diff --git a/.hgignore b/.hgignore
new file mode 100644
index 0000000..6294639
--- /dev/null
+++ b/.hgignore
@@ -0,0 +1,3 @@
+lib
+include
+.*\.pyc$
diff --git a/bin/flake8 b/bin/flake8
index 864c9ba..2001e00 100755
--- a/bin/flake8
+++ b/bin/flake8
@@ -1,5 +1,5 @@
 #!/home/tarek/dev/bitbucket.org/flake8-clean/bin/python
-from flake8 import main
+from flake8.run import main
 
 if __name__ == '__main__':
     main()
diff --git a/flake8/__init__.py b/flake8/__init__.py
index e9407cb..792d600 100644
--- a/flake8/__init__.py
+++ b/flake8/__init__.py
@@ -1,176 +1 @@
-
-"""
-Implementation of the command-line I{flake8} tool.
-"""
-import sys
-import os
-import _ast
-import pep8
-import mccabe
-import re
-
-
-checker = __import__('flake8.checker').checker
-
-
-def check(codeString, filename):
-    """
-    Check the Python source given by C{codeString} for flakes.
-
-    @param codeString: The Python source to check.
-    @type codeString: C{str}
-
-    @param filename: The name of the file the source came from, used to report
-        errors.
-    @type filename: C{str}
-
-    @return: The number of warnings emitted.
-    @rtype: C{int}
-    """
-    # First, compile into an AST and handle syntax errors.
-    try:
-        tree = compile(codeString, filename, "exec", _ast.PyCF_ONLY_AST)
-    except SyntaxError, value:
-        msg = value.args[0]
-
-        (lineno, offset, text) = value.lineno, value.offset, value.text
-
-        # If there's an encoding problem with the file, the text is None.
-        if text is None:
-            # Avoid using msg, since for the only known case, it contains a
-            # bogus message that claims the encoding the file declared was
-            # unknown.
-            print >> sys.stderr, "%s: problem decoding source" % (filename, )
-        else:
-            line = text.splitlines()[-1]
-
-            if offset is not None:
-                offset = offset - (len(text) - len(line))
-
-            print >> sys.stderr, '%s:%d: %s' % (filename, lineno, msg)
-            print >> sys.stderr, line
-
-            if offset is not None:
-                print >> sys.stderr, " " * offset, "^"
-
-        return 1
-    else:
-        # Okay, it's syntactically valid.  Now check it.
-        w = checker.Checker(tree, filename)
-        w.messages.sort(lambda a, b: cmp(a.lineno, b.lineno))
-        valid_warnings = 0
-
-        for warning in w.messages:
-            if _noqa(warning):
-                continue
-            print warning
-            valid_warnings += 1
-
-        return valid_warnings
-
-
-def _noqa(warning):
-    # XXX quick dirty hack, just need to keep the line in the warning
-    line = open(warning.filename).readlines()[warning.lineno-1]
-    return line.strip().lower().endswith('# noqa')
-
-
-def checkPath(filename):
-    """
-    Check the given path, printing out any warnings detected.
-
-    @return: the number of warnings printed
-    """
-    try:
-        return check(file(filename, 'U').read() + '\n', filename)
-    except IOError, msg:
-        print >> sys.stderr, "%s: %s" % (filename, msg.args[1])
-        return 1
-
-
-def check_file(path, complexity=10):
-    warnings = checkPath(path)
-    warnings += pep8.input_file(path)
-    warnings += mccabe.get_module_complexity(path, complexity)
-    return warnings
-
-
-def check_code(code, complexity=10):
-    warnings = check(code, '<stdin>')
-    warnings += mccabe.get_code_complexity(code, complexity)
-    return warnings
-
-
-_NOQA = re.compile(r'^# flake8: noqa', re.I | re.M)
-
-
-def skip_file(path):
-    """Returns True if this header is found in path
-
-    # flake8: noqa
-    """
-    f = open(path)
-    try:
-        content = f.read()
-    finally:
-        f.close()
-    return _NOQA.match(content) is not None
-
-
-def _get_python_files(paths):
-    for path in paths:
-        if os.path.isdir(path):
-            for dirpath, dirnames, filenames in os.walk(path):
-                for filename in filenames:
-                    if not filename.endswith('.py'):
-                        continue
-                    fullpath = os.path.join(dirpath, filename)
-                    if not skip_file(fullpath):
-                        yield fullpath
-
-        else:
-            if not skip_file(path):
-                yield path
-
-
-def main():
-    pep8.process_options()
-    warnings = 0
-    args = sys.argv[1:]
-    if args:
-        for path in _get_python_files(args):
-            warnings += check_file(path)
-    else:
-        stdin = sys.stdin.read()
-        warnings += check_code(stdin)
-
-    raise SystemExit(warnings > 0)
-
-
-def _get_files(repo, **kwargs):
-    for rev in xrange(repo[kwargs['node']], len(repo)):
-        for file_ in repo[rev].files():
-            if not file_.endswith('.py'):
-                continue
-            if skip_file(file_):
-                continue
-            yield file_
-
-
-def hg_hook(ui, repo, **kwargs):
-    pep8.process_options()
-    warnings = 0
-    for file_ in _get_files(repo, **kwargs):
-        warnings += check_file(file_)
-
-    strict = ui.config('flake8', 'strict')
-    if strict is None:
-        strict = True
-
-    if strict.lower() in ('1', 'true'):
-        return warnings
-
-    return 0
-
-if __name__ == '__main__':
-    main()
+#
diff --git a/flake8/pep8.py b/flake8/pep8.py
index fad2429..ec4576a 100644
--- a/flake8/pep8.py
+++ b/flake8/pep8.py
@@ -105,6 +105,8 @@ from optparse import OptionParser
 from keyword import iskeyword
 from fnmatch import fnmatch
 
