Move flake8 into src

This is an emerging best practice and there is little reason to not
follow it

29 files changed, 4358 insertions, 0 deletions

diff --git a/src/flake8/__init__.py b/src/flake8/__init__.py
new file mode 100644
index 0000000..d6c6915
--- /dev/null
+++ b/src/flake8/__init__.py
@@ -0,0 +1,82 @@
+"""Top-level module for Flake8.
+
+This module
+
+- initializes logging for the command-line tool
+- tracks the version of the package
+- provides a way to configure logging for the command-line tool
+
+.. autofunction:: flake8.configure_logging
+
+"""
+import logging
+try:
+    from logging import NullHandler
+except ImportError:
+    class NullHandler(logging.Handler):
+        """Shim for version of Python < 2.7."""
+
+        def emit(self, record):
+            """Do nothing."""
+            pass
+import sys
+
+LOG = logging.getLogger(__name__)
+LOG.addHandler(NullHandler())
+
+# Clean up after LOG config
+del NullHandler
+
+__version__ = '3.0.0b1'
+__version_info__ = tuple(int(i) for i in __version__.split('.') if i.isdigit())
+
+
+# There is nothing lower than logging.DEBUG (10) in the logging library,
+# but we want an extra level to avoid being too verbose when using -vv.
+_EXTRA_VERBOSE = 5
+logging.addLevelName(_EXTRA_VERBOSE, 'VERBOSE')
+
+_VERBOSITY_TO_LOG_LEVEL = {
+    # output more than warnings but not debugging info
+    1: logging.INFO,  # INFO is a numerical level of 20
+    # output debugging information
+    2: logging.DEBUG,  # DEBUG is a numerical level of 10
+    # output extra verbose debugging information
+    3: _EXTRA_VERBOSE,
+}
+
+LOG_FORMAT = ('%(name)-25s %(processName)-11s %(relativeCreated)6d '
+              '%(levelname)-8s %(message)s')
+
+
+def configure_logging(verbosity, filename=None, logformat=LOG_FORMAT):
+    """Configure logging for flake8.
+
+    :param int verbosity:
+        How verbose to be in logging information.
+    :param str filename:
+        Name of the file to append log information to.
+        If ``None`` this will log to ``sys.stderr``.
+        If the name is "stdout" or "stderr" this will log to the appropriate
+        stream.
+    """
+    if verbosity <= 0:
+        return
+    if verbosity > 3:
+        verbosity = 3
+
+    log_level = _VERBOSITY_TO_LOG_LEVEL[verbosity]
+
+    if not filename or filename in ('stderr', 'stdout'):
+        fileobj = getattr(sys, filename or 'stderr')
+        handler_cls = logging.StreamHandler
+    else:
+        fileobj = filename
+        handler_cls = logging.FileHandler
+
+    handler = handler_cls(fileobj)
+    handler.setFormatter(logging.Formatter(logformat))
+    LOG.addHandler(handler)
+    LOG.setLevel(log_level)
+    LOG.debug('Added a %s logging handler to logger root at %s',
+              filename, __name__)
diff --git a/src/flake8/__main__.py b/src/flake8/__main__.py
new file mode 100644
index 0000000..42bc428
--- /dev/null
+++ b/src/flake8/__main__.py
@@ -0,0 +1,4 @@
+"""Module allowing for ``python -m flake8 ...``."""
+from flake8.main import cli
+
+cli.main()
diff --git a/src/flake8/api/__init__.py b/src/flake8/api/__init__.py
new file mode 100644
index 0000000..9f95557
--- /dev/null
+++ b/src/flake8/api/__init__.py
@@ -0,0 +1,10 @@
+"""Module containing all public entry-points for Flake8.
+
+This is the only submodule in Flake8 with a guaranteed stable API. All other
+submodules are considered internal only and are subject to change.
+"""
+
+
+def get_style_guide(**kwargs):
+    """Stub out the only function I'm aware of people using."""
+    pass
diff --git a/src/flake8/checker.py b/src/flake8/checker.py
new file mode 100644
index 0000000..b875f44
--- /dev/null
+++ b/src/flake8/checker.py
@@ -0,0 +1,610 @@
+"""Checker Manager and Checker classes."""
+import errno
+import logging
+import os
+import sys
+import tokenize
+
+try:
+    import multiprocessing
+except ImportError:
+    multiprocessing = None
+
+try:
+    import Queue as queue
+except ImportError:
+    import queue
+
+from flake8 import defaults
+from flake8 import exceptions
+from flake8 import processor
+from flake8 import utils
+
+LOG = logging.getLogger(__name__)
+
+SERIAL_RETRY_ERRNOS = set([
+    # ENOSPC: Added by sigmavirus24
+    # > On some operating systems (OSX), multiprocessing may cause an
+    # > ENOSPC error while trying to trying to create a Semaphore.
+    # > In those cases, we should replace the customized Queue Report
+    # > class with pep8's StandardReport class to ensure users don't run
+    # > into this problem.
+    # > (See also: https://gitlab.com/pycqa/flake8/issues/74)
+    errno.ENOSPC,
+    # NOTE(sigmavirus24): When adding to this list, include the reasoning
+    # on the lines before the error code and always append your error
+    # code. Further, please always add a trailing `,` to reduce the visual
+    # noise in diffs.
+])
+
+
+class Manager(object):
+    """Manage the parallelism and checker instances for each plugin and file.
+
+    This class will be responsible for the following:
+
+    - Determining the parallelism of Flake8, e.g.:
+
+      * Do we use :mod:`multiprocessing` or is it unavailable?
+
+      * Do we automatically decide on the number of jobs to use or did the
+        user provide that?
+
+    - Falling back to a serial way of processing files if we run into an
+      OSError related to :mod:`multiprocessing`
+
+    - Organizing the results of each checker so we can group the output
+      together and make our output deterministic.
+    """
+
+    def __init__(self, style_guide, arguments, checker_plugins):
+        """Initialize our Manager instance.
+
+        :param style_guide:
+            The instantiated style guide for this instance of Flake8.
+        :type style_guide:
+            flake8.style_guide.StyleGuide
+        :param list arguments:
+            The extra arguments parsed from the CLI (if any)
+        :param checker_plugins:
+            The plugins representing checks parsed from entry-points.
+        :type checker_plugins:
+            flake8.plugins.manager.Checkers
+        """
+        self.arguments = arguments
+        self.style_guide = style_guide
+        self.options = style_guide.options
+        self.checks = checker_plugins
+        self.jobs = self._job_count()
+        self.process_queue = None
+        self.results_queue = None
+        self.statistics_queue = None
+        self.using_multiprocessing = self.jobs > 1
+        self.processes = []
+        self.checkers = []
+        self.statistics = {
+            'files': 0,
+            'logical lines': 0,
+            'physical lines': 0,
+            'tokens': 0,
+        }
+
+        if self.using_multiprocessing:
+            try:
+                self.process_queue = multiprocessing.Queue()
+                self.results_queue = multiprocessing.Queue()
+                self.statistics_queue = multiprocessing.Queue()
+            except OSError as oserr:
+                if oserr.errno not in SERIAL_RETRY_ERRNOS:
+                    raise
+                self.using_multiprocessing = False
+
+    @staticmethod
+    def _cleanup_queue(q):
+        while not q.empty():
+            q.get_nowait()
+
+    def _force_cleanup(self):
+        if self.using_multiprocessing:
+            for proc in self.processes:
+                proc.join(0.2)
+            self._cleanup_queue(self.process_queue)
+            self._cleanup_queue(self.results_queue)
+            self._cleanup_queue(self.statistics_queue)
+
+    def _process_statistics(self):
+        all_statistics = self.statistics
+        if self.using_multiprocessing:
+            total_number_of_checkers = len(self.checkers)
+            statistics_gathered = 0
+            while statistics_gathered < total_number_of_checkers:
+                try:
+                    statistics = self.statistics_queue.get(block=False)
+                    statistics_gathered += 1
+                except queue.Empty:
+                    break
+
+                for statistic in defaults.STATISTIC_NAMES:
+                    all_statistics[statistic] += statistics[statistic]
+        else:
+            statistics_generator = (checker.statistics
+                                    for checker in self.checkers)
+            for statistics in statistics_generator:
+                for statistic in defaults.STATISTIC_NAMES:
+                    all_statistics[statistic] += statistics[statistic]
+        all_statistics['files'] += len(self.checkers)
+
+    def _job_count(self):
+        # type: () -> Union[int, NoneType]
+        # First we walk through all of our error cases:
+        # - multiprocessing library is not present
+        # - we're running on windows in which case we know we have significant
+        #   implemenation issues
+        # - the user provided stdin and that's not something we can handle
+        #   well
+        # - we're processing a diff, which again does not work well with
+        #   multiprocessing and which really shouldn't require multiprocessing
+        # - the user provided some awful input
+        if not multiprocessing:
+            LOG.warning('The multiprocessing module is not available. '
+                        'Ignoring --jobs arguments.')
+            return 0
+
+        if (utils.is_windows() and
+                not utils.can_run_multiprocessing_on_windows()):
+            LOG.warning('The --jobs option is only available on Windows on '
+                        'Python 2.7.11+ and 3.3+. We have detected that you '
+                        'are running an unsupported version of Python on '
+                        'Windows. Ignoring --jobs arguments.')
+            return 0
+
+        if utils.is_using_stdin(self.arguments):
+            LOG.warning('The --jobs option is not compatible with supplying '
+                        'input using - . Ignoring --jobs arguments.')
+            return 0
+
+        if self.options.diff:
+            LOG.warning('The --diff option was specified with --jobs but '
+                        'they are not compatible. Ignoring --jobs arguments.')
+            return 0
+
+        jobs = self.options.jobs
+        if jobs != 'auto' and not jobs.isdigit():
+            LOG.warning('"%s" is not a valid parameter to --jobs. Must be one '
+                        'of "auto" or a numerical value, e.g., 4.', jobs)
+            return 0
+
+        # If the value is "auto", we want to let the multiprocessing library
+        # decide the number based on the number of CPUs. However, if that
+        # function is not implemented for this particular value of Python we
+        # default to 1
+        if jobs == 'auto':
+            try:
+                return multiprocessing.cpu_count()
+            except NotImplementedError:
+                return 0
+
+        # Otherwise, we know jobs should be an integer and we can just convert
+        # it to an integer
+        return int(jobs)
+
+    def _results(self):
+        seen_done = 0
+        LOG.info('Retrieving results')
+        while True:
+            result = self.results_queue.get()
+            if result == 'DONE':
+                seen_done += 1
+                if seen_done >= self.jobs:
+                    break
+                continue
+
+            yield result
+
+    def _handle_results(self, filename, results):
+        style_guide = self.style_guide
+        reported_results_count = 0
+        for (error_code, line_number, column, text, physical_line) in results:
+            reported_results_count += style_guide.handle_error(
+                code=error_code,
+                filename=filename,
+                line_number=line_number,
+                column_number=column,
+                text=text,
+                physical_line=physical_line,
+            )
+        return reported_results_count
+
+    def _run_checks_from_queue(self):
+        LOG.info('Running checks in parallel')
+        for checker in iter(self.process_queue.get, 'DONE'):
+            LOG.debug('Running checker for file "%s"', checker.filename)
+            checker.run_checks(self.results_queue, self.statistics_queue)
+        self.results_queue.put('DONE')
+
+    def is_path_excluded(self, path):
+        # type: (str) -> bool
+        """Check if a path is excluded.
+
+        :param str path:
+            Path to check against the exclude patterns.
+        :returns:
+            True if there are exclude patterns and the path matches,
+            otherwise False.
+        :rtype:
+            bool
+        """
+        exclude = self.options.exclude
+        if not exclude:
+            return False
+        basename = os.path.basename(path)
+        if utils.fnmatch(basename, exclude):
+            LOG.info('"%s" has been excluded', basename)
+            return True
+
+        absolute_path = os.path.abspath(path)
+        match = utils.fnmatch(absolute_path, exclude)
+        LOG.info('"%s" has %sbeen excluded', absolute_path,
+                 '' if match else 'not ')
+        return match
+
+    def make_checkers(self, paths=None):
+        # type: (List[str]) -> NoneType
+        """Create checkers for each file."""
+        if paths is None:
+            paths = self.arguments
+        filename_patterns = self.options.filename
+
+        # NOTE(sigmavirus24): Yes this is a little unsightly, but it's our
+        # best solution right now.
+        def should_create_file_checker(filename):
+            """Determine if we should create a file checker."""
+            matches_filename_patterns = utils.fnmatch(
+                filename, filename_patterns
+            )
+            is_stdin = filename == '-'
+            file_exists = os.path.exists(filename)
+            return (file_exists and matches_filename_patterns) or is_stdin
+
+        self.checkers = [
+            FileChecker(filename, self.checks, self.style_guide)
+            for argument in paths
+            for filename in utils.filenames_from(argument,
+                                                 self.is_path_excluded)
+            if should_create_file_checker(filename)
+        ]
+
+    def report(self):
+        # type: () -> (int, int)
+        """Report all of the errors found in the managed file checkers.
+
+        This iterates over each of the checkers and reports the errors sorted
+        by line number.
+
+        :returns:
+            A tuple of the total results found and the results reported.
+        :rtype:
+            tuple(int, int)
+        """
+        results_reported = results_found = 0
+        for checker in self.checkers:
+            results = sorted(checker.results, key=lambda tup: (tup[2], tup[3]))
+            results_reported += self._handle_results(checker.filename,
+                                                     results)
+            results_found += len(results)
+        return (results_found, results_reported)
+
+    def run_parallel(self):
+        """Run the checkers in parallel."""
+        LOG.info('Starting %d process workers', self.jobs)
+        for i in range(self.jobs):
+            proc = multiprocessing.Process(
+                target=self._run_checks_from_queue
+            )
+            proc.daemon = True
+            proc.start()
+            self.processes.append(proc)
+
+        final_results = {}
+        for (filename, results) in self._results():
+            final_results[filename] = results
+
+        for checker in self.checkers:
+            filename = checker.filename
+            checker.results = sorted(final_results.get(filename, []),
+                                     key=lambda tup: (tup[1], tup[2]))
+
+    def run_serial(self):
+        """Run the checkers in serial."""
+        for checker in self.checkers:
+            checker.run_checks(self.results_queue, self.statistics_queue)
+
+    def run(self):
+        """Run all the checkers.
+
+        This will intelligently decide whether to run the checks in parallel
+        or whether to run them in serial.
+
+        If running the checks in parallel causes a problem (e.g.,
+        https://gitlab.com/pycqa/flake8/issues/74) this also implements
+        fallback to serial processing.
+        """
+        try:
+            if self.using_multiprocessing:
+                self.run_parallel()
+            else:
+                self.run_serial()
+        except OSError as oserr:
+            if oserr.errno not in SERIAL_RETRY_ERRNOS:
+                LOG.exception(oserr)
+                raise
+            LOG.warning('Running in serial after OS exception, %r', oserr)
+            self.run_serial()
+
+    def start(self, paths=None):
+        """Start checking files.
+
+        :param list paths:
+            Path names to check. This is passed directly to
+            :meth:`~Manager.make_checkers`.
+        """
+        LOG.info('Making checkers')
+        self.make_checkers(paths)
+        if not self.using_multiprocessing:
+            return
+
+        LOG.info('Populating process queue')
+        for checker in self.checkers:
+            self.process_queue.put(checker)
+
+        for i in range(self.jobs):
+            self.process_queue.put('DONE')
+
+    def stop(self):
+        """Stop checking files."""
+        self._process_statistics()
+        for proc in self.processes:
+            LOG.info('Joining %s to the main process', proc.name)
+            proc.join()
+
+
+class FileChecker(object):
+    """Manage running checks for a file and aggregate the results."""
+
+    def __init__(self, filename, checks, style_guide):
+        """Initialize our file checker.
+
+        :param str filename:
+            Name of the file to check.
+        :param checks:
+            The plugins registered to check the file.
+        :type checks:
+            flake8.plugins.manager.Checkers
+        :param style_guide:
+            The initialized StyleGuide for this particular run.
+        :type style_guide:
+            flake8.style_guide.StyleGuide
+        """
+        self.filename = filename
+        self.checks = checks
+        self.style_guide = style_guide
+        self.results = []
+        self.processor = self._make_processor()
+        self.statistics = {
+            'tokens': 0,
+            'logical lines': 0,
+            'physical lines': len(self.processor.lines),
+        }
+
+    def _make_processor(self):
+        try:
+            return processor.FileProcessor(self.filename,
+                                           self.style_guide.options)
+        except IOError:
+            # If we can not read the file due to an IOError (e.g., the file
+            # does not exist or we do not have the permissions to open it)
+            # then we need to format that exception for the user.
