diff --git a/configs/Makefile b/configs/Makefile
index 31de5604e0..cee8bdafed 100644
--- a/configs/Makefile
+++ b/configs/Makefile
@@ -116,7 +116,7 @@ depend: .depend
 
 $(DUMMY_KCONFIG): $(BOARD_KCONFIG)
 	$(call DELFILE, $(DUMMY_KCONFIG))
-	$(Q) cp -f $(BOARD_KCONFIG) $(DUMMY_KCONFIG)
+	$(call COPYFILE, $(BOARD_KCONFIG), $(DUMMY_KCONFIG))
 
 dirlinks: $(DUMMY_KCONFIG)
 
diff --git a/tools/Config.mk b/tools/Config.mk
index b059bbabe3..eb95551f5f 100644
--- a/tools/Config.mk
+++ b/tools/Config.mk
@@ -268,6 +268,18 @@ define MOVEFILE
 endef
 endif
 
+# COPYFILE - Copy one file
+
+ifeq ($(CONFIG_WINDOWS_NATIVE),y)
+define COPYFILE
+	$(Q) if exist $1 (copy /y /b $1 $2)
+endef
+else
+define COPYFILE
+	$(Q) cp -f $1 $2
+endef
+endif
+
 # CATFILE - Cat and append a list of files
 #
 # USAGE: $(call CATFILE,dest,src1,src2,src3,...)
diff --git a/tools/configure.c b/tools/configure.c
index ba7f1d5600..629157b529 100644
--- a/tools/configure.c
+++ b/tools/configure.c
@@ -202,7 +202,7 @@ static void parse_args(int argc, char **argv)
 
   g_debug = false;
 
-  while ((ch = getopt(argc, argv, ":a:bcdfhlmnu")) > 0)
+  while ((ch = getopt(argc, argv, "a:bcdfghlmnu")) > 0)
     {
       switch (ch)
         {
@@ -917,6 +917,59 @@ static void substitute(char *str, int ch1, int ch2)
     }
 }
 
+static char *double_appdir_backslashes(char *old_appdir)
+{
+  char *new_appdir = NULL;
+  char *p_old = NULL;
+  char *p_new = NULL;
+  int oldlen = 0;
+  int occurrences = 0;
+  int alloclen = 0;
+
+  p_old = old_appdir;
+  while ((p_old = strchr(p_old, '\\')) != NULL)
+    {
+      occurrences++;
+      p_old++;
+    }
+
+  if (occurrences != 0)
+    {
+      oldlen = strlen(old_appdir);
+      alloclen = oldlen + occurrences + sizeof((char) '\0');
+      new_appdir = malloc(alloclen);
+
+      if (new_appdir != NULL)
+        {
+          p_old = old_appdir;
+          p_new = new_appdir;
+          while (oldlen)
+            {
+              if (*p_old != '\\')
+                {
+                  *p_new++ = *p_old;
+                }
+                else
+                {
+                  *p_new++ = '\\';
+                  *p_new++ = '\\';
+                }
+
+              ++p_old;
+              --oldlen;
+            }
+
+          *p_new = '\0';
+        }
+    }
+  else
+    {
+      new_appdir = strdup(old_appdir);
+    }
+
+  return new_appdir;
+}
+
 static void copy_optional(void)
 {
   int i;
@@ -1155,6 +1208,24 @@ static void configure(void)
             }
         }
 
+      /* Looks like prebuilt winnative kconfig-conf interprets "..\apps" as
+       * "..apps" (possibly '\a' as escape-sequence) so expand winnative path
+       * to double-backslashed variant "..\\apps".
+       */
+
+      if (g_winnative)
+        {
+          char *tmp_appdir = double_appdir_backslashes(appdir);
+          if (NULL == tmp_appdir)
+            {
+              fprintf(stderr, "ERROR: Failed to double appdir backslashes\n");
+              exit(EXIT_FAILURE);
+            }
+
+          free(appdir);
+          appdir = tmp_appdir;
+        }
+
       /* Open the file for appending */
 
       stream = fopen(destconfig, "a");
@@ -1185,7 +1256,7 @@ static void refresh(void)
       exit(EXIT_FAILURE);
     }
 
-  printf("  Refreshing...");
+  printf("  Refreshing...\n");
   fflush(stdout);
 
 #ifdef WIN32
diff --git a/tools/configure.sh b/tools/configure.sh
index 030d52340c..d51d73201f 100755
--- a/tools/configure.sh
+++ b/tools/configure.sh
@@ -235,7 +235,7 @@ fi
 # For checking the apps dir path, we need a POSIX version of the relative path.
 
 posappdir=`echo "${appdir}" | sed -e 's/\\\\/\\//g'`
-winappdir=`echo "${appdir}" | sed -e 's/\\//\\\\/g'`
+winappdir=`echo "${appdir}" | sed -e 's/\\//\\\\\\\/g'`
 
 # If appsdir was provided (or discovered) then make sure that the apps/
 # directory exists
diff --git a/tools/link.bat b/tools/link.bat
index 22ddaf14b1..21baa6c03e 100755
--- a/tools/link.bat
+++ b/tools/link.bat
@@ -89,7 +89,7 @@ goto :End
 )
 
 xcopy %src% %link% /c /q /s /e /y /i
-echo FAKELNK > include\apps\.fakelnk
+echo FAKELNK > %link%\.fakelnk
 goto :End
 
 :ShowUsage
diff --git a/tools/mkdeps.c b/tools/mkdeps.c
index 01db9c4e0c..3daae91f66 100644
--- a/tools/mkdeps.c
+++ b/tools/mkdeps.c
@@ -219,7 +219,7 @@ static void append(char **base, char *str)
     }
   else
     {
-      alloclen = strlen(oldbase) + strlen(str) + 2;
+      alloclen = strlen(oldbase) + strlen(str) + sizeof((char) ' ') + sizeof((char) '\0');
       newbase = (char *)malloc(alloclen);
       if (!newbase)
         {
@@ -227,7 +227,7 @@ static void append(char **base, char *str)
           exit(EXIT_FAILURE);
         }
 
-      snprintf(newbase, alloclen, "%s %s\n", oldbase, str);
+      snprintf(newbase, alloclen, "%s %s", oldbase, str);
       free(oldbase);
    }