+from flake8.util import skip_line
+
 DEFAULT_EXCLUDE = '.svn,CVS,.bzr,.hg,.git'
 DEFAULT_IGNORE = ['E24']
 
@@ -936,7 +938,7 @@ class Checker(object):
         """
         Report an error, according to options.
         """
-        if self.physical_line.strip().lower().endswith('# noqa'):
+        if skip_line(self.physical_line):
             return
         if options.quiet == 1 and not self.file_errors:
             message(self.filename)
diff --git a/flake8/checker.py b/flake8/pyflakes.py
similarity index 91%
rename from flake8/checker.py
rename to flake8/pyflakes.py
index c0c6077..a201a06 100644
--- a/flake8/checker.py
+++ b/flake8/pyflakes.py
@@ -5,8 +5,10 @@
 import __builtin__
 import os.path
 import _ast
+import sys
 
 from flake8 import messages
+from flake8.util import skip_warning
 
 # utility function to iterate over an AST node's children, adapted
 # from Python 2.6's standard ast module
@@ -616,3 +618,71 @@ class Checker(object):
             if node.module == '__future__':
                 importation.used = (self.scope, node.lineno)
             self.addBinding(node.lineno, importation)
+
+def checkPath(filename):
+    """
+    Check the given path, printing out any warnings detected.
+
+    @return: the number of warnings printed
+    """
+    try:
+        return check(file(filename, 'U').read() + '\n', filename)
+    except IOError, msg:
+        print >> sys.stderr, "%s: %s" % (filename, msg.args[1])
+        return 1
+
+def check(codeString, filename):
+    """
+    Check the Python source given by C{codeString} for flakes.
+
+    @param codeString: The Python source to check.
+    @type codeString: C{str}
+
+    @param filename: The name of the file the source came from, used to report
+        errors.
+    @type filename: C{str}
+
+    @return: The number of warnings emitted.
+    @rtype: C{int}
+    """
+    # First, compile into an AST and handle syntax errors.
+    try:
+        tree = compile(codeString, filename, "exec", _ast.PyCF_ONLY_AST)
+    except SyntaxError, value:
+        msg = value.args[0]
+
+        (lineno, offset, text) = value.lineno, value.offset, value.text
+
+        # If there's an encoding problem with the file, the text is None.
+        if text is None:
+            # Avoid using msg, since for the only known case, it contains a
+            # bogus message that claims the encoding the file declared was
+            # unknown.
+            print >> sys.stderr, "%s: problem decoding source" % (filename, )
+        else:
+            line = text.splitlines()[-1]
+
+            if offset is not None:
+                offset = offset - (len(text) - len(line))
+
+            print >> sys.stderr, '%s:%d: %s' % (filename, lineno, msg)
+            print >> sys.stderr, line
+
+            if offset is not None:
+                print >> sys.stderr, " " * offset, "^"
+
+        return 1
+    else:
+        # Okay, it's syntactically valid.  Now check it.
+        w = Checker(tree, filename)
+        w.messages.sort(lambda a, b: cmp(a.lineno, b.lineno))
+        valid_warnings = 0
+
+        for warning in w.messages:
+            if skip_warning(warning):
+                continue
+            print warning
+            valid_warnings += 1
+
+        return valid_warnings
+
diff --git a/flake8/run.py b/flake8/run.py
new file mode 100644
index 0000000..ce7728f
--- /dev/null
+++ b/flake8/run.py
@@ -0,0 +1,84 @@
+
+"""
+Implementation of the command-line I{flake8} tool.
+"""
+import sys
+import os
+
+from flake8.util import skip_file
+from flake8 import pep8
+from flake8 import pyflakes
+from flake8 import mccabe
+
+
+def check_file(path, complexity=10):
+
+    warnings = pyflakes.checkPath(path)
+    warnings += pep8.input_file(path)
+    warnings += mccabe.get_module_complexity(path, complexity)
+    return warnings
+
+
+def check_code(code, complexity=10):
+    warnings = pyflakes.check(code, '<stdin>')
+    warnings += mccabe.get_code_complexity(code, complexity)
+    return warnings
+
+
+def _get_python_files(paths):
+    for path in paths:
+        if os.path.isdir(path):
+            for dirpath, dirnames, filenames in os.walk(path):
+                for filename in filenames:
+                    if not filename.endswith('.py'):
+                        continue
+                    fullpath = os.path.join(dirpath, filename)
+                    if not skip_file(fullpath):
+                        yield fullpath
+
+        else:
+            if not skip_file(path):
+                yield path
+
+
+def main():
+    pep8.process_options()
+    warnings = 0
+    args = sys.argv[1:]
+    if args:
+        for path in _get_python_files(args):
+            warnings += check_file(path)
+    else:
+        stdin = sys.stdin.read()
+        warnings += check_code(stdin)
+
+    raise SystemExit(warnings > 0)
+
+
+def _get_files(repo, **kwargs):
+    for rev in xrange(repo[kwargs['node']], len(repo)):
+        for file_ in repo[rev].files():
+            if not file_.endswith('.py'):
+                continue
+            if skip_file(file_):
+                continue
+            yield file_
+
+
+def hg_hook(ui, repo, **kwargs):
+    pep8.process_options()
+    warnings = 0
+    for file_ in _get_files(repo, **kwargs):
+        warnings += check_file(file_)
+
+    strict = ui.config('flake8', 'strict')
+    if strict is None:
+        strict = True
+
+    if strict.lower() in ('1', 'true'):
+        return warnings
+
+    return 0
+
+if __name__ == '__main__':
+    main()
diff --git a/flake8/util.py b/flake8/util.py
new file mode 100644
index 0000000..87a340e
--- /dev/null
+++ b/flake8/util.py
@@ -0,0 +1,26 @@
+import re
+
+
+def skip_warning(warning):
+    # XXX quick dirty hack, just need to keep the line in the warning
+    line = open(warning.filename).readlines()[warning.lineno-1]
+    return skip_line(line)
+
+def skip_line(line):
+    return line.strip().lower().endswith('# noqa')
+
+
+_NOQA = re.compile(r'^# flake8: noqa', re.I | re.M)
+
+
+def skip_file(path):
+    """Returns True if this header is found in path
+
+    # flake8: noqa
+    """
+    f = open(path)
+    try:
+        content = f.read()
+    finally:
+        f.close()
+    return _NOQA.match(content) is not None