+            # NOTE(sigmavirus24): Historically, pep8 has always reported this
+            # as an E902. We probably *want* a better error code for this
+            # going forward.
+            (exc_type, exception) = sys.exc_info()[:2]
+            message = '{0}: {1}'.format(exc_type.__name__, exception)
+            self.report('E902', 0, 0, message)
+            return None
+
+    def report(self, error_code, line_number, column, text):
+        # type: (str, int, int, str) -> str
+        """Report an error by storing it in the results list."""
+        if error_code is None:
+            error_code, text = text.split(' ', 1)
+
+        physical_line = ''
+        # If we're recovering from a problem in _make_processor, we will not
+        # have this attribute.
+        if getattr(self, 'processor', None):
+            physical_line = self.processor.line_for(line_number)
+
+        error = (error_code, line_number, column, text, physical_line)
+        self.results.append(error)
+        return error_code
+
+    def run_check(self, plugin, **arguments):
+        """Run the check in a single plugin."""
+        LOG.debug('Running %r with %r', plugin, arguments)
+        self.processor.keyword_arguments_for(plugin.parameters, arguments)
+        return plugin.execute(**arguments)
+
+    def run_ast_checks(self):
+        """Run all checks expecting an abstract syntax tree."""
+        try:
+            ast = self.processor.build_ast()
+        except (ValueError, SyntaxError, TypeError):
+            (exc_type, exception) = sys.exc_info()[:2]
+            if len(exception.args) > 1:
+                offset = exception.args[1]
+                if len(offset) > 2:
+                    offset = offset[1:3]
+            else:
+                offset = (1, 0)
+
+            self.report('E999', offset[0], offset[1], '%s: %s' %
+                        (exc_type.__name__, exception.args[0]))
+            return
+
+        for plugin in self.checks.ast_plugins:
+            checker = self.run_check(plugin, tree=ast)
+            # NOTE(sigmavirus24): If we want to allow for AST plugins that are
+            # not classes exclusively, we can do the following:
+            # retrieve_results = getattr(checker, 'run', lambda: checker)
+            # Otherwise, we just call run on the checker
+            for (line_number, offset, text, check) in checker.run():
+                self.report(
+                    error_code=None,
+                    line_number=line_number,
+                    column=offset,
+                    text=text,
+                )
+
+    def run_logical_checks(self):
+        """Run all checks expecting a logical line."""
+        comments, logical_line, mapping = self.processor.build_logical_line()
+        if not mapping:
+            return
+        self.processor.update_state(mapping)
+
+        LOG.debug('Logical line: "%s"', logical_line.rstrip())
+
+        for plugin in self.checks.logical_line_plugins:
+            self.processor.update_checker_state_for(plugin)
+            results = self.run_check(plugin, logical_line=logical_line) or ()
+            for offset, text in results:
+                offset = find_offset(offset, mapping)
+                line_number, column_offset = offset
+                self.report(
+                    error_code=None,
+                    line_number=line_number,
+                    column=column_offset,
+                    text=text,
+                )
+
+        self.processor.next_logical_line()
+
+    def run_physical_checks(self, physical_line):
+        """Run all checks for a given physical line."""
+        for plugin in self.checks.physical_line_plugins:
+            self.processor.update_checker_state_for(plugin)
+            result = self.run_check(plugin, physical_line=physical_line)
+            if result is not None:
+                column_offset, text = result
+                error_code = self.report(
+                    error_code=None,
+                    line_number=self.processor.line_number,
+                    column=column_offset,
+                    text=text,
+                )
+
+                self.processor.check_physical_error(error_code, physical_line)
+
+    def process_tokens(self):
+        """Process tokens and trigger checks.
+
+        This can raise a :class:`flake8.exceptions.InvalidSyntax` exception.
+        Instead of using this directly, you should use
+        :meth:`flake8.checker.FileChecker.run_checks`.
+        """
+        parens = 0
+        statistics = self.statistics
+        file_processor = self.processor
+        for token in file_processor.generate_tokens():
+            statistics['tokens'] += 1
+            self.check_physical_eol(token)
+            token_type, text = token[0:2]
+            processor.log_token(LOG, token)
+            if token_type == tokenize.OP:
+                parens = processor.count_parentheses(parens, text)
+            elif parens == 0:
+                if processor.token_is_newline(token):
+                    self.handle_newline(token_type)
+                elif (processor.token_is_comment(token) and
+                        len(file_processor.tokens) == 1):
+                    self.handle_comment(token, text)
+
+        if file_processor.tokens:
+            # If any tokens are left over, process them
+            self.run_physical_checks(file_processor.lines[-1])
+            self.run_logical_checks()
+
+    def run_checks(self, results_queue, statistics_queue):
+        """Run checks against the file."""
+        if self.processor.should_ignore_file():
+            return
+
+        try:
+            self.process_tokens()
+        except exceptions.InvalidSyntax as exc:
+            self.report(exc.error_code, exc.line_number, exc.column_number,
+                        exc.error_message)
+
+        self.run_ast_checks()
+
+        if results_queue is not None:
+            results_queue.put((self.filename, self.results))
+
+        logical_lines = self.processor.statistics['logical lines']
+        self.statistics['logical lines'] = logical_lines
+        if statistics_queue is not None:
+            statistics_queue.put(self.statistics)
+
+    def handle_comment(self, token, token_text):
+        """Handle the logic when encountering a comment token."""
+        # The comment also ends a physical line
+        token = list(token)
+        token[1] = token_text.rstrip('\r\n')
+        token[3] = (token[2][0], token[2][1] + len(token[1]))
+        self.processor.tokens = [tuple(token)]
+        self.run_logical_checks()
+
+    def handle_newline(self, token_type):
+        """Handle the logic when encountering a newline token."""
+        if token_type == tokenize.NEWLINE:
+            self.run_logical_checks()
+            self.processor.reset_blank_before()
+        elif len(self.processor.tokens) == 1:
+            # The physical line contains only this token.
+            self.processor.visited_new_blank_line()
+            self.processor.delete_first_token()
+        else:
+            self.run_logical_checks()
+
+    def check_physical_eol(self, token):
+        """Run physical checks if and only if it is at the end of the line."""
+        if processor.is_eol_token(token):
+            # Obviously, a newline token ends a single physical line.
+            self.run_physical_checks(token[4])
+        elif processor.is_multiline_string(token):
+            # Less obviously, a string that contains newlines is a
+            # multiline string, either triple-quoted or with internal
+            # newlines backslash-escaped. Check every physical line in the
+            # string *except* for the last one: its newline is outside of
+            # the multiline string, so we consider it a regular physical
+            # line, and will check it like any other physical line.
+            #
+            # Subtleties:
+            # - have to wind self.line_number back because initially it
+            #   points to the last line of the string, and we want
+            #   check_physical() to give accurate feedback
+            line_no = token[2][0]
+            with self.processor.inside_multiline(line_number=line_no):
+                for line in self.processor.split_line(token):
+                    self.run_physical_checks(line + '\n')
+
+
+def find_offset(offset, mapping):
+    """Find the offset tuple for a single offset."""
+    if isinstance(offset, tuple):
+        return offset
+
+    for token_offset, position in mapping:
+        if offset <= token_offset:
+            break
+    return (position[0], position[1] + offset - token_offset)
diff --git a/src/flake8/defaults.py b/src/flake8/defaults.py
new file mode 100644
index 0000000..d9f5a0b
--- /dev/null
+++ b/src/flake8/defaults.py
@@ -0,0 +1,17 @@
+"""Constants that define defaults."""
+
+EXCLUDE = '.svn,CVS,.bzr,.hg,.git,__pycache__,.tox'
+IGNORE = 'E121,E123,E126,E226,E24,E704,W503,W504'
+SELECT = 'E,F,W,C'
+MAX_LINE_LENGTH = 79
+
+TRUTHY_VALUES = set(['true', '1', 't'])
+
+# Other constants
+WHITESPACE = frozenset(' \t')
+
+STATISTIC_NAMES = (
+    'logical lines',
+    'physical lines',
+    'tokens',
+)
diff --git a/src/flake8/exceptions.py b/src/flake8/exceptions.py
new file mode 100644
index 0000000..5ff55a2
--- /dev/null
+++ b/src/flake8/exceptions.py
@@ -0,0 +1,96 @@
+"""Exception classes for all of Flake8."""
+
+
+class Flake8Exception(Exception):
+    """Plain Flake8 exception."""
+
+    pass
+
+
+class FailedToLoadPlugin(Flake8Exception):
+    """Exception raised when a plugin fails to load."""
+
+    FORMAT = 'Flake8 failed to load plugin "%(name)s" due to %(exc)s.'
+
+    def __init__(self, *args, **kwargs):
+        """Initialize our FailedToLoadPlugin exception."""
+        self.plugin = kwargs.pop('plugin')
+        self.ep_name = self.plugin.name
+        self.original_exception = kwargs.pop('exception')
+        super(FailedToLoadPlugin, self).__init__(*args, **kwargs)
+
+    def __str__(self):
+        """Return a nice string for our exception."""
+        return self.FORMAT % {'name': self.ep_name,
+                              'exc': self.original_exception}
+
+
+class InvalidSyntax(Flake8Exception):
+    """Exception raised when tokenizing a file fails."""
+
+    def __init__(self, *args, **kwargs):
+        """Initialize our InvalidSyntax exception."""
+        self.original_exception = kwargs.pop('exception')
+        self.error_code = 'E902'
+        self.line_number = 1
+        self.column_number = 0
+        try:
+            self.error_message = self.original_exception.message
+        except AttributeError:
+            # On Python 3, the IOError is an OSError which has a
+            # strerror attribute instead of a message attribute
+            self.error_message = self.original_exception.strerror
+        super(InvalidSyntax, self).__init__(*args, **kwargs)
+
+
+class HookInstallationError(Flake8Exception):
+    """Parent exception for all hooks errors."""
+
+    pass
+
+
+class GitHookAlreadyExists(HookInstallationError):
+    """Exception raised when the git pre-commit hook file already exists."""
+
+    def __init__(self, *args, **kwargs):
+        """Initialize the path attribute."""
+        self.path = kwargs.pop('path')
+        super(GitHookAlreadyExists, self).__init__(*args, **kwargs)
+
+    def __str__(self):
+        """Provide a nice message regarding the exception."""
+        msg = ('The Git pre-commit hook ({0}) already exists. To convince '
+               'Flake8 to install the hook, please remove the existing '
+               'hook.')
+        return msg.format(self.path)
+
+
+class MercurialHookAlreadyExists(HookInstallationError):
+    """Exception raised when a mercurial hook is already configured."""
+
+    hook_name = None
+
+    def __init__(self, *args, **kwargs):
+        """Initialize the relevant attributes."""
+        self.path = kwargs.pop('path')
+        self.value = kwargs.pop('value')
+        super(MercurialHookAlreadyExists, self).__init__(*args, **kwargs)
+
+    def __str__(self):
+        """Return a nicely formatted string for these errors."""
+        msg = ('The Mercurial {0} hook already exists with "{1}" in {2}. '
+               'To convince Flake8 to install the hook, please remove the '
+               '{0} configuration from the [hooks] section of your hgrc.')
+        return msg.format(self.hook_name, self.value, self.path)
+
+
+class MercurialCommitHookAlreadyExists(MercurialHookAlreadyExists):
+    """Exception raised when the hg commit hook is already configured."""
+
+    hook_name = 'commit'
+
+
+class MercurialQRefreshHookAlreadyExists(MercurialHookAlreadyExists):
+    """Exception raised when the hg commit hook is already configured."""
+
+    hook_name = 'qrefresh'
diff --git a/src/flake8/formatting/__init__.py b/src/flake8/formatting/__init__.py
new file mode 100644
index 0000000..bf44801
--- /dev/null
+++ b/src/flake8/formatting/__init__.py
@@ -0,0 +1 @@
+"""Submodule containing the default formatters for Flake8."""
diff --git a/src/flake8/formatting/base.py b/src/flake8/formatting/base.py
new file mode 100644
index 0000000..4fda6f4
--- /dev/null
+++ b/src/flake8/formatting/base.py
@@ -0,0 +1,161 @@
+"""The base class and interface for all formatting plugins."""
+from __future__ import print_function
+
+
+class BaseFormatter(object):
+    """Class defining the formatter interface.
+
+    .. attribute:: options
+
+        The options parsed from both configuration files and the command-line.
+
+    .. attribute:: filename
+
+        If specified by the user, the path to store the results of the run.
+
+    .. attribute:: output_fd
+
+        Initialized when the :meth:`start` is called. This will be a file
+        object opened for writing.
+
+    .. attribute:: newline
+
+        The string to add to the end of a line. This is only used when the
+        output filename has been specified.
+    """
+
+    def __init__(self, options):
+        """Initialize with the options parsed from config and cli.
+
+        This also calls a hook, :meth:`after_init`, so subclasses do not need
+        to call super to call this method.
+
+        :param optparse.Values options:
+            User specified configuration parsed from both configuration files
+            and the command-line interface.
+        """
+        self.options = options
+        self.filename = options.output_file
+        self.output_fd = None
+        self.newline = '\n'
+        self.after_init()
+
+    def after_init(self):
+        """Initialize the formatter further."""
+        pass
+
+    def start(self):
+        """Prepare the formatter to receive input.
+
+        This defaults to initializing :attr:`output_fd` if :attr:`filename`
+        """
+        if self.filename:
+            self.output_fd = open(self.filename, 'w')
+
+    def handle(self, error):
+        """Handle an error reported by Flake8.
+
+        This defaults to calling :meth:`format`, :meth:`show_source`, and
+        then :meth:`write`. To extend how errors are handled, override this
+        method.
+
+        :param error:
+            This will be an instance of :class:`~flake8.style_guide.Error`.
+        :type error:
+            flake8.style_guide.Error
+        """
+        line = self.format(error)
+        source = self.show_source(error)
+        self.write(line, source)
+
+    def format(self, error):
+        """Format an error reported by Flake8.
+
+        This method **must** be implemented by subclasses.
+
+        :param error:
+            This will be an instance of :class:`~flake8.style_guide.Error`.
+        :type error:
+            flake8.style_guide.Error
+        :returns:
+            The formatted error string.
+        :rtype:
+            str
+        """
+        raise NotImplementedError('Subclass of BaseFormatter did not implement'
+                                  ' format.')
+
+    def show_benchmarks(self, benchmarks):
+        """Format and print the benchmarks."""
+        # NOTE(sigmavirus24): The format strings are a little confusing, even
+        # to me, so here's a quick explanation:
+        # We specify the named value first followed by a ':' to indicate we're
+        # formatting the value.
+        # Next we use '<' to indicate we want the value left aligned.
+        # Then '10' is the width of the area.
+        # For floats, finally, we only want only want at most 3 digits after
+        # the decimal point to be displayed. This is the precision and it
+        # can not be specified for integers which is why we need two separate
+        # format strings.
+        float_format = '{value:<10.3} {statistic}'.format
+        int_format = '{value:<10} {statistic}'.format
+        for statistic, value in benchmarks:
+            if isinstance(value, int):
+                benchmark = int_format(statistic=statistic, value=value)
+            else:
+                benchmark = float_format(statistic=statistic, value=value)
+            self._write(benchmark)
+
+    def show_source(self, error):
+        """Show the physical line generating the error.
+
+        This also adds an indicator for the particular part of the line that
+        is reported as generating the problem.
+
+        :param error:
+            This will be an instance of :class:`~flake8.style_guide.Error`.
+        :type error:
+            flake8.style_guide.Error
+        :returns:
+            The formatted error string if the user wants to show the source.
+            If the user does not want to show the source, this will return
+            ``None``.
+        :rtype:
+            str
+        """
+        if not self.options.show_source:
+            return None
+        pointer = (' ' * error.column_number) + '^'
+        # Physical lines have a newline at the end, no need to add an extra
+        # one
+        return error.physical_line + pointer
+
+    def _write(self, output):
+        """Handle logic of whether to use an output file or print()."""
+        if self.output_fd is not None:
+            self.output_fd.write(output + self.newline)
+        else:
+            print(output)
+
+    def write(self, line, source):
+        """Write the line either to the output file or stdout.
+
+        This handles deciding whether to write to a file or print to standard
+        out for subclasses. Override this if you want behaviour that differs
+        from the default.
+
+        :param str line:
+            The formatted string to print or write.
+        :param str source:
+            The source code that has been formatted and associated with the
+            line of output.
+        """
+        self._write(line)
+        if source:
+            self._write(source)
+
+    def stop(self):
+        """Clean up after reporting is finished."""
+        if self.output_fd is not None:
+            self.output_fd.close()
+            self.output_fd = None
diff --git a/src/flake8/formatting/default.py b/src/flake8/formatting/default.py
new file mode 100644
index 0000000..bef8c88
--- /dev/null
+++ b/src/flake8/formatting/default.py
@@ -0,0 +1,56 @@
+"""Default formatting class for Flake8."""
