diff --git a/urjtag/README b/urjtag/README
index 7890d15e..26677cc7 100644
--- a/urjtag/README
+++ b/urjtag/README
@@ -1,6 +1,6 @@
 $Id$
 
-The subdirectory urjtag/ or the UrJTAG package contains a branch that is used
+The subdirectory urjtag/ of the UrJTAG package contains a branch that is used
 for the conversion of UrJTAG to a library plus a separate command shell.
 Changes and commits to this branch will be frequent, and will affect nearly
 every aspect of the source tree, like file names, file locations, code layout,
diff --git a/urjtag/include/Makefile.am b/urjtag/include/Makefile.am
index d9c72419..718e5bdb 100644
--- a/urjtag/include/Makefile.am
+++ b/urjtag/include/Makefile.am
@@ -39,10 +39,10 @@ noinst_HEADERS = \
 	flash/mic.h \
 	flash/intel.h \
 	gettext.h \
-	instruction.h \
+	part_instruction.h \
 	parport.h \
 	part.h \
-	register.h \
+	tap_register.h \
 	bssignal.h \
 	tap_state.h \
 	jtag.h \
diff --git a/urjtag/include/cmd.h b/urjtag/include/cmd.h
index 820f0173..f709baaa 100644
--- a/urjtag/include/cmd.h
+++ b/urjtag/include/cmd.h
@@ -46,7 +46,6 @@ typedef struct
 
 extern const urj_cmd_t *urj_cmds[];
 
-char **urj_cmd_completion (const char *text, int start, int end);
 int urj_cmd_run (urj_chain_t *chain, char *params[]);
 int urj_cmd_params (char *params[]);
 int urj_cmd_get_number (char *s, unsigned int *i);
diff --git a/urjtag/include/data_register.h b/urjtag/include/data_register.h
index aeb18548..53c38af6 100644
--- a/urjtag/include/data_register.h
+++ b/urjtag/include/data_register.h
@@ -25,7 +25,7 @@
 #ifndef URJ_DATA_REGISTER_H
 #define URJ_DATA_REGISTER_H
 
-#include "register.h"
+#include "tap_register.h"
 
 #define URJ_DATA_REGISTER_MAXLEN        32
 
diff --git a/urjtag/include/flash.h b/urjtag/include/flash.h
index da0bdd15..addcb7e0 100644
--- a/urjtag/include/flash.h
+++ b/urjtag/include/flash.h
@@ -85,6 +85,8 @@ typedef struct
 #define URJ_FLASH_ERROR_BLOCK_LOCKED                    3
 #define URJ_FLASH_ERROR_UNKNOWN                         99
 
+extern urj_flash_cfi_array_t *urj_flash_cfi_array;
+
 void urj_flash_detectflash (urj_bus_t *bus, uint32_t adr);
 
 void urj_flashmem (urj_bus_t *bus, FILE * f, uint32_t addr, int);
diff --git a/urjtag/include/instruction.h b/urjtag/include/instruction.h
index 1ed019b3..0f676cda 100644
--- a/urjtag/include/instruction.h
+++ b/urjtag/include/instruction.h
@@ -22,27 +22,27 @@
  *
  */
 
-#ifndef URJ_INSTRUCTION_H
-#define URJ_INSTRUCTION_H
+#ifndef URJ_PART_INSTRUCTION_H
+#define URJ_PART_INSTRUCTION_H
 
-#include "register.h"
+#include "tap_register.h"
 #include "data_register.h"
 
 #define URJ_INSTRUCTION_MAXLEN_INSTRUCTION      20
 
-typedef struct urj_instruction urj_instruction_t;
+typedef struct urj_part_instruction urj_part_instruction_t;
 
-struct urj_instruction
+struct urj_part_instruction
 {
     char name[URJ_INSTRUCTION_MAXLEN_INSTRUCTION + 1];
     urj_tap_register_t *value;
     urj_tap_register_t *out;
     urj_data_register_t *data_register;
-    urj_instruction_t *next;
+    urj_part_instruction_t *next;
 };
 
-urj_instruction_t *urj_part_instruction_alloc (const char *name, int len,
-                                               const char *val);
-void urj_part_instruction_free (urj_instruction_t *i);
+urj_part_instruction_t *urj_part_instruction_alloc (const char *name, int len,
+                                                    const char *val);
+void urj_part_instruction_free (urj_part_instruction_t *i);
 
