diff --git a/tools/config.h.in b/tools/config.h.in
index f65d92d..603a42c 100644
--- a/tools/config.h.in
+++ b/tools/config.h.in
@@ -15,9 +15,6 @@
 #ifndef YANGLINT_CONFIG_H_
 #define YANGLINT_CONFIG_H_
 
-#define _DEFAULT_SOURCE
-#define _GNU_SOURCE
-
 #define PROJECT_VERSION "@LIBYANG_VERSION@" /**< libyang project version string */
 
 #endif /* YANGLINT_CONFIG_H_ */
diff --git a/tools/lint/commands.c b/tools/lint/commands.c
index 524eabb..17d0560 100644
--- a/tools/lint/commands.c
+++ b/tools/lint/commands.c
@@ -12,20 +12,19 @@
  *     https://opensource.org/licenses/BSD-3-Clause
  */
 
-#include "config.h"
-
-#include <string.h>
-#include <stdio.h>
-#include <errno.h>
-#include <ctype.h>
-#include <assert.h>
-#include <sys/types.h>
-#include <sys/stat.h>
-#include <unistd.h>
-#include <getopt.h>
-#include <libgen.h>
+#define _GNU_SOURCE
 
 #include "commands.h"
+
+#include <ctype.h>
+#include <errno.h>
+#include <getopt.h>
+#include <libgen.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <sys/stat.h>
+
 #include "libyang.h"
 
 COMMAND commands[];
diff --git a/tools/lint/commands.h b/tools/lint/commands.h
index 18d7fdc..247d373 100644
--- a/tools/lint/commands.h
+++ b/tools/lint/commands.h
@@ -21,8 +21,6 @@
 #  define UNUSED(x) UNUSED_ ## x
 #endif
 
-#include <stdlib.h>
-
 #include "libyang.h"
 
 #define PROMPT "> "
diff --git a/tools/lint/completion.c b/tools/lint/completion.c
index 3a5394c..4172a2b 100644
--- a/tools/lint/completion.c
+++ b/tools/lint/completion.c
@@ -12,19 +12,19 @@
  *     https://opensource.org/licenses/BSD-3-Clause
  */
 
-#include "config.h"
+#define _GNU_SOURCE
 
-#include <stdlib.h>
-#include <stdio.h>
-#include <sys/types.h>
-#include <dirent.h>
 #include <errno.h>
+#include <stdint.h>
+#include <stdio.h>
+#include <stdlib.h>
 #include <string.h>
 
-#include "commands.h"
-#include "./linenoise/linenoise.h"
 #include "libyang.h"
 
+#include "commands.h"
+#include "linenoise/linenoise.h"
+
 extern struct ly_ctx *ctx;
 
 static void
diff --git a/tools/lint/configuration.c b/tools/lint/configuration.c
index 095d2d0..5bda4ed 100644
--- a/tools/lint/configuration.c
+++ b/tools/lint/configuration.c
@@ -12,19 +12,17 @@
  *     https://opensource.org/licenses/BSD-3-Clause
  */
 
-#include "config.h"
-
-#include <stdlib.h>
-#include <stdio.h>
-#include <string.h>
-#include <errno.h>
-#include <unistd.h>
-#include <sys/stat.h>
-#include <sys/types.h>
-#include <pwd.h>
-
 #include "configuration.h"
-#include "./linenoise/linenoise.h"
+
+#include <errno.h>
+#include <pwd.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <sys/stat.h>
+#include <unistd.h>
+
+#include "linenoise/linenoise.h"
 
 /* Yanglint home (appended to ~/) */
 #define YL_DIR ".yanglint"
diff --git a/tools/lint/linenoise/linenoise.c b/tools/lint/linenoise/linenoise.c
index 135a712..f14d348 100644
--- a/tools/lint/linenoise/linenoise.c
+++ b/tools/lint/linenoise/linenoise.c
@@ -107,20 +107,19 @@
 
 #define _GNU_SOURCE
 
-#include <termios.h>
-#include <unistd.h>
-#include <stdlib.h>
-#include <stdio.h>
-#include <errno.h>
-#include <string.h>
-#include <stdlib.h>
+#include "linenoise.h"
+
 #include <ctype.h>
 #include <dirent.h>
-#include <sys/types.h>
+#include <errno.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <strings.h>
 #include <sys/ioctl.h>
 #include <sys/stat.h>
+#include <termios.h>
 #include <unistd.h>
-#include "linenoise.h"
 
 #define LINENOISE_DEFAULT_HISTORY_MAX_LEN 100
 #define LINENOISE_MAX_LINE 4096
diff --git a/tools/lint/linenoise/linenoise.h b/tools/lint/linenoise/linenoise.h
index c708990..2bebcf3 100644
--- a/tools/lint/linenoise/linenoise.h
+++ b/tools/lint/linenoise/linenoise.h
@@ -39,6 +39,8 @@
 #ifndef __LINENOISE_H
 #define __LINENOISE_H
 
+#include <stddef.h>
+
 #ifdef __cplusplus
 extern "C" {
 #endif
diff --git a/tools/lint/main.c b/tools/lint/main.c
index 6b257da..d1121a0 100644
--- a/tools/lint/main.c
+++ b/tools/lint/main.c
@@ -12,7 +12,7 @@
  *     https://opensource.org/licenses/BSD-3-Clause
  */
 
-#include "config.h"
+#define _GNU_SOURCE
 
 #include <stdio.h>
 #include <stdlib.h>
@@ -20,12 +20,16 @@
 #include <string.h>
 #include <unistd.h>
 
-#include "commands.h"
-#include "configuration.h"
-#include "completion.h"
-#include "./linenoise/linenoise.h"
 #include "libyang.h"
 
+#include "tools/config.h"
+
+#include "commands.h"
+#include "completion.h"
+#include "configuration.h"
+#include "linenoise/linenoise.h"
+
+
 int done;
 struct ly_ctx *ctx = NULL;
 
diff --git a/tools/lint/main_ni.c b/tools/lint/main_ni.c
index 67bd6ae..8da6a87 100644
--- a/tools/lint/main_ni.c
+++ b/tools/lint/main_ni.c
@@ -12,7 +12,7 @@
  *     https://opensource.org/licenses/BSD-3-Clause
  */
 
-#include "config.h"
+#define _GNU_SOURCE
 
 #include <stdio.h>
 #include <stdlib.h>
@@ -25,9 +25,13 @@
 #include <string.h>
 #include <unistd.h>
 
-#include "commands.h"
 #include "libyang.h"
 
+#include "tools/config.h"
+
+#include "commands.h"
+
+
 volatile uint8_t verbose = 0;
 
 #if 0
diff --git a/tools/re/main.c b/tools/re/main.c
index b664bf9..8773907 100644
--- a/tools/re/main.c
+++ b/tools/re/main.c
@@ -12,7 +12,7 @@
  *     https://opensource.org/licenses/BSD-3-Clause
  */
 
-#include "config.h"
+#define _GNU_SOURCE
 
 #include <errno.h>
 #include <fcntl.h>
@@ -24,8 +24,9 @@
 #include <getopt.h>
 #include <unistd.h>
 
-#include "context.h"
-#include "plugins_types.h"
+#include "libyang.h"
+
+#include "tools/config.h"
 
 void
 help(void)