+from flake8.formatting import base
+
+
+class SimpleFormatter(base.BaseFormatter):
+    """Simple abstraction for Default and Pylint formatter commonality.
+
+    Sub-classes of this need to define an ``error_format`` attribute in order
+    to succeed. The ``format`` method relies on that attribute and expects the
+    ``error_format`` string to use the old-style formatting strings with named
+    parameters:
+
+    * code
+    * text
+    * path
+    * row
+    * col
+
+    """
+
+    error_format = None
+
+    def format(self, error):
+        """Format and write error out.
+
+        If an output filename is specified, write formatted errors to that
+        file. Otherwise, print the formatted error to standard out.
+        """
+        return self.error_format % {
+            "code": error.code,
+            "text": error.text,
+            "path": error.filename,
+            "row": error.line_number,
+            "col": error.column_number,
+        }
+
+
+class Default(SimpleFormatter):
+    """Default formatter for Flake8.
+
+    This also handles backwards compatibility for people specifying a custom
+    format string.
+    """
+
+    error_format = '%(path)s:%(row)d:%(col)d: %(code)s %(text)s'
+
+    def after_init(self):
+        """Check for a custom format string."""
+        if self.options.format.lower() != 'default':
+            self.error_format = self.options.format
+
+
+class Pylint(SimpleFormatter):
+    """Pylint formatter for Flake8."""
+
+    error_format = '%(path)s:%(row)d: [%(code)s] %(text)s'
diff --git a/src/flake8/main/__init__.py b/src/flake8/main/__init__.py
new file mode 100644
index 0000000..d3aa1de
--- /dev/null
+++ b/src/flake8/main/__init__.py
@@ -0,0 +1 @@
+"""Module containing the logic for the Flake8 entry-points."""
diff --git a/src/flake8/main/application.py b/src/flake8/main/application.py
new file mode 100644
index 0000000..225c701
--- /dev/null
+++ b/src/flake8/main/application.py
@@ -0,0 +1,296 @@
+"""Module containing the application logic for Flake8."""
+from __future__ import print_function
+
+import logging
+import sys
+import time
+
+import flake8
+from flake8 import checker
+from flake8 import defaults
+from flake8 import style_guide
+from flake8 import utils
+from flake8.main import options
+from flake8.options import aggregator
+from flake8.options import manager
+from flake8.plugins import manager as plugin_manager
+
+LOG = logging.getLogger(__name__)
+
+
+class Application(object):
+    """Abstract our application into a class."""
+
+    def __init__(self, program='flake8', version=flake8.__version__):
+        # type: (str, str) -> NoneType
+        """Initialize our application.
+
+        :param str program:
+            The name of the program/application that we're executing.
+        :param str version:
+            The version of the program/application we're executing.
+        """
+        #: The timestamp when the Application instance was instantiated.
+        self.start_time = time.time()
+        #: The timestamp when the Application finished reported errors.
+        self.end_time = None
+        #: The name of the program being run
+        self.program = program
+        #: The version of the program being run
+        self.version = version
+        #: The instance of :class:`flake8.options.manager.OptionManager` used
+        #: to parse and handle the options and arguments passed by the user
+        self.option_manager = manager.OptionManager(
+            prog='flake8', version=flake8.__version__
+        )
+        options.register_default_options(self.option_manager)
+
+        # We haven't found or registered our plugins yet, so let's defer
+        # printing the version until we aggregate options from config files
+        # and the command-line. First, let's clone our arguments on the CLI,
+        # then we'll attempt to remove ``--version`` so that we can avoid
+        # triggering the "version" action in optparse. If it's not there, we
+        # do not need to worry and we can continue. If it is, we successfully
+        # defer printing the version until just a little bit later.
+        # Similarly we have to defer printing the help text until later.
+        args = sys.argv[:]
+        try:
+            args.remove('--version')
+        except ValueError:
+            pass
+        try:
+            args.remove('--help')
+        except ValueError:
+            pass
+        try:
+            args.remove('-h')
+        except ValueError:
+            pass
+
+        preliminary_opts, _ = self.option_manager.parse_args(args)
+        # Set the verbosity of the program
+        flake8.configure_logging(preliminary_opts.verbose,
+                                 preliminary_opts.output_file)
+
+        #: The instance of :class:`flake8.plugins.manager.Checkers`
+        self.check_plugins = None
+        #: The instance of :class:`flake8.plugins.manager.Listeners`
+        self.listening_plugins = None
+        #: The instance of :class:`flake8.plugins.manager.ReportFormatters`
+        self.formatting_plugins = None
+        #: The user-selected formatter from :attr:`formatting_plugins`
+        self.formatter = None
+        #: The :class:`flake8.plugins.notifier.Notifier` for listening plugins
+        self.listener_trie = None
+        #: The :class:`flake8.style_guide.StyleGuide` built from the user's
+        #: options
+        self.guide = None
+        #: The :class:`flake8.checker.Manager` that will handle running all of
+        #: the checks selected by the user.
+        self.file_checker_manager = None
+
+        #: The user-supplied options parsed into an instance of
+        #: :class:`optparse.Values`
+        self.options = None
+        #: The left over arguments that were not parsed by
+        #: :attr:`option_manager`
+        self.args = None
+        #: The number of errors, warnings, and other messages after running
+        #: flake8 and taking into account ignored errors and lines.
+        self.result_count = 0
+        #: The total number of errors before accounting for ignored errors and
+        #: lines.
+        self.total_result_count = 0
+
+        #: Whether the program is processing a diff or not
+        self.running_against_diff = False
+        #: The parsed diff information
+        self.parsed_diff = {}
+
+    def exit(self):
+        # type: () -> NoneType
+        """Handle finalization and exiting the program.
+
+        This should be the last thing called on the application instance. It
+        will check certain options and exit appropriately.
+        """
+        if self.options.count:
+            print(self.result_count)
+
+        if not self.options.exit_zero:
+            raise SystemExit(self.result_count > 0)
+
+    def find_plugins(self):
+        # type: () -> NoneType
+        """Find and load the plugins for this application.
+
+        If :attr:`check_plugins`, :attr:`listening_plugins`, or
+        :attr:`formatting_plugins` are ``None`` then this method will update
+        them with the appropriate plugin manager instance. Given the expense
+        of finding plugins (via :mod:`pkg_resources`) we want this to be
+        idempotent and so only update those attributes if they are ``None``.
+        """
+        if self.check_plugins is None:
+            self.check_plugins = plugin_manager.Checkers()
+
+        if self.listening_plugins is None:
+            self.listening_plugins = plugin_manager.Listeners()
+
+        if self.formatting_plugins is None:
+            self.formatting_plugins = plugin_manager.ReportFormatters()
+
+        self.check_plugins.load_plugins()
+        self.listening_plugins.load_plugins()
+        self.formatting_plugins.load_plugins()
+
+    def register_plugin_options(self):
+        # type: () -> NoneType
+        """Register options provided by plugins to our option manager."""
+        self.check_plugins.register_options(self.option_manager)
+        self.check_plugins.register_plugin_versions(self.option_manager)
+        self.listening_plugins.register_options(self.option_manager)
+        self.formatting_plugins.register_options(self.option_manager)
+
+    def parse_configuration_and_cli(self, argv=None):
+        # type: (Union[NoneType, List[str]]) -> NoneType
+        """Parse configuration files and the CLI options.
+
+        :param list argv:
+            Command-line arguments passed in directly.
+        """
+        if self.options is None and self.args is None:
+            self.options, self.args = aggregator.aggregate_options(
+                self.option_manager, argv
+            )
+
+        self.running_against_diff = self.options.diff
+        if self.running_against_diff:
+            self.parsed_diff = utils.parse_unified_diff()
+
+        self.check_plugins.provide_options(self.option_manager, self.options,
+                                           self.args)
+        self.listening_plugins.provide_options(self.option_manager,
+                                               self.options,
+                                               self.args)
+        self.formatting_plugins.provide_options(self.option_manager,
+                                                self.options,
+                                                self.args)
+
+    def make_formatter(self):
+        # type: () -> NoneType
+        """Initialize a formatter based on the parsed options."""
+        if self.formatter is None:
+            self.formatter = self.formatting_plugins.get(
+                self.options.format, self.formatting_plugins['default']
+            ).execute(self.options)
+
+    def make_notifier(self):
+        # type: () -> NoneType
+        """Initialize our listener Notifier."""
+        if self.listener_trie is None:
+            self.listener_trie = self.listening_plugins.build_notifier()
+
+    def make_guide(self):
+        # type: () -> NoneType
+        """Initialize our StyleGuide."""
+        if self.guide is None:
+            self.guide = style_guide.StyleGuide(
+                self.options, self.listener_trie, self.formatter
+            )
+
+        if self.running_against_diff:
+            self.guide.add_diff_ranges(self.parsed_diff)
+
+    def make_file_checker_manager(self):
+        # type: () -> NoneType
+        """Initialize our FileChecker Manager."""
+        if self.file_checker_manager is None:
+            self.file_checker_manager = checker.Manager(
+                style_guide=self.guide,
+                arguments=self.args,
+                checker_plugins=self.check_plugins,
+            )
+
+    def run_checks(self):
+        # type: () -> NoneType
+        """Run the actual checks with the FileChecker Manager.
+
+        This method encapsulates the logic to make a
+        :class:`~flake8.checker.Manger` instance run the checks it is
+        managing.
+        """
+        files = None
+        if self.running_against_diff:
+            files = list(sorted(self.parsed_diff.keys()))
+        self.file_checker_manager.start(files)
+        self.file_checker_manager.run()
+        LOG.info('Finished running')
+        self.file_checker_manager.stop()
+        self.end_time = time.time()
+
+    def report_benchmarks(self):
+        """Aggregate, calculate, and report benchmarks for this run."""
+        if not self.options.benchmark:
+            return
+
+        time_elapsed = self.end_time - self.start_time
+        statistics = [('seconds elapsed', time_elapsed)]
+        add_statistic = statistics.append
+        for statistic in (defaults.STATISTIC_NAMES + ('files',)):
+            value = self.file_checker_manager.statistics[statistic]
+            total_description = 'total ' + statistic + ' processed'
+            add_statistic((total_description, value))
+            per_second_description = statistic + ' processed per second'
+            add_statistic((per_second_description, int(value / time_elapsed)))
+
+        self.formatter.show_benchmarks(statistics)
+
+    def report_errors(self):
+        # type: () -> NoneType
+        """Report all the errors found by flake8 3.0.
+
+        This also updates the :attr:`result_count` attribute with the total
+        number of errors, warnings, and other messages found.
+        """
+        LOG.info('Reporting errors')
+        results = self.file_checker_manager.report()
+        self.total_result_count, self.result_count = results
+        LOG.info('Found a total of %d results and reported %d',
+                 self.total_result_count, self.result_count)
+
+    def initialize(self, argv):
+        # type: () -> NoneType
+        """Initialize the application to be run.
+
+        This finds the plugins, registers their options, and parses the
+        command-line arguments.
+        """
+        self.find_plugins()
+        self.register_plugin_options()
+        self.parse_configuration_and_cli(argv)
+        self.make_formatter()
+        self.make_notifier()
+        self.make_guide()
+        self.make_file_checker_manager()
+
+    def _run(self, argv):
+        # type: (Union[NoneType, List[str]]) -> NoneType
+        self.initialize(argv)
+        self.run_checks()
+        self.report_errors()
+        self.report_benchmarks()
+
+    def run(self, argv=None):
+        # type: (Union[NoneType, List[str]]) -> NoneType
+        """Run our application.
+
+        This method will also handle KeyboardInterrupt exceptions for the
+        entirety of the flake8 application. If it sees a KeyboardInterrupt it
+        will forcibly clean up the :class:`~flake8.checker.Manager`.
+        """
+        try:
+            self._run(argv)
+        except KeyboardInterrupt as exc:
+            LOG.critical('Caught keyboard interrupt from user')
+            LOG.exception(exc)
+            self.file_checker_manager._force_cleanup()
diff --git a/src/flake8/main/cli.py b/src/flake8/main/cli.py
new file mode 100644
index 0000000..29bd159
--- /dev/null
+++ b/src/flake8/main/cli.py
@@ -0,0 +1,17 @@
+"""Command-line implementation of flake8."""
+from flake8.main import application
+
+
+def main(argv=None):
+    # type: (Union[NoneType, List[str]]) -> NoneType
+    """Main entry-point for the flake8 command-line tool.
+
+    This handles the creation of an instance of :class:`Application`, runs it,
+    and then exits the application.
+
+    :param list argv:
+        The arguments to be passed to the application for parsing.
+    """
+    app = application.Application()
+    app.run(argv)
+    app.exit()
diff --git a/src/flake8/main/git.py b/src/flake8/main/git.py
new file mode 100644
index 0000000..bae0233
--- /dev/null
+++ b/src/flake8/main/git.py
@@ -0,0 +1,207 @@
+"""Module containing the main git hook interface and helpers.
+
+.. autofunction:: hook
+.. autofunction:: install
+
+"""
+import contextlib
+import os
+import shutil
+import stat
+import subprocess
+import sys
+import tempfile
+
+from flake8 import defaults
+from flake8 import exceptions
+
+__all__ = ('hook', 'install')
+
+
+def hook(lazy=False, strict=False):
+    """Execute Flake8 on the files in git's index.
+
+    Determine which files are about to be committed and run Flake8 over them
+    to check for violations.
+
+    :param bool lazy:
+        Find files not added to the index prior to committing. This is useful
+        if you frequently use ``git commit -a`` for example. This defaults to
+        False since it will otherwise include files not in the index.
+    :param bool strict:
+        If True, return the total number of errors/violations found by Flake8.
+        This will cause the hook to fail.
+    :returns:
+        Total number of errors found during the run.
+    :rtype:
+        int
+    """
+    # NOTE(sigmavirus24): Delay import of application until we need it.
+    from flake8.main import application
+    app = application.Application()
+    with make_temporary_directory() as tempdir:
+        filepaths = list(copy_indexed_files_to(tempdir, lazy))
+        app.initialize(filepaths)
+        app.run_checks()
+
+    app.report_errors()
+    if strict:
+        return app.result_count
+    return 0
+
+
+def install():
+    """Install the git hook script.
+
+    This searches for the ``.git`` directory and will install an executable
+    pre-commit python script in the hooks sub-directory if one does not
+    already exist.
+
+    :returns:
+        True if successful, False if the git directory doesn't exist.
+    :rtype:
+        bool
+    :raises:
+        flake8.exceptions.GitHookAlreadyExists
+    """
+    git_directory = find_git_directory()
+    if git_directory is None or not os.path.exists(git_directory):
+        return False
+
+    hooks_directory = os.path.join(git_directory, 'hooks')
+    if not os.path.exists(hooks_directory):
+        os.mkdir(hooks_directory)
+
+    pre_commit_file = os.path.abspath(
+        os.path.join(hooks_directory, 'pre-commit')
+    )
+    if os.path.exists(pre_commit_file):
+        raise exceptions.GitHookAlreadyExists(
+            'File already exists',
+            path=pre_commit_file,
+        )
+
+    executable = get_executable()
+
+    with open(pre_commit_file, 'w') as fd:
+        fd.write(_HOOK_TEMPLATE.format(executable=executable))
+
+    # NOTE(sigmavirus24): The following sets:
+    # - read, write, and execute permissions for the owner
+    # - read permissions for people in the group
+    # - read permissions for other people
+    # The owner needs the file to be readable, writable, and executable
+    # so that git can actually execute it as a hook.