 #endif /* URJ_INSTRUCTION_H */
diff --git a/urjtag/include/jtag.h b/urjtag/include/jtag.h
index 78bc7b65..050119ae 100644
--- a/urjtag/include/jtag.h
+++ b/urjtag/include/jtag.h
@@ -40,8 +40,8 @@
 
 
 extern urj_bus_t *urj_bus;
-extern int big_endian;
-extern int debug_mode;
+extern int urj_big_endian;
+extern int urj_debug_mode;
 
 const char *urj_cmd_jtag_get_data_dir (void);
 
diff --git a/urjtag/include/part.h b/urjtag/include/part.h
index af147ff0..5ce852f5 100644
--- a/urjtag/include/part.h
+++ b/urjtag/include/part.h
@@ -28,7 +28,7 @@
 #include <stdio.h>
 
 #include "bssignal.h"
-#include "instruction.h"
+#include "part_instruction.h"
 #include "data_register.h"
 #include "bsbit.h"
 
@@ -48,8 +48,8 @@ struct urj_part
     urj_part_signal_t *signals;
     urj_part_salias_t *saliases;
     int instruction_length;
-    urj_instruction_t *instructions;
-    urj_instruction_t *active_instruction;
+    urj_part_instruction_t *instructions;
+    urj_part_instruction_t *active_instruction;
     urj_data_register_t *data_registers;
     int boundary_length;
     urj_bsbit_t **bsbits;
@@ -58,8 +58,8 @@ struct urj_part
 urj_part_t *urj_part_alloc (const urj_tap_register_t *id);
 void urj_part_free (urj_part_t *p);
 urj_part_t *read_part (FILE * f, urj_tap_register_t *idr);
-urj_instruction_t *urj_part_find_instruction (urj_part_t *p,
-                                              const char *iname);
+urj_part_instruction_t *urj_part_find_instruction (urj_part_t *p,
+                                                   const char *iname);
 urj_data_register_t *urj_part_find_data_register (urj_part_t *p,
                                                   const char *drname);
 urj_part_signal_t *urj_part_find_signal (urj_part_t *p,
diff --git a/urjtag/include/tap.h b/urjtag/include/tap.h
index 6472d450..3c05ff72 100644
--- a/urjtag/include/tap.h
+++ b/urjtag/include/tap.h
@@ -25,7 +25,7 @@
 #ifndef URJ_TAP_H
 #define URJ_TAP_H
 
-#include "register.h"
+#include "tap_register.h"
 #include "chain.h"
 
 void urj_tap_reset (urj_chain_t *chain);
diff --git a/urjtag/include/register.h b/urjtag/include/tap_register.h
similarity index 97%
rename from urjtag/include/register.h
rename to urjtag/include/tap_register.h
index 218c4a9c..a53fe7e8 100644
--- a/urjtag/include/register.h
+++ b/urjtag/include/tap_register.h
@@ -22,8 +22,8 @@
  *
  */
 
-#ifndef URJ_REGISTER_H
-#define URJ_REGISTER_H
+#ifndef URJ_TAP_REGISTER_H
+#define URJ_TAP_REGISTER_H
 
 typedef struct urj_tap_register
 {
diff --git a/urjtag/src/bus/fjmem.c b/urjtag/src/bus/fjmem.c
index bfa1720f..13d0787b 100644
--- a/urjtag/src/bus/fjmem.c
+++ b/urjtag/src/bus/fjmem.c
@@ -85,7 +85,7 @@ fjmem_detect_reg_len (urj_chain_t *chain, urj_part_t *part, char *opcode,
                       int len)
 {
     urj_data_register_t *dr;
-    urj_instruction_t *i;
+    urj_part_instruction_t *i;
     int l, fjmem_reg_len;
     char *tdo_bit;
 
diff --git a/urjtag/src/bus/readmem.c b/urjtag/src/bus/readmem.c
index b39c0f09..3c52b74b 100644
--- a/urjtag/src/bus/readmem.c
+++ b/urjtag/src/bus/readmem.c
@@ -101,7 +101,7 @@ urj_bus_readmem (urj_bus_t *bus, FILE * f, uint32_t addr, uint32_t len)
             data = URJ_BUS_READ_END (bus);
 
         for (j = step; j > 0; j--)
-            if (big_endian)
+            if (urj_big_endian)
                 b[bc++] = (data >> ((j - 1) * 8)) & 0xFF;
             else
             {
diff --git a/urjtag/src/bus/writemem.c b/urjtag/src/bus/writemem.c
index b0ac3f4a..2ac3b6ac 100644
--- a/urjtag/src/bus/writemem.c
+++ b/urjtag/src/bus/writemem.c
@@ -116,7 +116,7 @@ urj_bus_writemem (urj_bus_t *bus, FILE * f, uint32_t addr, uint32_t len)
         data = 0;
         for (j = step; j > 0; j--)
         {
-            if (big_endian)
+            if (urj_big_endian)
             {
                 data |= b[bidx++];
                 data <<= 8;
diff --git a/urjtag/src/cmd/cmd_cmd.c b/urjtag/src/cmd/cmd_cmd.c
index 76c3bce9..cfca4f15 100644
--- a/urjtag/src/cmd/cmd_cmd.c
+++ b/urjtag/src/cmd/cmd_cmd.c
@@ -26,9 +26,6 @@
 
