makefiles
+++ b/tools/make_makefiles
@@ -202,7 +202,7 @@ sub parse_makefile($)
 
         if (/\@[A-Z_]+\@/)  # config.status substitution variable
         {
-            ${$make{"=flags"}}{"config"} = 1;
+            die "Configure substitution is not allowed in $file";
         }
         if (/^\s*(MODULE|IMPORTLIB|TESTDLL|PARENTSRC|APPMODE)\s*=\s*(.*)/)
         {
diff --git a/tools/makedep.c b/tools/makedep.c
index 469b833eff8..14a26ef4f89 100644
--- a/tools/makedep.c
+++ b/tools/makedep.c
@@ -180,7 +180,6 @@ struct makefile
 static struct makefile *top_makefile;
 
 static const char *output_makefile_name = "Makefile";
-static const char *input_makefile_name;
 static const char *input_file_name;
 static const char *output_file_name;
 static const char *temp_file_name;
@@ -193,8 +192,7 @@ static const char Usage[] =
     "Usage: makedep [options] directories\n"
     "Options:\n"
     "   -R from to  Compute the relative path between two directories\n"
-    "   -fxxx       Store output in file 'xxx' (default: Makefile)\n"
-    "   -ixxx       Read input from file 'xxx' (default: Makefile.in)\n";
+    "   -fxxx       Store output in file 'xxx' (default: Makefile)\n";
 
 
 #ifndef __GNUC__
@@ -1558,11 +1556,9 @@ static FILE *open_input_makefile( const struct makefile *make )
     FILE *ret;
 
     if (make->base_dir)
-    {
-        input_file_name = base_dir_path( make, input_makefile_name );
-        if (strendswith( input_makefile_name, ".in" )) input_file_name = root_dir_path( input_file_name );
-    }
-    else input_file_name = output_makefile_name;  /* always use output name for main Makefile */
+        input_file_name = root_dir_path( base_dir_path( make, strmake( "%s.in", output_makefile_name )));
+    else
+        input_file_name = output_makefile_name;  /* always use output name for main Makefile */
 
     input_line = 0;
     if (!(ret = fopen( input_file_name, "r" ))) fatal_perror( "open" );
@@ -3208,9 +3204,6 @@ static int parse_option( const char *opt )
     case 'f':
         if (opt[2]) output_makefile_name = opt + 2;
         break;
-    case 'i':
-        if (opt[2]) input_makefile_name = opt + 2;
-        break;
     case 'R':
         relative_dir_mode = 1;
         break;
@@ -3271,8 +3264,6 @@ int main( int argc, char *argv[] )
 
     for (i = 0; i < HASH_SIZE; i++) list_init( &files[i] );
 
-    if (!input_makefile_name) input_makefile_name = strmake( "%s.in", output_makefile_name );
-
     top_makefile = parse_makefile( NULL, "# End of common header" );
 
     linguas      = get_expanded_make_var_array( top_makefile, "LINGUAS" );