+    pre_commit_permissions = stat.S_IRWXU | stat.S_IRGRP | stat.S_IROTH
+    os.chmod(pre_commit_file, pre_commit_permissions)
+    return True
+
+
+def get_executable():
+    if sys.executable is not None:
+        return sys.executable
+    return '/usr/bin/env python'
+
+
+def find_git_directory():
+    rev_parse = piped_process(['git', 'rev-parse', '--git-dir'])
+
+    (stdout, _) = rev_parse.communicate()
+    stdout = to_text(stdout)
+
+    if rev_parse.returncode == 0:
+        return stdout.strip()
+    return None
+
+
+def copy_indexed_files_to(temporary_directory, lazy):
+    modified_files = find_modified_files(lazy)
+    for filename in modified_files:
+        contents = get_staged_contents_from(filename)
+        yield copy_file_to(temporary_directory, filename, contents)
+
+
+def copy_file_to(destination_directory, filepath, contents):
+    directory, filename = os.path.split(os.path.abspath(filepath))
+    temporary_directory = make_temporary_directory_from(destination_directory,
+                                                        directory)
+    if not os.path.exists(temporary_directory):
+        os.makedirs(temporary_directory)
+    temporary_filepath = os.path.join(temporary_directory, filename)
+    with open(temporary_filepath, 'wb') as fd:
+        fd.write(contents)
+    return temporary_filepath
+
+
+def make_temporary_directory_from(destination, directory):
+    prefix = os.path.commonprefix([directory, destination])
+    common_directory_path = os.path.relpath(directory, start=prefix)
+    return os.path.join(destination, common_directory_path)
+
+
+def find_modified_files(lazy):
+    diff_index = piped_process(
+        ['git', 'diff-index', '--cached', '--name-only',
+         '--diff-filter=ACMRTUXB', 'HEAD'],
+    )
+
+    (stdout, _) = diff_index.communicate()
+    stdout = to_text(stdout)
+    return stdout.splitlines()
+
+
+def get_staged_contents_from(filename):
+    git_show = piped_process(['git', 'show', ':{0}'.format(filename)])
+    (stdout, _) = git_show.communicate()
+    return stdout
+
+
+@contextlib.contextmanager
+def make_temporary_directory():
+    temporary_directory = tempfile.mkdtemp()
+    yield temporary_directory
+    shutil.rmtree(temporary_directory, ignore_errors=True)
+
+
+def to_text(string):
+    """Ensure that the string is text."""
+    if callable(getattr(string, 'decode', None)):
+        return string.decode('utf-8')
+    return string
+
+
+def piped_process(command):
+    return subprocess.Popen(
+        command,
+        stdout=subprocess.PIPE,
+        stderr=subprocess.PIPE,
+    )
+
+
+def git_config_for(parameter):
+    config = piped_process(['git', 'config', '--get', '--bool', parameter])
+    (stdout, _) = config.communicate()
+    return to_text(stdout)
+
+
+def config_for(parameter):
+    environment_variable = 'flake8_{0}'.format(parameter).upper()
+    git_variable = 'flake8.{0}'.format(parameter)
+    value = os.environ.get(environment_variable, git_config_for(git_variable))
+    return value.lower() in defaults.TRUTHY_VALUES
+
+
+_HOOK_TEMPLATE = """#!{executable}
+import os
+import sys
+
+from flake8.main import git
+
+if __name__ == '__main__':
+    sys.exit(
+        git.hook(
+            strict=git.config_for('strict'),
+            lazy=git.config_for('lazy'),
+        )
+    )
+"""
diff --git a/src/flake8/main/mercurial.py b/src/flake8/main/mercurial.py
new file mode 100644
index 0000000..d067612
--- /dev/null
+++ b/src/flake8/main/mercurial.py
@@ -0,0 +1,128 @@
+"""Module containing the main mecurial hook interface and helpers.
+
+.. autofunction:: hook
+.. autofunction:: install
+
+"""
+import configparser
+import os
+import subprocess
+
+from flake8 import exceptions as exc
+
+__all__ = ('hook', 'install')
+
+
+def hook(ui, repo, **kwargs):
+    """Execute Flake8 on the repository provided by Mercurial.
+
+    To understand the parameters read more of the Mercurial documentation
+    around Hooks: https://www.mercurial-scm.org/wiki/Hook.
+
+    We avoid using the ``ui`` attribute because it can cause issues with
+    the GPL license tha Mercurial is under. We don't import it, but we
+    avoid using it all the same.
+    """
+    from flake8.main import application
+    hgrc = find_hgrc(create_if_missing=False)
+    if hgrc is None:
+        print('Cannot locate your root mercurial repository.')
+        raise SystemExit(True)
+
+    hgconfig = configparser_for(hgrc)
+    strict = hgconfig.get('flake8', 'strict', fallback=True)
+
+    filenames = list(get_filenames_from(repo, kwargs))
+
+    app = application.Application()
+    app.run(filenames)
+
+    if strict:
+        return app.result_count
+    return 0
+
+
+def install():
+    """Ensure that the mercurial hooks are installed."""
+    hgrc = find_hgrc(create_if_missing=True)
+    if hgrc is None:
+        return False
+
+    hgconfig = configparser_for(hgrc)
+
+    if not hgconfig.has_section('hooks'):
+        hgconfig.add_section('hooks')
+
+    if hgconfig.has_option('hooks', 'commit'):
+        raise exc.MercurialCommitHookAlreadyExists(
+            path=hgrc,
+            value=hgconfig.get('hooks', 'commit'),
+        )
+
+    if hgconfig.has_option('hooks', 'qrefresh'):
+        raise exc.MercurialQRefreshHookAlreadyExists(
+            path=hgrc,
+            value=hgconfig.get('hooks', 'qrefresh'),
+        )
+
+    hgconfig.set('hooks', 'commit', 'python:flake8.main.mercurial.hook')
+    hgconfig.set('hooks', 'qrefresh', 'python:flake8.main.mercurial.hook')
+
+    if not hgconfig.has_section('flake8'):
+        hgconfig.add_section('flake8')
+
+    if not hgconfig.has_option('flake8', 'strict'):
+        hgconfig.set('flake8', 'strict', False)
+
+    with open(hgrc, 'w') as fd:
+        hgconfig.write(fd)
+
+    return True
+
+
+def get_filenames_from(repository, kwargs):
+    seen_filenames = set()
+    node = kwargs['node']
+    for revision in range(repository[node], len(repository)):
+        for filename in repository[revision].files():
+            full_filename = os.path.join(repository.root, filename)
+            have_seen_filename = full_filename in seen_filenames
+            filename_does_not_exist = not os.path.exists(full_filename)
+            if have_seen_filename or filename_does_not_exist:
+                continue
+
+            seen_filenames.add(full_filename)
+            if full_filename.endswith('.py'):
+                yield full_filename
+
+
+def find_hgrc(create_if_missing=False):
+    root = subprocess.Popen(
+        ['hg', 'root'],
+        stdout=subprocess.PIPE,
+        stderr=subprocess.PIPE,
+    )
+
+    (hg_directory, _) = root.communicate()
+    if callable(getattr(hg_directory, 'decode', None)):
+        hg_directory = hg_directory.decode('utf-8')
+
+    if not os.path.isdir(hg_directory):
+        return None
+
+    hgrc = os.path.abspath(
+        os.path.join(hg_directory, '.hg', 'hgrc')
+    )
+    if not os.path.exists(hgrc):
+        if create_if_missing:
+            open(hgrc, 'w').close()
+        else:
+            return None
+
+    return hgrc
+
+
+def configparser_for(path):
+    parser = configparser.ConfigParser(interpolation=None)
+    parser.read(path)
+    return parser
diff --git a/src/flake8/main/options.py b/src/flake8/main/options.py
new file mode 100644
index 0000000..c725c38
--- /dev/null
+++ b/src/flake8/main/options.py
@@ -0,0 +1,201 @@
+"""Contains the logic for all of the default options for Flake8."""
+from flake8 import defaults
+from flake8.main import vcs
+
+
+def register_default_options(option_manager):
+    """Register the default options on our OptionManager.
+
+    The default options include:
+
+    - ``-v``/``--verbose``
+    - ``-q``/``--quiet``
+    - ``--count``
+    - ``--diff``
+    - ``--exclude``
+    - ``--filename``
+    - ``--format``
+    - ``--hang-closing``
+    - ``--ignore``
+    - ``--max-line-length``
+    - ``--select``
+    - ``--disable-noqa``
+    - ``--show-source``
+    - ``--statistics``
+    - ``--enable-extensions``
+    - ``--exit-zero``
+    - ``-j``/``--jobs``
+    - ``--output-file``
+    - ``--append-config``
+    - ``--config``
+    - ``--isolated``
+    """
+    add_option = option_manager.add_option
+
+    # pep8 options
+    add_option(
+        '-v', '--verbose', default=0, action='count',
+        parse_from_config=True,
+        help='Print more information about what is happening in flake8.'
+             ' This option is repeatable and will increase verbosity each '
+             'time it is repeated.',
+    )
+    add_option(
+        '-q', '--quiet', default=0, action='count',
+        parse_from_config=True,
+        help='Report only file names, or nothing. This option is repeatable.',
+    )
+
+    add_option(
+        '--count', action='store_true', parse_from_config=True,
+        help='Print total number of errors and warnings to standard error and'
+             ' set the exit code to 1 if total is not empty.',
+    )
+
+    add_option(
+        '--diff', action='store_true',
+        help='Report changes only within line number ranges in the unified '
+             'diff provided on standard in by the user.',
+    )
+
+    add_option(
+        '--exclude', metavar='patterns', default=defaults.EXCLUDE,
+        comma_separated_list=True, parse_from_config=True,
+        normalize_paths=True,
+        help='Comma-separated list of files or directories to exclude.'
+             ' (Default: %default)',
+    )
+
+    add_option(
+        '--filename', metavar='patterns', default='*.py',
+        parse_from_config=True, comma_separated_list=True,
+        help='Only check for filenames matching the patterns in this comma-'
+             'separated list. (Default: %default)',
+    )
+
+    add_option(
+        '--stdin-display-name', default='stdin',
+        help='The name used when reporting errors from code passed via stdin.'
+             ' This is useful for editors piping the file contents to flake8.'
+             ' (Default: %default)',
+    )
+
+    # TODO(sigmavirus24): Figure out --first/--repeat
+
+    # NOTE(sigmavirus24): We can't use choices for this option since users can
+    # freely provide a format string and that will break if we restrict their
+    # choices.
+    add_option(
+        '--format', metavar='format', default='default',
+        parse_from_config=True,
+        help='Format errors according to the chosen formatter.',
+    )
+
+    add_option(
+        '--hang-closing', action='store_true', parse_from_config=True,
+        help='Hang closing bracket instead of matching indentation of opening'
+             " bracket's line.",
+    )
+
+    add_option(
+        '--ignore', metavar='errors', default=defaults.IGNORE,
+        parse_from_config=True, comma_separated_list=True,
+        help='Comma-separated list of errors and warnings to ignore (or skip).'
+             ' For example, ``--ignore=E4,E51,W234``. (Default: %default)',
+    )
+
+    add_option(
+        '--max-line-length', type='int', metavar='n',
+        default=defaults.MAX_LINE_LENGTH, parse_from_config=True,
+        help='Maximum allowed line length for the entirety of this run. '
+             '(Default: %default)',
+    )
+
+    add_option(
+        '--select', metavar='errors', default=defaults.SELECT,
+        parse_from_config=True, comma_separated_list=True,
+        help='Comma-separated list of errors and warnings to enable.'
+             ' For example, ``--select=E4,E51,W234``. (Default: %default)',
+    )
+
+    add_option(
+        '--disable-noqa', default=False, parse_from_config=True,
+        action='store_true',
+        help='Disable the effect of "# noqa". This will report errors on '
+             'lines with "# noqa" at the end.'
+    )
+
+    # TODO(sigmavirus24): Decide what to do about --show-pep8
+
+    add_option(
+        '--show-source', action='store_true', parse_from_config=True,
+        help='Show the source generate each error or warning.',
+    )
+
+    add_option(
+        '--statistics', action='store_true', parse_from_config=True,
+        help='Count errors and warnings.',
+    )
+
+    # Flake8 options
+    add_option(
+        '--enable-extensions', default='', parse_from_config=True,
+        comma_separated_list=True, type='string',
+        help='Enable plugins and extensions that are otherwise disabled '
+             'by default',
+    )
+
+    add_option(
+        '--exit-zero', action='store_true',
+        help='Exit with status code "0" even if there are errors.',
+    )
+
+    add_option(
+        '--install-hook', action='callback', type='choice',
+        choices=vcs.choices(), callback=vcs.install,
+        help='Install a hook that is run prior to a commit for the supported '
+             'version control systema.'
+    )
+
+    add_option(
+        '-j', '--jobs', type='string', default='auto', parse_from_config=True,
+        help='Number of subprocesses to use to run checks in parallel. '
+             'This is ignored on Windows. The default, "auto", will '
+             'auto-detect the number of processors available to use.'
+             ' (Default: %default)',
+    )
+
+    add_option(
+        '--output-file', default=None, type='string', parse_from_config=True,
+        # callback=callbacks.redirect_stdout,
+        help='Redirect report to a file.',
+    )
+
+    # Config file options
+
+    add_option(
+        '--append-config', action='append',
+        help='Provide extra config files to parse in addition to the files '
+             'found by Flake8 by default. These files are the last ones read '
+             'and so they take the highest precedence when multiple files '
+             'provide the same option.',
+    )
+
+    add_option(
+        '--config', default=None,
+        help='Path to the config file that will be the authoritative config '
+             'source. This will cause Flake8 to ignore all other '
+             'configuration files.'
+    )
+
+    add_option(
+        '--isolated', default=False, action='store_true',
+        help='Ignore all found configuration files.',
+    )
+
+    # Benchmarking
+
+    add_option(
+        '--benchmark', default=False, action='store_true',
+        help='Print benchmark information about this run of Flake8',
+    )
diff --git a/src/flake8/main/setuptools_command.py b/src/flake8/main/setuptools_command.py
new file mode 100644
index 0000000..1c27bf6
--- /dev/null
+++ b/src/flake8/main/setuptools_command.py
@@ -0,0 +1,77 @@
+"""The logic for Flake8's integration with setuptools."""
+import os
+
+import setuptools
+
+from flake8.main import application as app
+
+
+class Flake8(setuptools.Command):
+    """Run Flake8 via setuptools/distutils for registered modules."""
+
+    description = 'Run Flake8 on modules registered in setup.py'
+    # NOTE(sigmavirus24): If we populated this with a list of tuples, users
+    # could do something like ``python setup.py flake8 --ignore=E123,E234``
+    # but we would have to redefine it and we can't define it dynamically.
+    # Since I refuse to copy-and-paste the options here or maintain two lists
+    # of options, and since this will break when users use plugins that
+    # provide command-line options, we are leaving this empty. If users want
+    # to configure this command, they can do so through config files.
+    user_options = []
+
+    def initialize_options(self):
+        """Override this method to initialize our application."""
+        pass
+
+    def finalize_options(self):
+        """Override this to parse the parameters."""
+        pass
+
+    def package_files(self):
+        """Collect the files/dirs included in the registered modules."""
+        seen_package_directories = ()
+        directories = self.distribution.package_dir or {}
+        empty_directory_exists = '' in directories
+        packages = self.distribution.packages or []
+        for package in packages:
+            package_directory = package
+            if package in directories:
+                package_directory = directories[package]
+            elif empty_directory_exists:
+                package_directory = os.path.join(directories[''],
+                                                 package_directory)
+
+            # NOTE(sigmavirus24): Do not collect submodules, e.g.,
+            # if we have:
+            #  - flake8/
+            #  - flake8/plugins/
+            # Flake8 only needs ``flake8/`` to be provided. It will
+            # recurse on its own.
+            if package_directory.startswith(seen_package_directories):
+                continue
+
+            seen_package_directories += (package_directory,)
+            yield package_directory
+
+    def module_files(self):
+        """Collect the files listed as py_modules."""
+        modules = self.distribution.py_modules or []
+        filename_from = '{0}.py'.format
+        for module in modules:
+            yield filename_from(module)
+
+    def distribution_files(self):
+        """Collect package and module files."""
+        for package in self.package_files():
+            yield package
+
+        for module in self.module_files():
+            yield module
+
+        yield 'setup.py'
+
+    def run(self):
+        """Run the Flake8 application."""
+        flake8 = app.Application()
+        flake8.run(list(self.distribution_files()))
+        flake8.exit()
diff --git a/src/flake8/main/vcs.py b/src/flake8/main/vcs.py
new file mode 100644
index 0000000..6f7499e
--- /dev/null
+++ b/src/flake8/main/vcs.py
@@ -0,0 +1,39 @@
+"""Module containing some of the logic for our VCS installation logic."""
+from flake8 import exceptions as exc
+from flake8.main import git
+from flake8.main import mercurial
+
+
+# NOTE(sigmavirus24): In the future, we may allow for VCS hooks to be defined
+# as plugins, e.g., adding a flake8.vcs entry-point. In that case, this
+# dictionary should disappear, and this module might contain more code for
+# managing those bits (in conjuntion with flake8.plugins.manager).
+_INSTALLERS = {
+    'git': git.install,
+    'mercurial': mercurial.install,
+}
+
+
+def install(option, option_string, value, parser):
+    """Determine which version control hook to install.
+
+    For more information about the callback signature, see:
+    https://docs.python.org/2/library/optparse.html#optparse-option-callbacks
+    """
+    installer = _INSTALLERS.get(value)
+    errored = False
+    successful = False
+    try:
+        successful = installer()
+    except exc.HookInstallationError as hook_error:
+        print(str(hook_error))
+        errored = True
+
+    if not successful:
+        print('Could not find the {0} directory'.format(value))
+    raise SystemExit(not successful and errored)
+
+
+def choices():
+    """Return the list of VCS choices."""