 #include <stdio.h>
 #include <string.h>
-#ifdef HAVE_LIBREADLINE
-#include <readline/readline.h>
-#endif
 
 #include "jtag.h"
 
@@ -127,42 +124,6 @@ const urj_cmd_t *urj_cmds[] = {
     NULL                        /* last must be NULL */
 };
 
-#ifdef HAVE_LIBREADLINE
-static char *
-cmd_find_next (const char *text, int state)
-{
-    static size_t cmd_idx, len;
-
-    if (!state)
-    {
-        cmd_idx = 0;
-        len = strlen (text);
-    }
-
-    while (urj_cmds[cmd_idx])
-    {
-        char *name = urj_cmds[cmd_idx++]->name;
-        if (!strncmp (name, text, len))
-            return strdup (name);
-    }
-
-    return NULL;
-}
-
-#ifdef HAVE_READLINE_COMPLETION
-char **
-urj_cmd_completion (const char *text, int start, int end)
-{
-    char **ret = NULL;
-
-    if (start == 0)
-        ret = rl_completion_matches (text, cmd_find_next);
-
-    return ret;
-}
-#endif
-#endif
-
 int
 urj_cmd_test_cable (urj_chain_t *chain)
 {
diff --git a/urjtag/src/cmd/cmd_debug.c b/urjtag/src/cmd/cmd_debug.c
index 350341c8..5b656a0d 100644
--- a/urjtag/src/cmd/cmd_debug.c
+++ b/urjtag/src/cmd/cmd_debug.c
@@ -45,7 +45,7 @@ cmd_debug_run (urj_chain_t *chain, char *params[])
     if (urj_cmd_get_number (params[1], &i))
         return 1;
 
-    debug_mode = i;
+    urj_debug_mode = i;
     return 1;
 }
 
diff --git a/urjtag/src/cmd/cmd_dr.c b/urjtag/src/cmd/cmd_dr.c
index a232480f..a8608375 100644
--- a/urjtag/src/cmd/cmd_dr.c
+++ b/urjtag/src/cmd/cmd_dr.c
@@ -27,7 +27,7 @@
 #include <stdio.h>
 #include <string.h>
 
-#include "register.h"
+#include "tap_register.h"
 #include "jtag.h"
 
 #include "cmd.h"
diff --git a/urjtag/src/cmd/cmd_endian.c b/urjtag/src/cmd/cmd_endian.c
index 0afc59d8..1bacd32f 100644
--- a/urjtag/src/cmd/cmd_endian.c
+++ b/urjtag/src/cmd/cmd_endian.c
@@ -39,7 +39,7 @@ cmd_endian_run (urj_chain_t *chain, char *params[])
 
     if (!params[1])
     {
-        if (big_endian)
+        if (urj_big_endian)
             printf (_("Endianess for external files: big\n"));
         else
             printf (_("Endianess for external files: little\n"));
@@ -49,12 +49,12 @@ cmd_endian_run (urj_chain_t *chain, char *params[])
 
     if (strcasecmp (params[1], "little") == 0)
     {
-        big_endian = 0;
+        urj_big_endian = 0;
         return 1;
     }
     if (strcasecmp (params[1], "big") == 0)
     {
-        big_endian = 1;
+        urj_big_endian = 1;
         return 1;
     }
 
diff --git a/urjtag/src/cmd/cmd_instruction.c b/urjtag/src/cmd/cmd_instruction.c
index 69d330f2..3a4328c9 100644
--- a/urjtag/src/cmd/cmd_instruction.c
+++ b/urjtag/src/cmd/cmd_instruction.c
@@ -85,7 +85,7 @@ cmd_instruction_run (urj_chain_t *chain, char *params[])
 
     if (urj_cmd_params (params) == 4)
     {
-        urj_instruction_t *i;
+        urj_part_instruction_t *i;
 
         if (strlen (params[2]) != part->instruction_length)
         {
diff --git a/urjtag/src/cmd/cmd_parse.c b/urjtag/src/cmd/cmd_parse.c
index 2e315275..f723c23b 100644
--- a/urjtag/src/cmd/cmd_parse.c
+++ b/urjtag/src/cmd/cmd_parse.c
@@ -110,7 +110,7 @@ urj_cmd_jtag_parse_line (urj_chain_t *chain, char *line)
     a[tcnt] = NULL;
 
