diff --git a/rst2code.py b/rst2code.py
old mode 100644
new mode 100755
index f8cf1eb..c3d9467
--- a/rst2code.py
+++ b/rst2code.py
@@ -21,7 +21,6 @@
 import sys
 from docutils.core import publish_doctree
 import logging
-logging.basicConfig(level=logging.WARNING)
 import re
 import shutil, os
 
@@ -182,6 +181,7 @@ def __init__(self, msg):
         self.msg = msg
 
 def main(argv=None):
+    global OUTPUT_DIR
     if argv is None:
         argv = sys.argv[1:]
     try:
@@ -189,23 +189,28 @@ def main(argv=None):
             parser = argparse.ArgumentParser("Write code from rst files")
             parser.add_argument('outdir', metavar="OUTPUT_DIR", type=str, nargs=1,
                                 help="Output directory base for code")
-            parser.add_argument('srcfiles', metavar="SRC_FILES", type=str, nargs="+",
+            parser.add_argument('srcfiles', metavar="SRC_FILES", type=str, nargs=argparse.REMAINDER,
                                 help="Source files (.rst files)")
-            parser.add_argument('--debug', '-d')
+            parser.add_argument('--debug', '-d', action='store_true')
             args = parser.parse_args(argv)
-
         except Exception as msg:
              raise Usage(msg)
 
 
         # process arguments
         DEBUG = args.debug
-        OUTPUT_DIR = args.outdir
+        if DEBUG:
+            logging.basicConfig(level=logging.DEBUG)
+        else:
+            logging.basicConfig(level=logging.WARNING)
+        OUTPUT_DIR = args.outdir[0]
         SRC_FILES = args.srcfiles
 
         for filename in SRC_FILES:
             scan_file(filename)
         process_blocks()
+        clean_output_dir()
+        write_files()
         return 0
 
     except Usage as err:
@@ -220,9 +225,16 @@ def main(argv=None):
 
 
 def sphinx_get_doctree(app, doctree, docname):
+
+    if app.config.rst2code_debug:
+        logging.basicConfig(level=logging.DEBUG)
+    else:
+        logging.basicConfig(level=logging.WARNING)
+
     logging.debug("Got doctree")
     scan_doctree(doctree,docname)
 def sphinx_build_finished(app, exception):
+    global OUTPUT_DIR
     env = app.builder.env
     OUTPUT_DIR = app.config.rst2code_output_dir
     process_blocks()
@@ -231,5 +243,6 @@ def sphinx_build_finished(app, exception):
 def setup(app):
     app.add_config_value("rst2code_output_dir", "./src", "env")
     app.add_config_value("rst2code_max_iterations", 10, "env")
+    app.add_config_value("rst2code_debug", False, "env")
     app.connect('doctree-resolved',sphinx_get_doctree)
     app.connect('build-finished', sphinx_build_finished)
diff --git a/source/cmdline.rst b/source/cmdline.rst
index 1502e24..3496d92 100644
--- a/source/cmdline.rst
+++ b/source/cmdline.rst
@@ -20,6 +20,7 @@ of input files ::
             self.msg = msg
 
     def main(argv=None):
+        global OUTPUT_DIR
         if argv is None:
             argv = sys.argv[1:]
         try:
@@ -27,23 +28,28 @@ of input files ::
                 parser = argparse.ArgumentParser("Write code from rst files")
                 parser.add_argument('outdir', metavar="OUTPUT_DIR", type=str, nargs=1,
                                     help="Output directory base for code")
-                parser.add_argument('srcfiles', metavar="SRC_FILES", type=str, nargs="+",
+                parser.add_argument('srcfiles', metavar="SRC_FILES", type=str, nargs=argparse.REMAINDER,
                                     help="Source files (.rst files)")
-                parser.add_argument('--debug', '-d')
+                parser.add_argument('--debug', '-d', action='store_true')
                 args = parser.parse_args(argv)
-    
             except Exception as msg:
                  raise Usage(msg)
     
     
             # process arguments
             DEBUG = args.debug
-            OUTPUT_DIR = args.outdir
+            if DEBUG:
+                logging.basicConfig(level=logging.DEBUG)
+            else:
+                logging.basicConfig(level=logging.WARNING)
+            OUTPUT_DIR = args.outdir[0]
             SRC_FILES = args.srcfiles
     
             for filename in SRC_FILES:
                 scan_file(filename)
             process_blocks()
+            clean_output_dir()
+            write_files()
             return 0
     
         except Usage as err:
diff --git a/source/index.rst b/source/index.rst
index 33f4c52..8eb9efa 100644
--- a/source/index.rst
+++ b/source/index.rst
@@ -36,7 +36,6 @@ Logging can be enabled for debug / trace purposes ::
 
     #@@imports@@
     import logging
-    logging.basicConfig(level=logging.WARNING)  
 
 Code blocks
 -----------
diff --git a/source/sphinx.rst b/source/sphinx.rst
index 3bff092..90f185d 100644
--- a/source/sphinx.rst
+++ b/source/sphinx.rst
@@ -7,6 +7,12 @@ gives us processed doctree ::
 
     #@@sphinx_extension@@
     def sphinx_get_doctree(app, doctree, docname):
+
+        if app.config.rst2code_debug:
+            logging.basicConfig(level=logging.DEBUG)
+        else:
+            logging.basicConfig(level=logging.WARNING)
+
         logging.debug("Got doctree")
         scan_doctree(doctree,docname)
 
@@ -14,6 +20,7 @@ We wait for "build-finished" event to create source code files (SEE? maybe we sh
 
     #@@sphinx_extension@@
     def sphinx_build_finished(app, exception):
+        global OUTPUT_DIR
         env = app.builder.env
         OUTPUT_DIR = app.config.rst2code_output_dir
         process_blocks()
@@ -27,6 +34,7 @@ To use rst2code within sphinx, [configuration]... So we need a "setup" function
     def setup(app):
         app.add_config_value("rst2code_output_dir", "./src", "env")
         app.add_config_value("rst2code_max_iterations", 10, "env")
+        app.add_config_value("rst2code_debug", False, "env")
         app.connect('doctree-resolved',sphinx_get_doctree)
         app.connect('build-finished', sphinx_build_finished)