+    return list(_INSTALLERS.keys())
diff --git a/src/flake8/options/__init__.py b/src/flake8/options/__init__.py
new file mode 100644
index 0000000..cc20daa
--- /dev/null
+++ b/src/flake8/options/__init__.py
@@ -0,0 +1,12 @@
+"""Package containing the option manager and config management logic.
+
+- :mod:`flake8.options.config` contains the logic for finding, parsing, and
+  merging configuration files.
+
+- :mod:`flake8.options.manager` contains the logic for managing customized
+  Flake8 command-line and configuration options.
+
+- :mod:`flake8.options.aggregator` uses objects from both of the above modules
+  to aggregate configuration into one object used by plugins and Flake8.
+
+"""
diff --git a/src/flake8/options/aggregator.py b/src/flake8/options/aggregator.py
new file mode 100644
index 0000000..99d0cfe
--- /dev/null
+++ b/src/flake8/options/aggregator.py
@@ -0,0 +1,74 @@
+"""Aggregation function for CLI specified options and config file options.
+
+This holds the logic that uses the collected and merged config files and
+applies the user-specified command-line configuration on top of it.
+"""
+import logging
+
+from flake8 import utils
+from flake8.options import config
+
+LOG = logging.getLogger(__name__)
+
+
+def aggregate_options(manager, arglist=None, values=None):
+    """Aggregate and merge CLI and config file options.
+
+    :param flake8.option.manager.OptionManager manager:
+        The instance of the OptionManager that we're presently using.
+    :param list arglist:
+        The list of arguments to pass to ``manager.parse_args``. In most cases
+        this will be None so ``parse_args`` uses ``sys.argv``. This is mostly
+        available to make testing easier.
+    :param optparse.Values values:
+        Previously parsed set of parsed options.
+    :returns:
+        Tuple of the parsed options and extra arguments returned by
+        ``manager.parse_args``.
+    :rtype:
+        tuple(optparse.Values, list)
+    """
+    # Get defaults from the option parser
+    default_values, _ = manager.parse_args([], values=values)
+    # Get original CLI values so we can find additional config file paths and
+    # see if --config was specified.
+    original_values, original_args = manager.parse_args(arglist)
+    extra_config_files = utils.normalize_paths(original_values.append_config)
+
+    # Make our new configuration file mergerator
+    config_parser = config.MergedConfigParser(
+        option_manager=manager,
+        extra_config_files=extra_config_files,
+        args=original_args,
+    )
+
+    # Get the parsed config
+    parsed_config = config_parser.parse(original_values.config,
+                                        original_values.isolated)
+
+    # Extend the default ignore value with the extended default ignore list,
+    # registered by plugins.
+    extended_default_ignore = manager.extended_default_ignore.copy()
+    LOG.debug('Extended default ignore list: %s',
+              list(extended_default_ignore))
+    extended_default_ignore.update(default_values.ignore)
+    default_values.ignore = list(extended_default_ignore)
+    LOG.debug('Merged default ignore list: %s', default_values.ignore)
+
+    # Merge values parsed from config onto the default values returned
+    for config_name, value in parsed_config.items():
+        dest_name = config_name
+        # If the config name is somehow different from the destination name,
+        # fetch the destination name from our Option
+        if not hasattr(default_values, config_name):
+            dest_name = config_parser.config_options[config_name].dest
+
+        LOG.debug('Overriding default value of (%s) for "%s" with (%s)',
+                  getattr(default_values, dest_name, None),
+                  dest_name,
+                  value)
+        # Override the default values with the config values
+        setattr(default_values, dest_name, value)
+
+    # Finally parse the command-line options
+    return manager.parse_args(arglist, default_values)
diff --git a/src/flake8/options/config.py b/src/flake8/options/config.py
new file mode 100644
index 0000000..48719a8
--- /dev/null
+++ b/src/flake8/options/config.py
@@ -0,0 +1,279 @@
+"""Config handling logic for Flake8."""
+import configparser
+import logging
+import os.path
+import sys
+
+LOG = logging.getLogger(__name__)
+
+__all__ = ('ConfigFileFinder', 'MergedConfigParser')
+
+
+class ConfigFileFinder(object):
+    """Encapsulate the logic for finding and reading config files."""
+
+    PROJECT_FILENAMES = ('setup.cfg', 'tox.ini')
+
+    def __init__(self, program_name, args, extra_config_files):
+        """Initialize object to find config files.
+
+        :param str program_name:
+            Name of the current program (e.g., flake8).
+        :param list args:
+            The extra arguments passed on the command-line.
+        :param list extra_config_files:
+            Extra configuration files specified by the user to read.
+        """
+        # The values of --append-config from the CLI
+        extra_config_files = extra_config_files or []
+        self.extra_config_files = [
+            # Ensure the paths are absolute paths for local_config_files
+            os.path.abspath(f) for f in extra_config_files
+        ]
+
+        # Platform specific settings
+        self.is_windows = sys.platform == 'win32'
+        self.xdg_home = os.environ.get('XDG_CONFIG_HOME',
+                                       os.path.expanduser('~/.config'))
+
+        # Look for '.<program_name>' files
+        self.program_config = '.' + program_name
+        self.program_name = program_name
+
+        # List of filenames to find in the local/project directory
+        self.project_filenames = ('setup.cfg', 'tox.ini', self.program_config)
+
+        self.local_directory = os.path.abspath(os.curdir)
+
+        if not args:
+            args = ['.']
+        self.parent = self.tail = os.path.abspath(os.path.commonprefix(args))
+
+    @staticmethod
+    def _read_config(files):
+        config = configparser.RawConfigParser()
+        try:
+            found_files = config.read(files)
+        except configparser.ParsingError:
+            LOG.exception("There was an error trying to parse a config "
+                          "file. The files we were attempting to parse "
+                          "were: %r", files)
+            found_files = []
+        return (config, found_files)
+
+    def cli_config(self, files):
+        """Read and parse the config file specified on the command-line."""
+        config, found_files = self._read_config(files)
+        if found_files:
+            LOG.debug('Found cli configuration files: %s', found_files)
+        return config
+
+    def generate_possible_local_files(self):
+        """Find and generate all local config files."""
+        tail = self.tail
+        parent = self.parent
+        local_dir = self.local_directory
+        while tail:
+            for project_filename in self.project_filenames:
+                filename = os.path.abspath(os.path.join(parent,
+                                                        project_filename))
+                yield filename
+            if parent == local_dir:
+                break
+            (parent, tail) = os.path.split(parent)
+
+    def local_config_files(self):
+        """Find all local config files which actually exist.
+
+        Filter results from
+        :meth:`~ConfigFileFinder.generate_possible_local_files` based
+        on whether the filename exists or not.
+
+        :returns:
+            List of files that exist that are local project config files with
+            extra config files appended to that list (which also exist).
+        :rtype:
+            [str]
+        """
+        exists = os.path.exists
+        return [
+            filename
+            for filename in self.generate_possible_local_files()
+            if os.path.exists(filename)
+        ] + [f for f in self.extra_config_files if exists(f)]
+
+    def local_configs(self):
+        """Parse all local config files into one config object."""
+        config, found_files = self._read_config(self.local_config_files())
+        if found_files:
+            LOG.debug('Found local configuration files: %s', found_files)
+        return config
+
+    def user_config_file(self):
+        """Find the user-level config file."""
+        if self.is_windows:
+            return os.path.expanduser('~\\' + self.program_config)
+        return os.path.join(self.xdg_home, self.program_name)
+
+    def user_config(self):
+        """Parse the user config file into a config object."""
+        config, found_files = self._read_config(self.user_config_file())
+        if found_files:
+            LOG.debug('Found user configuration files: %s', found_files)
+        return config
+
+
+class MergedConfigParser(object):
+    """Encapsulate merging different types of configuration files.
+
+    This parses out the options registered that were specified in the
+    configuration files, handles extra configuration files, and returns
+    dictionaries with the parsed values.
+    """
+
+    #: Set of types that should use the
+    #: :meth:`~configparser.RawConfigParser.getint` method.
+    GETINT_TYPES = set(['int', 'count'])
+    #: Set of actions that should use the
+    #: :meth:`~configparser.RawConfigParser.getbool` method.
+    GETBOOL_ACTIONS = set(['store_true', 'store_false'])
+
+    def __init__(self, option_manager, extra_config_files=None, args=None):
+        """Initialize the MergedConfigParser instance.
+
+        :param flake8.option.manager.OptionManager option_manager:
+            Initialized OptionManager.
+        :param list extra_config_files:
+            List of extra config files to parse.
+        :params list args:
+            The extra parsed arguments from the command-line.
+        """
+        #: Our instance of flake8.options.manager.OptionManager
+        self.option_manager = option_manager
+        #: The prog value for the cli parser
+        self.program_name = option_manager.program_name
+        #: Parsed extra arguments
+        self.args = args
+        #: Mapping of configuration option names to
+        #: :class:`~flake8.options.manager.Option` instances
+        self.config_options = option_manager.config_options_dict
+        #: List of extra config files
+        self.extra_config_files = extra_config_files or []
+        #: Our instance of our :class:`~ConfigFileFinder`
+        self.config_finder = ConfigFileFinder(self.program_name, self.args,
+                                              self.extra_config_files)
+
+    @staticmethod
+    def _normalize_value(option, value):
+        final_value = option.normalize(value)
+        LOG.debug('%r has been normalized to %r for option "%s"',
+                  value, final_value, option.config_name)
+        return final_value
+
+    def _parse_config(self, config_parser):
+        config_dict = {}
+        for option_name in config_parser.options(self.program_name):
+            if option_name not in self.config_options:
+                LOG.debug('Option "%s" is not registered. Ignoring.',
+                          option_name)
+                continue
+            option = self.config_options[option_name]
+
+            # Use the appropriate method to parse the config value
+            method = config_parser.get
+            if option.type in self.GETINT_TYPES:
+                method = config_parser.getint
+            elif option.action in self.GETBOOL_ACTIONS:
+                method = config_parser.getboolean
+
+            value = method(self.program_name, option_name)
+            LOG.debug('Option "%s" returned value: %r', option_name, value)
+
+            final_value = self._normalize_value(option, value)
+            config_dict[option_name] = final_value
+
+        return config_dict
+
+    def is_configured_by(self, config):
+        """Check if the specified config parser has an appropriate section."""
+        return config.has_section(self.program_name)
+
+    def parse_local_config(self):
+        """Parse and return the local configuration files."""
+        config = self.config_finder.local_configs()
+        if not self.is_configured_by(config):
+            LOG.debug('Local configuration files have no %s section',
+                      self.program_name)
+            return {}
+
+        LOG.debug('Parsing local configuration files.')
+        return self._parse_config(config)
+
+    def parse_user_config(self):
+        """Parse and return the user configuration files."""
+        config = self.config_finder.user_config()
+        if not self.is_configured_by(config):
+            LOG.debug('User configuration files have no %s section',
+                      self.program_name)
+            return {}
+
+        LOG.debug('Parsing user configuration files.')
+        return self._parse_config(config)
+
+    def parse_cli_config(self, config_path):
+        """Parse and return the file specified by --config."""
+        config = self.config_finder.cli_config(config_path)
+        if not self.is_configured_by(config):
+            LOG.debug('CLI configuration files have no %s section',
+                      self.program_name)
+            return {}
+
+        LOG.debug('Parsing CLI configuration files.')
+        return self._parse_config(config)
+
+    def merge_user_and_local_config(self):
+        """Merge the parsed user and local configuration files.
+
+        :returns:
+            Dictionary of the parsed and merged configuration options.
+        :rtype:
+            dict
+        """
+        user_config = self.parse_user_config()
+        config = self.parse_local_config()
+
+        for option, value in user_config.items():
+            config.setdefault(option, value)
+
+        return config
+
+    def parse(self, cli_config=None, isolated=False):
+        """Parse and return the local and user config files.
+
+        First this copies over the parsed local configuration and then
+        iterates over the options in the user configuration and sets them if
+        they were not set by the local configuration file.
+
+        :param str cli_config:
+            Value of --config when specified at the command-line. Overrides
+            all other config files.
+        :param bool isolated:
+            Determines if we should parse configuration files at all or not.
+            If running in isolated mode, we ignore all configuration files
+        :returns:
+            Dictionary of parsed configuration options
+        :rtype:
+            dict
+        """
+        if isolated:
+            LOG.debug('Refusing to parse configuration files due to user-'
+                      'requested isolation')
+            return {}
+
+        if cli_config:
+            LOG.debug('Ignoring user and locally found configuration files. '
+                      'Reading only configuration from "%s" specified via '
+                      '--config by the user', cli_config)
+            return self.parse_cli_config(cli_config)
+
+        return self.merge_user_and_local_config()
diff --git a/src/flake8/options/manager.py b/src/flake8/options/manager.py
new file mode 100644
index 0000000..439cba2
--- /dev/null
+++ b/src/flake8/options/manager.py
@@ -0,0 +1,256 @@
+"""Option handling and Option management logic."""
+import logging
+import optparse  # pylint: disable=deprecated-module
+
+from flake8 import utils
+
+LOG = logging.getLogger(__name__)
+
+
+class Option(object):
+    """Our wrapper around an optparse.Option object to add features."""
+
+    def __init__(self, short_option_name=None, long_option_name=None,
+                 # Options below here are taken from the optparse.Option class
+                 action=None, default=None, type=None, dest=None,
+                 nargs=None, const=None, choices=None, callback=None,
+                 callback_args=None, callback_kwargs=None, help=None,
+                 metavar=None,
+                 # Options below here are specific to Flake8
+                 parse_from_config=False, comma_separated_list=False,
+                 normalize_paths=False):
+        """Initialize an Option instance wrapping optparse.Option.
+
+        The following are all passed directly through to optparse.
+
+        :param str short_option_name:
+            The short name of the option (e.g., ``-x``). This will be the
+            first argument passed to :class:`~optparse.Option`.
+        :param str long_option_name:
+            The long name of the option (e.g., ``--xtra-long-option``). This
+            will be the second argument passed to :class:`~optparse.Option`.
+        :param str action:
+            Any action allowed by :mod:`optparse`.
+        :param default:
+            Default value of the option.
+        :param type:
+            Any type allowed by :mod:`optparse`.
+        :param dest:
+            Attribute name to store parsed option value as.
+        :param nargs:
+            Number of arguments to parse for this option.
+        :param const:
+            Constant value to store on a common destination. Usually used in
+            conjuntion with ``action="store_const"``.
+        :param iterable choices:
+            Possible values for the option.
+        :param callable callback:
+            Callback used if the action is ``"callback"``.
+        :param iterable callback_args:
+            Additional positional arguments to the callback callable.
+        :param dictionary callback_kwargs:
+            Keyword arguments to the callback callable.
+        :param str help:
+            Help text displayed in the usage information.
+        :param str metavar:
+            Name to use instead of the long option name for help text.
+
+        The following parameters are for Flake8's option handling alone.
+
+        :param bool parse_from_config:
+            Whether or not this option should be parsed out of config files.
+        :param bool comma_separated_list:
+            Whether the option is a comma separated list when parsing from a
+            config file.
+        :param bool normalize_paths:
+            Whether the option is expecting a path or list of paths and should
+            attempt to normalize the paths to absolute paths.
+        """
+        self.short_option_name = short_option_name
+        self.long_option_name = long_option_name
+        self.option_args = [
+            x for x in (short_option_name, long_option_name) if x is not None
+        ]
+        self.option_kwargs = {
+            'action': action,
+            'default': default,
+            'type': type,
+            'dest': self._make_dest(dest),
+            'nargs': nargs,
+            'const': const,
+            'choices': choices,
+            'callback': callback,
+            'callback_args': callback_args,
+            'callback_kwargs': callback_kwargs,
+            'help': help,
+            'metavar': metavar,
+        }
+        # Set attributes for our option arguments
+        for key, value in self.option_kwargs.items():
+            setattr(self, key, value)
+
+        # Set our custom attributes
+        self.parse_from_config = parse_from_config
+        self.comma_separated_list = comma_separated_list
+        self.normalize_paths = normalize_paths
+
+        self.config_name = None
+        if parse_from_config:
+            if not long_option_name:
+                raise ValueError('When specifying parse_from_config=True, '
+                                 'a long_option_name must also be specified.')
+            self.config_name = long_option_name[2:].replace('-', '_')
+
+        self._opt = None
+
+    def __repr__(self):
+        """Simple representation of an Option class."""
+        return (
+            'Option({0}, {1}, action={action}, default={default}, '
+            'dest={dest}, type={type}, callback={callback}, help={help},'
+            ' callback={callback}, callback_args={callback_args}, '
+            'callback_kwargs={callback_kwargs}, metavar={metavar})'
+        ).format(self.short_option_name, self.long_option_name,
+                 **self.option_kwargs)
+
+    def _make_dest(self, dest):
+        if dest:
+            return dest
+
+        if self.long_option_name:
+            return self.long_option_name[2:].replace('-', '_')
+        return self.short_option_name[1]
+
+    def normalize(self, value):
+        """Normalize the value based on the option configuration."""