     r = urj_cmd_run (chain, a);
-    if (debug_mode & 1)
+    if (urj_debug_mode & 1)
         printf ("Return in urj_cmd_jtag_parse_line r=%d\n", r);
     free (a);
     free (sline);
@@ -172,7 +172,7 @@ urj_cmd_jtag_parse_file (urj_chain_t *chain, const char *filename)
     go = urj_cmd_jtag_parse_stream (chain, f);
 
     fclose (f);
-    if (debug_mode & 1)
+    if (urj_debug_mode & 1)
         printf ("File Closed gp=%d\n", go);
     return go;
 }
diff --git a/urjtag/src/cmd/cmd_print.c b/urjtag/src/cmd/cmd_print.c
index a2c0c8c2..9d40dfe1 100644
--- a/urjtag/src/cmd/cmd_print.c
+++ b/urjtag/src/cmd/cmd_print.c
@@ -104,7 +104,7 @@ cmd_print_run (urj_chain_t *chain, char *params[])
         if (strcasecmp (params[1], "instructions") == 0)
         {
             urj_part_t *part;
-            urj_instruction_t *inst;
+            urj_part_instruction_t *inst;
 
             snprintf (format, 128, _(" Active %%-%ds %%-%ds"),
                       URJ_INSTRUCTION_MAXLEN_INSTRUCTION,
diff --git a/urjtag/src/flash/flash.c b/urjtag/src/flash/flash.c
index f3a005b5..09296969 100644
--- a/urjtag/src/flash/flash.c
+++ b/urjtag/src/flash/flash.c
@@ -65,7 +65,6 @@ urj_flash_driver_t *urj_flash_flash_drivers[] = {
     NULL
 };
 
-extern urj_flash_cfi_array_t *urj_flash_cfi_array;
 static urj_flash_driver_t *flash_driver = NULL;
 
 static void
@@ -363,7 +362,7 @@ urj_flashmem (urj_bus_t *bus, FILE * f, uint32_t addr, int noverify)
 
             data = 0;
             for (j = 0; j < flash_driver->bus_width; j++)
-                if (big_endian)
+                if (urj_big_endian)
                     data = (data << 8) | b[bc + j];
                 else
                     data |= b[bc + j] << (j * 8);
@@ -420,7 +419,7 @@ urj_flashmem (urj_bus_t *bus, FILE * f, uint32_t addr, int noverify)
 
             data = 0;
             for (j = 0; j < flash_driver->bus_width; j++)
-                if (big_endian)
+                if (urj_big_endian)
                     data = (data << 8) | b[bc + j];
                 else
                     data |= b[bc + j] << (j * 8);
diff --git a/urjtag/src/jtag.c b/urjtag/src/jtag.c
index df9a736c..55f2d287 100644
--- a/urjtag/src/jtag.c
+++ b/urjtag/src/jtag.c
@@ -50,15 +50,15 @@
 #include "bus.h"
 #include "cmd.h"
 #include "jtag.h"
+#include "flash.h"
 
 #ifndef HAVE_GETLINE
 ssize_t urj_lib_getline (char **lineptr, size_t *n, FILE * stream);
 #endif
 
-int debug_mode = 0;
-int big_endian = 0;
-int interactive = 0;
-extern urj_flash_cfi_array_t *urj_flash_cfi_array;
+int urj_debug_mode = 0;
+int urj_big_endian = 0;
+static int urj_interactive = 0;
 
 #define JTAGDIR         ".jtag"
 #define HISTORYFILE     "history"
@@ -92,6 +92,41 @@ jtag_create_jtagdir (void)
 }
 
 #ifdef HAVE_LIBREADLINE
+
+static char *
+cmd_find_next (const char *text, int state)
+{
+    static size_t cmd_idx, len;
+
+    if (!state)
+    {
+        cmd_idx = 0;
+        len = strlen (text);
+    }
+
+    while (urj_cmds[cmd_idx])
+    {
+        char *name = urj_cmds[cmd_idx++]->name;
+        if (!strncmp (name, text, len))
+            return strdup (name);
+    }
+
+    return NULL;
+}
+
+#ifdef HAVE_READLINE_COMPLETION
+static char **
+urj_cmd_completion (const char *text, int start, int end)
+{
+    char **ret = NULL;
+
+    if (start == 0)
+        ret = rl_completion_matches (text, cmd_find_next);
+
+    return ret;
+}
+#endif /* def HAVE_READLINE_COMPLETION */
+
 #ifdef HAVE_READLINE_HISTORY
 