+        if self.normalize_paths:
+            # Decide whether to parse a list of paths or a single path
+            normalize = utils.normalize_path
+            if self.comma_separated_list:
+                normalize = utils.normalize_paths
+            return normalize(value)
+        elif self.comma_separated_list:
+            return utils.parse_comma_separated_list(value)
+        return value
+
+    def to_optparse(self):
+        """Convert a Flake8 Option to an optparse Option."""
+        if self._opt is None:
+            self._opt = optparse.Option(*self.option_args,
+                                        **self.option_kwargs)
+        return self._opt
+
+
+class OptionManager(object):
+    """Manage Options and OptionParser while adding post-processing."""
+
+    def __init__(self, prog=None, version=None,
+                 usage='%prog [options] file file ...'):
+        """Initialize an instance of an OptionManager.
+
+        :param str prog:
+            Name of the actual program (e.g., flake8).
+        :param str version:
+            Version string for the program.
+        :param str usage:
+            Basic usage string used by the OptionParser.
+        """
+        self.parser = optparse.OptionParser(prog=prog, version=version,
+                                            usage=usage)
+        self.config_options_dict = {}
+        self.options = []
+        self.program_name = prog
+        self.version = version
+        self.registered_plugins = set()
+        self.extended_default_ignore = set()
+
+    @staticmethod
+    def format_plugin(plugin_tuple):
+        """Convert a plugin tuple into a dictionary mapping name to value."""
+        return dict(zip(["name", "version"], plugin_tuple))
+
+    def add_option(self, *args, **kwargs):
+        """Create and register a new option.
+
+        See parameters for :class:`~flake8.options.manager.Option` for
+        acceptable arguments to this method.
+
+        .. note::
+
+            ``short_option_name`` and ``long_option_name`` may be specified
+            positionally as they are with optparse normally.
+        """
+        if len(args) == 1 and args[0].startswith('--'):
+            args = (None, args[0])
+        option = Option(*args, **kwargs)
+        self.parser.add_option(option.to_optparse())
+        self.options.append(option)
+        if option.parse_from_config:
+            self.config_options_dict[option.config_name] = option
+        LOG.debug('Registered option "%s".', option)
+
+    def remove_from_default_ignore(self, error_codes):
+        """Remove specified error codes from the default ignore list.
+
+        :param list error_codes:
+            List of strings that are the error/warning codes to attempt to
+            remove from the extended default ignore list.
+        """
+        LOG.debug('Removing %r from the default ignore list', error_codes)
+        for error_code in error_codes:
+            try:
+                self.extend_default_ignore.remove(error_code)
+            except ValueError:
+                LOG.debug('Attempted to remove %s from default ignore'
+                          ' but it was not a member of the list.', error_code)
+
+    def extend_default_ignore(self, error_codes):
+        """Extend the default ignore list with the error codes provided.
+
+        :param list error_codes:
+            List of strings that are the error/warning codes with which to
+            extend the default ignore list.
+        """
+        LOG.debug('Extending default ignore list with %r', error_codes)
+        self.extended_default_ignore.update(error_codes)
+
+    def generate_versions(self, format_str='%(name)s: %(version)s'):
+        """Generate a comma-separated list of versions of plugins."""
+        return ', '.join(
+            format_str % self.format_plugin(plugin)
+            for plugin in self.registered_plugins
+        )
+
+    def update_version_string(self):
+        """Update the flake8 version string."""
+        self.parser.version = (self.version + ' (' +
+                               self.generate_versions() + ')')
+
+    def generate_epilog(self):
+        """Create an epilog with the version and name of each of plugin."""
+        plugin_version_format = '%(name)s: %(version)s'
+        self.parser.epilog = 'Installed plugins: ' + self.generate_versions(
+            plugin_version_format
+        )
+
+    def parse_args(self, args=None, values=None):
+        """Simple proxy to calling the OptionParser's parse_args method."""
+        self.generate_epilog()
+        self.update_version_string()
+        options, xargs = self.parser.parse_args(args, values)
+        for option in self.options:
+            old_value = getattr(options, option.dest)
+            setattr(options, option.dest, option.normalize(old_value))
+
+        return options, xargs
+
+    def register_plugin(self, name, version):
+        """Register a plugin relying on the OptionManager.
+
+        :param str name:
+            The name of the checker itself. This will be the ``name``
+            attribute of the class or function loaded from the entry-point.
+        :param str version:
+            The version of the checker that we're using.
+        """
+        self.registered_plugins.add((name, version))
diff --git a/src/flake8/plugins/__init__.py b/src/flake8/plugins/__init__.py
new file mode 100644
index 0000000..fda6a44
--- /dev/null
+++ b/src/flake8/plugins/__init__.py
@@ -0,0 +1 @@
+"""Submodule of built-in plugins and plugin managers."""
diff --git a/src/flake8/plugins/_trie.py b/src/flake8/plugins/_trie.py
new file mode 100644
index 0000000..4871abb
--- /dev/null
+++ b/src/flake8/plugins/_trie.py
@@ -0,0 +1,97 @@
+"""Independent implementation of a Trie tree."""
+
+__all__ = ('Trie', 'TrieNode')
+
+
+def _iterate_stringlike_objects(string):
+    for i in range(len(string)):
+        yield string[i:i + 1]
+
+
+class Trie(object):
+    """The object that manages the trie nodes."""
+
+    def __init__(self):
+        """Initialize an empty trie."""
+        self.root = TrieNode(None, None)
+
+    def add(self, path, node_data):
+        """Add the node data to the path described."""
+        node = self.root
+        for prefix in _iterate_stringlike_objects(path):
+            child = node.find_prefix(prefix)
+            if child is None:
+                child = node.add_child(prefix, [])
+            node = child
+        node.data.append(node_data)
+
+    def find(self, path):
+        """Find a node based on the path provided."""
+        node = self.root
+        for prefix in _iterate_stringlike_objects(path):
+            child = node.find_prefix(prefix)
+            if child is None:
+                return None
+            node = child
+        return node
+
+    def traverse(self):
+        """Traverse this tree.
+
+        This performs a depth-first pre-order traversal of children in this
+        tree. It returns the results consistently by first sorting the
+        children based on their prefix and then traversing them in
+        alphabetical order.
+        """
+        return self.root.traverse()
+
+
+class TrieNode(object):
+    """The majority of the implementation details of a Trie."""
+
+    def __init__(self, prefix, data, children=None):
+        """Initialize a TrieNode with data and children."""
+        self.children = children or {}
+        self.data = data
+        self.prefix = prefix
+
+    def __repr__(self):
+        """Generate an easy to read representation of the node."""
+        return 'TrieNode(prefix={0}, data={1})'.format(
+            self.prefix, self.data
+        )
+
+    def find_prefix(self, prefix):
+        """Find the prefix in the children of this node.
+
+        :returns: A child matching the prefix or None.
+        :rtype: :class:`~TrieNode` or None
+        """
+        return self.children.get(prefix, None)
+
+    def add_child(self, prefix, data, children=None):
+        """Create and add a new child node.
+
+        :returns: The newly created node
+        :rtype: :class:`~TrieNode`
+        """
+        new_node = TrieNode(prefix, data, children)
+        self.children[prefix] = new_node
+        return new_node
+
+    def traverse(self):
+        """Traverse children of this node.
+
+        This performs a depth-first pre-order traversal of the remaining
+        children in this sub-tree. It returns the results consistently by
+        first sorting the children based on their prefix and then traversing
+        them in alphabetical order.
+        """
+        if not self.children:
+            return
+
+        for prefix in sorted(self.children.keys()):
+            child = self.children[prefix]
+            yield child
+            for child in child.traverse():
+                yield child
diff --git a/src/flake8/plugins/manager.py b/src/flake8/plugins/manager.py
new file mode 100644
index 0000000..d08d542
--- /dev/null
+++ b/src/flake8/plugins/manager.py
@@ -0,0 +1,458 @@
+"""Plugin loading and management logic and classes."""
+import collections
+import logging
+
+import pkg_resources
+
+from flake8 import exceptions
+from flake8 import utils
+from flake8.plugins import notifier
+
+LOG = logging.getLogger(__name__)
+
+__all__ = (
+    'Checkers',
+    'Listeners',
+    'Plugin',
+    'PluginManager',
+    'ReportFormatters',
+)
+
+NO_GROUP_FOUND = object()
+
+
+class Plugin(object):
+    """Wrap an EntryPoint from setuptools and other logic."""
+
+    def __init__(self, name, entry_point):
+        """"Initialize our Plugin.
+
+        :param str name:
+            Name of the entry-point as it was registered with setuptools.
+        :param entry_point:
+            EntryPoint returned by setuptools.
+        :type entry_point:
+            setuptools.EntryPoint
+        """
+        self.name = name
+        self.entry_point = entry_point
+        self._plugin = None
+        self._parameters = None
+        self._group = None
+        self._plugin_name = None
+        self._version = None
+
+    def __repr__(self):
+        """Provide an easy to read description of the current plugin."""
+        return 'Plugin(name="{0}", entry_point="{1}")'.format(
+            self.name, self.entry_point
+        )
+
+    def is_in_a_group(self):
+        """Determine if this plugin is in a group.
+
+        :returns:
+            True if the plugin is in a group, otherwise False.
+        :rtype:
+            bool
+        """
+        return self.group() is not None
+
+    def group(self):
+        """Find and parse the group the plugin is in."""
+        if self._group is None:
+            name = self.name.split('.', 1)
+            if len(name) > 1:
+                self._group = name[0]
+            else:
+                self._group = NO_GROUP_FOUND
+        if self._group is NO_GROUP_FOUND:
+            return None
+        return self._group
+
+    @property
+    def parameters(self):
+        """List of arguments that need to be passed to the plugin."""
+        if self._parameters is None:
+            self._parameters = utils.parameters_for(self)
+        return self._parameters
+
+    @property
+    def plugin(self):
+        """The loaded (and cached) plugin associated with the entry-point.
+
+        This property implicitly loads the plugin and then caches it.
+        """
+        self.load_plugin()
+        return self._plugin
+
+    @property
+    def version(self):
+        """Return the version of the plugin."""
+        if self._version is None:
+            if self.is_in_a_group():
+                self._version = version_for(self)
+            else:
+                self._version = self.plugin.version
+
+        return self._version
+
+    @property
+    def plugin_name(self):
+        """Return the name of the plugin."""
+        if self._plugin_name is None:
+            if self.is_in_a_group():
+                self._plugin_name = self.group()
+            else:
+                self._plugin_name = self.plugin.name
+
+        return self._plugin_name
+
+    @property
+    def off_by_default(self):
+        """Return whether the plugin is ignored by default."""
+        return getattr(self.plugin, 'off_by_default', False)
+
+    def execute(self, *args, **kwargs):
+        r"""Call the plugin with \*args and \*\*kwargs."""
+        return self.plugin(*args, **kwargs)  # pylint: disable=not-callable
+
+    def _load(self, verify_requirements):
+        # Avoid relying on hasattr() here.
+        resolve = getattr(self.entry_point, 'resolve', None)
+        require = getattr(self.entry_point, 'require', None)
+        if resolve and require:
+            if verify_requirements:
+                LOG.debug('Verifying plugin "%s"\'s requirements.',
+                          self.name)
+                require()
+            self._plugin = resolve()
+        else:
+            self._plugin = self.entry_point.load(
+                require=verify_requirements
+            )
+
+    def load_plugin(self, verify_requirements=False):
+        """Retrieve the plugin for this entry-point.
+
+        This loads the plugin, stores it on the instance and then returns it.
+        It does not reload it after the first time, it merely returns the
+        cached plugin.
+
+        :param bool verify_requirements:
+            Whether or not to make setuptools verify that the requirements for
+            the plugin are satisfied.
+        :returns:
+            Nothing
+        """
+        if self._plugin is None:
+            LOG.info('Loading plugin "%s" from entry-point.', self.name)
+            try:
+                self._load(verify_requirements)
+            except Exception as load_exception:
+                LOG.exception(load_exception, exc_info=True)
+                failed_to_load = exceptions.FailedToLoadPlugin(
+                    plugin=self,
+                    exception=load_exception,
+                )
+                LOG.critical(str(failed_to_load))
+                raise failed_to_load
+
+    def enable(self, optmanager):
+        """Remove plugin name from the default ignore list."""
+        optmanager.remove_from_default_ignore([self.name])
+
+    def disable(self, optmanager):
+        """Add the plugin name to the default ignore list."""
+        optmanager.extend_default_ignore([self.name])
+
+    def provide_options(self, optmanager, options, extra_args):
+        """Pass the parsed options and extra arguments to the plugin."""
+        parse_options = getattr(self.plugin, 'parse_options', None)
+        if parse_options is not None:
+            LOG.debug('Providing options to plugin "%s".', self.name)
+            try:
+                parse_options(optmanager, options, extra_args)
+            except TypeError:
+                parse_options(options)
+
+        if self.name in options.enable_extensions:
+            self.enable(optmanager)
+
+    def register_options(self, optmanager):
+        """Register the plugin's command-line options on the OptionManager.
+
+        :param optmanager:
+            Instantiated OptionManager to register options on.
+        :type optmanager:
+            flake8.options.manager.OptionManager
+        :returns:
+            Nothing
+        """
+        add_options = getattr(self.plugin, 'add_options', None)
+        if add_options is not None:
+            LOG.debug(
+                'Registering options from plugin "%s" on OptionManager %r',
+                self.name, optmanager
+            )
+            add_options(optmanager)
+
+        if self.off_by_default:
+            self.disable(optmanager)
+
+
+class PluginManager(object):  # pylint: disable=too-few-public-methods
+    """Find and manage plugins consistently."""
+
+    def __init__(self, namespace, verify_requirements=False):
+        """Initialize the manager.
+
+        :param str namespace:
+            Namespace of the plugins to manage, e.g., 'flake8.extension'.
+        :param bool verify_requirements:
+            Whether or not to make setuptools verify that the requirements for
+            the plugin are satisfied.
+        """
+        self.namespace = namespace
+        self.verify_requirements = verify_requirements
+        self.plugins = {}
+        self.names = []
+        self._load_all_plugins()
+
+    def _load_all_plugins(self):
+        LOG.info('Loading entry-points for "%s".', self.namespace)
+        for entry_point in pkg_resources.iter_entry_points(self.namespace):
+            name = entry_point.name
+            self.plugins[name] = Plugin(name, entry_point)
+            self.names.append(name)
+            LOG.debug('Loaded %r for plugin "%s".', self.plugins[name], name)
+
+    def map(self, func, *args, **kwargs):
+        r"""Call ``func`` with the plugin and \*args and \**kwargs after.
+
+        This yields the return value from ``func`` for each plugin.
+
+        :param collections.Callable func:
+            Function to call with each plugin. Signature should at least be:
+
+            .. code-block:: python
+
+                def myfunc(plugin):
+                     pass
+
+            Any extra positional or keyword arguments specified with map will
+            be passed along to this function after the plugin. The plugin
+            passed is a :class:`~flake8.plugins.manager.Plugin`.
+        :param args:
+            Positional arguments to pass to ``func`` after each plugin.
+        :param kwargs:
+            Keyword arguments to pass to ``func`` after each plugin.
+        """
+        for name in self.names:
+            yield func(self.plugins[name], *args, **kwargs)
+
+    def versions(self):
+        # () -> (str, str)
+        """Generate the versions of plugins.
+
+        :returns:
+            Tuples of the plugin_name and version
+        :rtype:
+            tuple
+        """
+        plugins_seen = set()
+        for entry_point_name in self.names:
+            plugin = self.plugins[entry_point_name]
+            plugin_name = plugin.plugin_name
+            if plugin.plugin_name in plugins_seen:
+                continue
+            plugins_seen.add(plugin_name)
+            yield (plugin_name, plugin.version)
+
+
+def version_for(plugin):
+    # (Plugin) -> Union[str, NoneType]
+    """Determine the version of a plugin by it's module.
+
+    :param plugin:
+        The loaded plugin
+    :type plugin:
+        Plugin
+    :returns:
+        version string for the module
+    :rtype:
+        str
+    """
+    module_name = plugin.plugin.__module__
+    try:
+        module = __import__(module_name)
+    except ImportError:
+        return None
+
+    return getattr(module, '__version__', None)
+
+
+class PluginTypeManager(object):
+    """Parent class for most of the specific plugin types."""
+
+    namespace = None
+
+    def __init__(self):
+        """Initialize the plugin type's manager."""
+        self.manager = PluginManager(self.namespace)
+        self.plugins_loaded = False
+
+    def __contains__(self, name):
+        """Check if the entry-point name is in this plugin type manager."""
+        LOG.debug('Checking for "%s" in plugin type manager.', name)
+        return name in self.plugins
+
+    def __getitem__(self, name):
+        """Retrieve a plugin by its name."""
+        LOG.debug('Retrieving plugin for "%s".', name)
+        return self.plugins[name]
+
+    def get(self, name, default=None):
+        """Retrieve the plugin referred to by ``name`` or return the default.
+
+        :param str name:
+            Name of the plugin to retrieve.
+        :param default:
+            Default value to return.
+        :returns:
+            Plugin object referred to by name, if it exists.
+        :rtype:
+            :class:`Plugin`
+        """
+        if name in self:
+            return self[name]
+        return default
+
+    @property
+    def names(self):
+        """Proxy attribute to underlying manager."""
+        return self.manager.names
+
+    @property
+    def plugins(self):
+        """Proxy attribute to underlying manager."""
+        return self.manager.plugins
+
+    @staticmethod
+    def _generate_call_function(method_name, optmanager, *args, **kwargs):
+        def generated_function(plugin):
+            """Function that attempts to call a specific method on a plugin."""
+            method = getattr(plugin, method_name, None)
+            if (method is not None and
+                    isinstance(method, collections.Callable)):
+                return method(optmanager, *args, **kwargs)
+        return generated_function
+
+    def load_plugins(self):
+        """Load all plugins of this type that are managed by this manager."""
+        if self.plugins_loaded:
+            return
+
+        def load_plugin(plugin):
+            """Call each plugin's load_plugin method."""
+            return plugin.load_plugin()
+
+        plugins = list(self.manager.map(load_plugin))
+        # Do not set plugins_loaded if we run into an exception
+        self.plugins_loaded = True
+        return plugins
+
+    def register_plugin_versions(self, optmanager):
+        """Register the plugins and their versions with the OptionManager."""
+        self.load_plugins()
+        for (plugin_name, version) in self.manager.versions():
+            optmanager.register_plugin(name=plugin_name, version=version)
+
+    def register_options(self, optmanager):
+        """Register all of the checkers' options to the OptionManager."""
+        self.load_plugins()
+        call_register_options = self._generate_call_function(
+            'register_options', optmanager,
+        )
+
+        list(self.manager.map(call_register_options))
+
+    def provide_options(self, optmanager, options, extra_args):
+        """Provide parsed options and extra arguments to the plugins."""
+        call_provide_options = self._generate_call_function(
+            'provide_options', optmanager, options, extra_args,
+        )
+
+        list(self.manager.map(call_provide_options))
+
+
+class NotifierBuilderMixin(object):  # pylint: disable=too-few-public-methods
+    """Mixin class that builds a Notifier from a PluginManager."""
+
+    def build_notifier(self):
+        """Build a Notifier for our Listeners.
+
+        :returns:
+            Object to notify our listeners of certain error codes and
+            warnings.
+        :rtype:
+            :class:`~flake8.notifier.Notifier`
+        """
+        notifier_trie = notifier.Notifier()
+        for name in self.names:
+            notifier_trie.register_listener(name, self.manager[name])
+        return notifier_trie
+
+
+class Checkers(PluginTypeManager):
+    """All of the checkers registered through entry-ponits."""
+
+    namespace = 'flake8.extension'
+
+    def checks_expecting(self, argument_name):
+        """Retrieve checks that expect an argument with the specified name.
+
+        Find all checker plugins that are expecting a specific argument.
+        """
+        for plugin in self.plugins.values():
+            if argument_name == plugin.parameters[0]:
+                yield plugin
+
+    @property
+    def ast_plugins(self):
+        """List of plugins that expect the AST tree."""
+        plugins = getattr(self, '_ast_plugins', [])
+        if not plugins:
+            plugins = list(self.checks_expecting('tree'))
+            self._ast_plugins = plugins
+        return plugins
+
+    @property
+    def logical_line_plugins(self):
+        """List of plugins that expect the logical lines."""
+        plugins = getattr(self, '_logical_line_plugins', [])
+        if not plugins:
+            plugins = list(self.checks_expecting('logical_line'))
+            self._logical_line_plugins = plugins
+        return plugins
+
+    @property
+    def physical_line_plugins(self):
+        """List of plugins that expect the physical lines."""
+        plugins = getattr(self, '_physical_line_plugins', [])
+        if not plugins:
+            plugins = list(self.checks_expecting('physical_line'))
+            self._physical_line_plugins = plugins
+        return plugins
+
+
+class Listeners(PluginTypeManager, NotifierBuilderMixin):
+    """All of the listeners registered through entry-points."""
+
+    namespace = 'flake8.listen'
+
+
+class ReportFormatters(PluginTypeManager):
+    """All of the report formatters registered through entry-points."""
+
+    namespace = 'flake8.report'
diff --git a/src/flake8/plugins/notifier.py b/src/flake8/plugins/notifier.py
new file mode 100644
index 0000000..dc255c4
--- /dev/null
+++ b/src/flake8/plugins/notifier.py
@@ -0,0 +1,46 @@
+"""Implementation of the class that registers and notifies listeners."""
+from flake8.plugins import _trie
+
+
+class Notifier(object):
+    """Object that tracks and notifies listener objects."""
+
+    def __init__(self):
+        """Initialize an empty notifier object."""
+        self.listeners = _trie.Trie()
+
+    def listeners_for(self, error_code):
+        """Retrieve listeners for an error_code.
+
+        There may be listeners registered for E1, E100, E101, E110, E112, and
+        E126. To get all the listeners for one of E100, E101, E110, E112, or
+        E126 you would also need to incorporate the listeners for E1 (since
+        they're all in the same class).
+
+        Example usage:
+
+        .. code-block:: python
+
+            from flake8 import notifier
+
+            n = notifier.Notifier()
+            # register listeners
+            for listener in n.listeners_for('W102'):
+                listener.notify(...)
+        """
+        path = error_code
+        while path:
+            node = self.listeners.find(path)
+            listeners = getattr(node, 'data', [])
+            for listener in listeners:
+                yield listener
+            path = path[:-1]
+
+    def notify(self, error_code, *args, **kwargs):
+        """Notify all listeners for the specified error code."""
+        for listener in self.listeners_for(error_code):
+            listener.notify(error_code, *args, **kwargs)
+
+    def register_listener(self, error_code, listener):
+        """Register a listener for a specific error_code."""
+        self.listeners.add(error_code, listener)
diff --git a/src/flake8/plugins/pyflakes.py b/src/flake8/plugins/pyflakes.py
new file mode 100644
index 0000000..72d45fa
--- /dev/null
+++ b/src/flake8/plugins/pyflakes.py
@@ -0,0 +1,140 @@
+"""Plugin built-in to Flake8 to treat pyflakes as a plugin."""
+# -*- coding: utf-8 -*-
+from __future__ import absolute_import
+
+try:
+    # The 'demandimport' breaks pyflakes and flake8.plugins.pyflakes
+    from mercurial import demandimport
+except ImportError:
+    pass
+else:
+    demandimport.disable()
+import os
+
+import pyflakes
+import pyflakes.checker
+
+from flake8 import utils
+
+
+def patch_pyflakes():
+    """Add error codes to Pyflakes messages."""
+    codes = dict([line.split()[::-1] for line in (
+        'F401 UnusedImport',
+        'F402 ImportShadowedByLoopVar',
+        'F403 ImportStarUsed',
+        'F404 LateFutureImport',
+        'F810 Redefined',
+        'F811 RedefinedWhileUnused',
+        'F812 RedefinedInListComp',
+        'F821 UndefinedName',
+        'F822 UndefinedExport',
+        'F823 UndefinedLocal',
+        'F831 DuplicateArgument',
+        'F841 UnusedVariable',
+    )])
+
+    for name, obj in vars(pyflakes.messages).items():
+        if name[0].isupper() and obj.message:
+            obj.flake8_msg = '%s %s' % (codes.get(name, 'F999'), obj.message)
+patch_pyflakes()
+
+
+class FlakesChecker(pyflakes.checker.Checker):
+    """Subclass the Pyflakes checker to conform with the flake8 API."""
+
+    name = 'pyflakes'
+    version = pyflakes.__version__
+
+    def __init__(self, tree, filename):
+        """Initialize the PyFlakes plugin with an AST tree and filename."""
+        filename = utils.normalize_paths(filename)[0]
+        with_doctest = self.with_doctest
+        included_by = [include for include in self.include_in_doctest
+                       if include != '' and filename.startswith(include)]
+        if included_by:
+            with_doctest = True
+
+        for exclude in self.exclude_from_doctest:
+            if exclude != '' and filename.startswith(exclude):
+                with_doctest = False
+                overlaped_by = [include for include in included_by
+                                if include.startswith(exclude)]
+
+                if overlaped_by:
+                    with_doctest = True
+
+        super(FlakesChecker, self).__init__(tree, filename,
+                                            withDoctest=with_doctest)
+
+    @classmethod
+    def add_options(cls, parser):
+        """Register options for PyFlakes on the Flake8 OptionManager."""
+        parser.add_option(
+            '--builtins', parse_from_config=True, comma_separated_list=True,
+            help="define more built-ins, comma separated",
+        )
+        parser.add_option(
+            '--doctests', default=False, action='store_true',
+            parse_from_config=True,
+            help="check syntax of the doctests",
+        )
+        parser.add_option(
+            '--include-in-doctest', default='',
+            dest='include_in_doctest', parse_from_config=True,
+            comma_separated_list=True, normalize_paths=True,
+            help='Run doctests only on these files',
+            type='string',
+        )
+        parser.add_option(
+            '--exclude-from-doctest', default='',
+            dest='exclude_from_doctest', parse_from_config=True,
+            comma_separated_list=True, normalize_paths=True,
+            help='Skip these files when running doctests',
+            type='string',
+        )
+
+    @classmethod
+    def parse_options(cls, options):
+        """Parse option values from Flake8's OptionManager."""
+        if options.builtins:
+            cls.builtIns = cls.builtIns.union(options.builtins)
+        cls.with_doctest = options.doctests
+
+        included_files = []
+        for included_file in options.include_in_doctest:
+            if included_file == '':
+                continue
+            if not included_file.startswith((os.sep, './', '~/')):
+                included_files.append('./' + included_file)
+            else:
+                included_files.append(included_file)
+        cls.include_in_doctest = utils.normalize_paths(included_files)
+
+        excluded_files = []
+        for excluded_file in options.exclude_from_doctest:
+            if excluded_file == '':
+                continue
+            if not excluded_file.startswith((os.sep, './', '~/')):
+                excluded_files.append('./' + excluded_file)
+            else:
+                excluded_files.append(excluded_file)
+        cls.exclude_from_doctest = utils.normalize_paths(excluded_files)
+
+        inc_exc = set(cls.include_in_doctest).intersection(
+            cls.exclude_from_doctest
+        )
+        if inc_exc:
+            raise ValueError('"%s" was specified in both the '
+                             'include-in-doctest and exclude-from-doctest '
+                             'options. You are not allowed to specify it in '
+                             'both for doctesting.' % inc_exc)
+
+    def run(self):
+        """Run the plugin."""
+        for message in self.messages:
+            col = getattr(message, 'col', 0)
+            yield (message.lineno,
+                   col,
+                   (message.flake8_msg % message.message_args),
+                   message.__class__)
diff --git a/src/flake8/processor.py b/src/flake8/processor.py
new file mode 100644
index 0000000..0c33cc2
--- /dev/null
+++ b/src/flake8/processor.py
@@ -0,0 +1,430 @@
+"""Module containing our file processor that tokenizes a file for checks."""
+import contextlib
+import io
+import logging
+import re
+import sys
+import tokenize
+
+import flake8
+from flake8 import defaults
+from flake8 import exceptions
+from flake8 import utils
+
+LOG = logging.getLogger(__name__)
+PyCF_ONLY_AST = 1024
+NEWLINE = frozenset([tokenize.NL, tokenize.NEWLINE])
+# Work around Python < 2.6 behaviour, which does not generate NL after
+# a comment which is on a line by itself.
+COMMENT_WITH_NL = tokenize.generate_tokens(['#\n'].pop).send(None)[1] == '#\n'
+
+SKIP_TOKENS = frozenset([tokenize.NL, tokenize.NEWLINE, tokenize.INDENT,
+                         tokenize.DEDENT])
+
+
+class FileProcessor(object):
+    """Processes a file and holdes state.
+
+    This processes a file by generating tokens, logical and physical lines,
+    and AST trees. This also provides a way of passing state about the file
+    to checks expecting that state. Any public attribute on this object can
+    be requested by a plugin. The known public attributes are:
+
+    - :attr:`blank_before`
+    - :attr:`blank_lines`
+    - :attr:`checker_state`
+    - :attr:`indect_char`
+    - :attr:`indent_level`
+    - :attr:`line_number`
+    - :attr:`logical_line`
+    - :attr:`max_line_length`
+    - :attr:`multiline`
+    - :attr:`noqa`
+    - :attr:`previous_indent_level`
+    - :attr:`previous_logical`
+    - :attr:`tokens`
+    - :attr:`total_lines`
+    - :attr:`verbose`
+    """
+
+    NOQA_FILE = re.compile(r'\s*# flake8[:=]\s*noqa', re.I)
+
+    def __init__(self, filename, options, lines=None):
+        """Initialice our file processor.
+
+        :param str filename:
+            Name of the file to process
+        """
+        self.filename = filename
+        self.lines = lines
+        if lines is None:
+            self.lines = self.read_lines()
+        self.strip_utf_bom()
+        self.options = options
+
+        # Defaults for public attributes
+        #: Number of preceding blank lines
+        self.blank_before = 0
+        #: Number of blank lines
+        self.blank_lines = 0
+        #: Checker states for each plugin?
+        self._checker_states = {}
+        #: Current checker state
+        self.checker_state = None
+        #: User provided option for hang closing
+        self.hang_closing = options.hang_closing
+        #: Character used for indentation
+        self.indent_char = None
+        #: Current level of indentation
+        self.indent_level = 0
+        #: Line number in the file
+        self.line_number = 0
+        #: Current logical line
+        self.logical_line = ''
+        #: Maximum line length as configured by the user
+        self.max_line_length = options.max_line_length
+        #: Whether the current physical line is multiline
+        self.multiline = False
+        #: Whether or not we're observing NoQA
+        self.noqa = False
+        #: Previous level of indentation
+        self.previous_indent_level = 0
+        #: Previous logical line
+        self.previous_logical = ''
+        #: Current set of tokens
+        self.tokens = []
+        #: Total number of lines in the file
+        self.total_lines = len(self.lines)
+        #: Verbosity level of Flake8
+        self.verbose = options.verbose
+        #: Statistics dictionary
+        self.statistics = {
+            'logical lines': 0,
+        }
+
+    @contextlib.contextmanager
+    def inside_multiline(self, line_number):
+        """Context-manager to toggle the multiline attribute."""
+        self.line_number = line_number
+        self.multiline = True
+        yield
+        self.multiline = False
+
+    def reset_blank_before(self):
+        """Reset the blank_before attribute to zero."""
+        self.blank_before = 0
+
+    def delete_first_token(self):
+        """Delete the first token in the list of tokens."""
+        del self.tokens[0]
+
+    def visited_new_blank_line(self):
+        """Note that we visited a new blank line."""
+        self.blank_lines += 1
+
+    def update_state(self, mapping):
+        """Update the indent level based on the logical line mapping."""
+        (start_row, start_col) = mapping[0][1]
+        start_line = self.lines[start_row - 1]
+        self.indent_level = expand_indent(start_line[:start_col])
+        if self.blank_before < self.blank_lines:
+            self.blank_before = self.blank_lines
+
+    def update_checker_state_for(self, plugin):
+        """Update the checker_state attribute for the plugin."""
+        if 'checker_state' in plugin.parameters:
+            self.checker_state = self._checker_states.setdefault(
+                plugin.name, {}
+            )
+
+    def next_logical_line(self):
+        """Record the previous logical line.
+
+        This also resets the tokens list and the blank_lines count.
+        """
+        if self.logical_line:
+            self.previous_indent_level = self.indent_level
+            self.previous_logical = self.logical_line
+        self.blank_lines = 0
+        self.tokens = []
+
+    def build_logical_line_tokens(self):
+        """Build the mapping, comments, and logical line lists."""