 static void
@@ -145,7 +180,8 @@ jtag_save_history (void)
 }
 
 #endif /* HAVE_READLINE_HISTORY */
-#endif
+
+#endif /* HAVE_READLINE */
 
 static int
 jtag_readline_multiple_commands_support (urj_chain_t *chain, char *line)        /* multiple commands should be separated with '::' */
@@ -345,7 +381,7 @@ main (int argc, char *const argv[])
             break;
 
         case 'i':
-            interactive = 1;
+            urj_interactive = 1;
             break;
 
         case 'h':
@@ -433,7 +469,7 @@ main (int argc, char *const argv[])
             }
         }
 
-        if (!interactive)
+        if (!urj_interactive)
             return 0;
     }
 
diff --git a/urjtag/src/part/instruction.c b/urjtag/src/part/instruction.c
index 2ae266a8..2ceed238 100644
--- a/urjtag/src/part/instruction.c
+++ b/urjtag/src/part/instruction.c
@@ -28,12 +28,12 @@
 #include <stdio.h>
 #include <string.h>
 
-#include "instruction.h"
+#include "part_instruction.h"
 
-urj_instruction_t *
+urj_part_instruction_t *
 urj_part_instruction_alloc (const char *name, int len, const char *val)
 {
-    urj_instruction_t *i;
+    urj_part_instruction_t *i;
 
     if (!name || !val)
         return NULL;
@@ -69,7 +69,7 @@ urj_part_instruction_alloc (const char *name, int len, const char *val)
 }
 
 void
-urj_part_instruction_free (urj_instruction_t *i)
+urj_part_instruction_free (urj_part_instruction_t *i)
 {
     if (!i)
         return;
diff --git a/urjtag/src/part/part.c b/urjtag/src/part/part.c
index f6168d06..9e30bb94 100644
--- a/urjtag/src/part/part.c
+++ b/urjtag/src/part/part.c
@@ -87,7 +87,7 @@ urj_part_free (urj_part_t *p)
     /* instructions */
     while (p->instructions)
     {
-        urj_instruction_t *i = p->instructions;
+        urj_part_instruction_t *i = p->instructions;
         p->instructions = i->next;
         urj_part_instruction_free (i);
     }
@@ -108,10 +108,10 @@ urj_part_free (urj_part_t *p)
     free (p);
 }
 
-urj_instruction_t *
+urj_part_instruction_t *
 urj_part_find_instruction (urj_part_t *p, const char *iname)
 {
-    urj_instruction_t *i;
+    urj_part_instruction_t *i;
 
     if (!p || !iname)
         return NULL;
diff --git a/urjtag/src/svf/svf.h b/urjtag/src/svf/svf.h
index ec7b8ee5..0311ec73 100644
--- a/urjtag/src/svf/svf.h
+++ b/urjtag/src/svf/svf.h
@@ -95,7 +95,7 @@ struct parser_priv
     struct svf_parser_params parser_params;
     void *scanner;
     urj_part_t *part;
-    urj_instruction_t *ir;
+    urj_part_instruction_t *ir;
     urj_data_register_t *dr;
     urj_svf_sxr_t sir_params;
     urj_svf_sxr_t sdr_params;
diff --git a/urjtag/src/tap/detect.c b/urjtag/src/tap/detect.c
index 1beb9226..5b115930 100644
--- a/urjtag/src/tap/detect.c
+++ b/urjtag/src/tap/detect.c
@@ -34,7 +34,7 @@
 
 #include <bsdl.h>
 
-#include "register.h"
+#include "tap_register.h"
 #include "tap.h"
 #include "cable.h"
 #include "part.h"
diff --git a/urjtag/src/tap/register.c b/urjtag/src/tap/register.c
index 16cad952..e906452e 100644
--- a/urjtag/src/tap/register.c
+++ b/urjtag/src/tap/register.c
@@ -25,7 +25,7 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "register.h"
+#include "tap_register.h"
 
 urj_tap_register_t *
 urj_tap_register_alloc (int len)
diff --git a/urjtag/src/tap/tap.c b/urjtag/src/tap/tap.c
index 0e5ce6a1..5145509a 100644
--- a/urjtag/src/tap/tap.c
+++ b/urjtag/src/tap/tap.c
@@ -26,7 +26,7 @@
 
 #include <stdio.h>
 
-#include "register.h"
+#include "tap_register.h"
 #include "tap.h"
 #include "tap_state.h"
 #include "chain.h"