+        logical = []
+        comments = []
+        length = 0
+        previous_row = previous_column = mapping = None
+        for token_type, text, start, end, line in self.tokens:
+            if token_type in SKIP_TOKENS:
+                continue
+            if not mapping:
+                mapping = [(0, start)]
+            if token_type == tokenize.COMMENT:
+                comments.append(text)
+                continue
+            if token_type == tokenize.STRING:
+                text = mutate_string(text)
+            if previous_row:
+                (start_row, start_column) = start
+                if previous_row != start_row:
+                    row_index = previous_row - 1
+                    column_index = previous_column - 1
+                    previous_text = self.lines[row_index][column_index]
+                    if (previous_text == ',' or
+                            (previous_text not in '{[(' and
+                             text not in '}])')):
+                        text = ' ' + text
+                elif previous_column != start_column:
+                    text = line[previous_column:start_column] + text
+            logical.append(text)
+            length += len(text)
+            mapping.append((length, end))
+            (previous_row, previous_column) = end
+        return comments, logical, mapping
+
+    def build_ast(self):
+        """Build an abstract syntax tree from the list of lines."""
+        return compile(''.join(self.lines), '', 'exec', PyCF_ONLY_AST)
+
+    def build_logical_line(self):
+        """Build a logical line from the current tokens list."""
+        comments, logical, mapping_list = self.build_logical_line_tokens()
+        self.logical_line = ''.join(logical)
+        self.statistics['logical lines'] += 1
+        return ''.join(comments), self.logical_line, mapping_list
+
+    def split_line(self, token):
+        """Split a physical line's line based on new-lines.
+
+        This also auto-increments the line number for the caller.
+        """
+        for line in token[1].split('\n')[:-1]:
+            yield line
+            self.line_number += 1
+
+    def keyword_arguments_for(self, parameters, arguments=None):
+        """Generate the keyword arguments for a list of parameters."""
+        if arguments is None:
+            arguments = {}
+        for param in parameters:
+            if param in arguments:
+                continue
+            try:
+                arguments[param] = getattr(self, param)
+            except AttributeError as exc:
+                LOG.exception(exc)
+                raise
+        return arguments
+
+    def check_physical_error(self, error_code, line):
+        """Update attributes based on error code and line."""
+        if error_code == 'E101':
+            self.indent_char = line[0]
+
+    def generate_tokens(self):
+        """Tokenize the file and yield the tokens.
+
+        :raises flake8.exceptions.InvalidSyntax:
+            If a :class:`tokenize.TokenError` is raised while generating
+            tokens.
+        """
+        try:
+            for token in tokenize.generate_tokens(self.next_line):
+                if token[2][0] > self.total_lines:
+                    break
+                self.tokens.append(token)
+                yield token
+        # NOTE(sigmavirus24): pycodestyle was catching both a SyntaxError
+        # and a tokenize.TokenError. In looking a the source on Python 2 and
+        # Python 3, the SyntaxError should never arise from generate_tokens.
+        # If we were using tokenize.tokenize, we would have to catch that. Of
+        # course, I'm going to be unsurprised to be proven wrong at a later
+        # date.
+        except tokenize.TokenError as exc:
+            raise exceptions.InvalidSyntax(exc.message, exception=exc)
+
+    def line_for(self, line_number):
+        """Retrieve the physical line at the specified line number."""
+        return self.lines[line_number - 1]
+
+    def next_line(self):
+        """Get the next line from the list."""
+        if self.line_number >= self.total_lines:
+            return ''
+        line = self.lines[self.line_number]
+        self.line_number += 1
+        if self.indent_char is None and line[:1] in defaults.WHITESPACE:
+            self.indent_char = line[0]
+        return line
+
+    def read_lines(self):
+        # type: () -> List[str]
+        """Read the lines for this file checker."""
+        if self.filename is None or self.filename == '-':
+            self.filename = 'stdin'
+            return self.read_lines_from_stdin()
+        return self.read_lines_from_filename()
+
+    def _readlines_py2(self):
+        # type: () -> List[str]
+        with open(self.filename, 'rU') as fd:
+            return fd.readlines()
+
+    def _readlines_py3(self):
+        # type: () -> List[str]
+        try:
+            with open(self.filename, 'rb') as fd:
+                (coding, lines) = tokenize.detect_encoding(fd.readline)
+                textfd = io.TextIOWrapper(fd, coding, line_buffering=True)
+                return ([l.decode(coding) for l in lines] +
+                        textfd.readlines())
+        except (LookupError, SyntaxError, UnicodeError):
+            # If we can't detect the codec with tokenize.detect_encoding, or
+            # the detected encoding is incorrect, just fallback to latin-1.
+            with open(self.filename, encoding='latin-1') as fd:
+                return fd.readlines()
+
+    def read_lines_from_filename(self):
+        # type: () -> List[str]
+        """Read the lines for a file."""
+        if (2, 6) <= sys.version_info < (3, 0):
+            readlines = self._readlines_py2
+        elif (3, 0) <= sys.version_info < (4, 0):
+            readlines = self._readlines_py3
+        return readlines()
+
+    def read_lines_from_stdin(self):
+        # type: () -> List[str]
+        """Read the lines from standard in."""
+        return utils.stdin_get_value().splitlines(True)
+
+    def should_ignore_file(self):
+        # type: () -> bool
+        """Check if ``# flake8: noqa`` is in the file to be ignored.
+
+        :returns:
+            True if a line matches :attr:`FileProcessor.NOQA_FILE`,
+            otherwise False
+        :rtype:
+            bool
+        """
+        ignore_file = self.NOQA_FILE.search
+        return any(ignore_file(line) for line in self.lines)
+
+    def strip_utf_bom(self):
+        # type: () -> NoneType
+        """Strip the UTF bom from the lines of the file."""
+        if not self.lines:
+            # If we have nothing to analyze quit early
+            return
+
+        first_byte = ord(self.lines[0][0])
+        if first_byte not in (0xEF, 0xFEFF):
+            return
+
+        # If the first byte of the file is a UTF-8 BOM, strip it
+        if first_byte == 0xFEFF:
+            self.lines[0] = self.lines[0][1:]
+        elif self.lines[0][:3] == '\xEF\xBB\xBF':
+            self.lines[0] = self.lines[0][3:]
+
+
+def is_eol_token(token):
+    """Check if the token is an end-of-line token."""
+    return token[0] in NEWLINE or token[4][token[3][1]:].lstrip() == '\\\n'
+
+if COMMENT_WITH_NL:  # If on Python 2.6
+    def is_eol_token(token, _is_eol_token=is_eol_token):
+        """Check if the token is an end-of-line token."""
+        return (_is_eol_token(token) or
+                (token[0] == tokenize.COMMENT and token[1] == token[4]))
+
+
+def is_multiline_string(token):
+    """Check if this is a multiline string."""
+    return token[0] == tokenize.STRING and '\n' in token[1]
+
+
+def token_is_newline(token):
+    """Check if the token type is a newline token type."""
+    return token[0] in NEWLINE
+
+
+def token_is_comment(token):
+    """Check if the token type is a comment."""
+    return COMMENT_WITH_NL and token[0] == tokenize.COMMENT
+
+
+def count_parentheses(current_parentheses_count, token_text):
+    """Count the number of parentheses."""
+    current_parentheses_count = current_parentheses_count or 0
+    if token_text in '([{':
+        return current_parentheses_count + 1
+    elif token_text in '}])':
+        return current_parentheses_count - 1
+    return current_parentheses_count
+
+
+def log_token(log, token):
+    """Log a token to a provided logging object."""
+    if token[2][0] == token[3][0]:
+        pos = '[%s:%s]' % (token[2][1] or '', token[3][1])
+    else:
+        pos = 'l.%s' % token[3][0]
+    log.log(flake8._EXTRA_VERBOSE, 'l.%s\t%s\t%s\t%r' %
+            (token[2][0], pos, tokenize.tok_name[token[0]],
+                token[1]))
+
+
+# NOTE(sigmavirus24): This was taken wholesale from
+# https://github.com/PyCQA/pycodestyle
+def expand_indent(line):
+    r"""Return the amount of indentation.
+
+    Tabs are expanded to the next multiple of 8.
+
+    >>> expand_indent('    ')
+    4
+    >>> expand_indent('\t')
+    8
+    >>> expand_indent('       \t')
+    8
+    >>> expand_indent('        \t')
+    16
+    """
+    if '\t' not in line:
+        return len(line) - len(line.lstrip())
+    result = 0
+    for char in line:
+        if char == '\t':
+            result = result // 8 * 8 + 8
+        elif char == ' ':
+            result += 1
+        else:
+            break
+    return result
+
+
+# NOTE(sigmavirus24): This was taken wholesale from
+# https://github.com/PyCQA/pycodestyle. The in-line comments were edited to be
+# more descriptive.
+def mutate_string(text):
+    """Replace contents with 'xxx' to prevent syntax matching.
+
+    >>> mute_string('"abc"')
+    '"xxx"'
+    >>> mute_string("'''abc'''")
+    "'''xxx'''"
+    >>> mute_string("r'abc'")
+    "r'xxx'"
+    """
+    # NOTE(sigmavirus24): If there are string modifiers (e.g., b, u, r)
+    # use the last "character" to determine if we're using single or double
+    # quotes and then find the first instance of it
+    start = text.index(text[-1]) + 1
+    end = len(text) - 1
+    # Check for triple-quoted strings
+    if text[-3:] in ('"""', "'''"):
+        start += 2
+        end -= 2
+    return text[:start] + 'x' * (end - start) + text[end:]
diff --git a/src/flake8/style_guide.py b/src/flake8/style_guide.py
new file mode 100644
index 0000000..89890ba
--- /dev/null
+++ b/src/flake8/style_guide.py
@@ -0,0 +1,283 @@
+"""Implementation of the StyleGuide used by Flake8."""
+import collections
+import enum
+import linecache
+import logging
+import re
+
+from flake8 import utils
+
+__all__ = (
+    'StyleGuide',
+)
+
+LOG = logging.getLogger(__name__)
+
+
+# TODO(sigmavirus24): Determine if we need to use enum/enum34
+class Selected(enum.Enum):
+    """Enum representing an explicitly or implicitly selected code."""
+
+    Explicitly = 'explicitly selected'
+    Implicitly = 'implicitly selected'
+
+
+class Ignored(enum.Enum):
+    """Enum representing an explicitly or implicitly ignored code."""
+
+    Explicitly = 'explicitly ignored'
+    Implicitly = 'implicitly ignored'
+
+
+class Decision(enum.Enum):
+    """Enum representing whether a code should be ignored or selected."""
+
+    Ignored = 'ignored error'
+    Selected = 'selected error'
+
+
+Error = collections.namedtuple(
+    'Error',
+    [
+        'code',
+        'filename',
+        'line_number',
+        'column_number',
+        'text',
+        'physical_line',
+    ],
+)
+
+
+class StyleGuide(object):
+    """Manage a Flake8 user's style guide."""
+
+    NOQA_INLINE_REGEXP = re.compile(
+        # We're looking for items that look like this:
+        # ``# noqa``
+        # ``# noqa: E123``
+        # ``# noqa: E123,W451,F921``
+        # ``# NoQA: E123,W451,F921``
+        # ``# NOQA: E123,W451,F921``
+        # We do not care about the ``: `` that follows ``noqa``
+        # We do not care about the casing of ``noqa``
+        # We want a comma-separated list of errors
+        '# noqa(?:: )?(?P<codes>[A-Z0-9,]+)?$',
+        re.IGNORECASE
+    )
+
+    def __init__(self, options, listener_trie, formatter):
+        """Initialize our StyleGuide.
+
+        .. todo:: Add parameter documentation.
+        """
+        self.options = options
+        self.listener = listener_trie
+        self.formatter = formatter
+        self._selected = tuple(options.select)
+        self._ignored = tuple(options.ignore)
+        self._decision_cache = {}
+        self._parsed_diff = {}
+
+    def is_user_selected(self, code):
+        # type: (str) -> Union[Selected, Ignored]
+        """Determine if the code has been selected by the user.
+
+        :param str code:
+            The code for the check that has been run.
+        :returns:
+            Selected.Implicitly if the selected list is empty,
+            Selected.Explicitly if the selected list is not empty and a match
+            was found,
+            Ignored.Implicitly if the selected list is not empty but no match
+            was found.
+        """
+        if not self._selected:
+            return Selected.Implicitly
+
+        if code.startswith(self._selected):
+            return Selected.Explicitly
+
+        return Ignored.Implicitly
+
+    def is_user_ignored(self, code):
+        # type: (str) -> Union[Selected, Ignored]
+        """Determine if the code has been ignored by the user.
+
+        :param str code:
+            The code for the check that has been run.
+        :returns:
+            Selected.Implicitly if the ignored list is empty,
+            Ignored.Explicitly if the ignored list is not empty and a match was
+            found,
+            Selected.Implicitly if the ignored list is not empty but no match
+            was found.
+        """
+        if self._ignored and code.startswith(self._ignored):
+            return Ignored.Explicitly
+
+        return Selected.Implicitly
+
+    def _decision_for(self, code):
+        # type: (Error) -> Decision
+        startswith = code.startswith
+        selected = sorted([s for s in self._selected if startswith(s)])[0]
+        ignored = sorted([i for i in self._ignored if startswith(i)])[0]
+
+        if selected.startswith(ignored):
+            return Decision.Selected
+        return Decision.Ignored
+
+    def should_report_error(self, code):
+        # type: (str) -> Decision
+        """Determine if the error code should be reported or ignored.
+
+        This method only cares about the select and ignore rules as specified
+        by the user in their configuration files and command-line flags.
+
+        This method does not look at whether the specific line is being
+        ignored in the file itself.
+
+        :param str code:
+            The code for the check that has been run.
+        """
+        decision = self._decision_cache.get(code)
+        if decision is None:
+            LOG.debug('Deciding if "%s" should be reported', code)
+            selected = self.is_user_selected(code)
+            ignored = self.is_user_ignored(code)
+            LOG.debug('The user configured "%s" to be "%s", "%s"',
+                      code, selected, ignored)
+
+            if ((selected is Selected.Explicitly or
+                 selected is Selected.Implicitly) and
+                    ignored is Selected.Implicitly):
+                decision = Decision.Selected
+            elif (selected is Selected.Explicitly and
+                  ignored is Ignored.Explicitly):
+                decision = self._decision_for(code)
+            elif (selected is Ignored.Implicitly or
+                  ignored is Ignored.Explicitly):
+                decision = Decision.Ignored  # pylint: disable=R0204
+
+            self._decision_cache[code] = decision
+            LOG.debug('"%s" will be "%s"', code, decision)
+        return decision
+
+    def is_inline_ignored(self, error):
+        # type: (Error) -> bool
+        """Determine if an comment has been added to ignore this line."""
+        physical_line = error.physical_line
+        # TODO(sigmavirus24): Determine how to handle stdin with linecache
+        if self.options.disable_noqa:
+            return False
+
+        if physical_line is None:
+            physical_line = linecache.getline(error.filename,
+                                              error.line_number)
+        noqa_match = self.NOQA_INLINE_REGEXP.search(physical_line)
+        if noqa_match is None:
+            LOG.debug('%r is not inline ignored', error)
+            return False
+
+        codes_str = noqa_match.groupdict()['codes']
+        if codes_str is None:
+            LOG.debug('%r is ignored by a blanket ``# noqa``', error)
+            return True
+
+        codes = set(utils.parse_comma_separated_list(codes_str))
+        if error.code in codes or error.code.startswith(tuple(codes)):
+            LOG.debug('%r is ignored specifically inline with ``# noqa: %s``',
+                      error, codes_str)
+            return True
+
+        LOG.debug('%r is not ignored inline with ``# noqa: %s``',
+                  error, codes_str)
+        return False
+
+    def is_in_diff(self, error):
+        # type: (Error) -> bool
+        """Determine if an error is included in a diff's line ranges.
+
+        This function relies on the parsed data added via
+        :meth:`~StyleGuide.add_diff_ranges`. If that has not been called and
+        we are not evaluating files in a diff, then this will always return
+        True. If there are diff ranges, then this will return True if the
+        line number in the error falls inside one of the ranges for the file
+        (and assuming the file is part of the diff data). If there are diff
+        ranges, this will return False if the file is not part of the diff
+        data or the line number of the error is not in any of the ranges of
+        the diff.
+
+        :returns:
+            True if there is no diff or if the error is in the diff's line
+            number ranges. False if the error's line number falls outside
+            the diff's line number ranges.
+        :rtype:
+            bool
+        """
+        if not self._parsed_diff:
+            return True
+
+        # NOTE(sigmavirus24): The parsed diff will be a defaultdict with
+        # a set as the default value (if we have received it from
+        # flake8.utils.parse_unified_diff). In that case ranges below
+        # could be an empty set (which is False-y) or if someone else
+        # is using this API, it could be None. If we could guarantee one
+        # or the other, we would check for it more explicitly.
+        line_numbers = self._parsed_diff.get(error.filename)
+        if not line_numbers:
+            return False
+
+        return error.line_number in line_numbers
+
+    def handle_error(self, code, filename, line_number, column_number, text,
+                     physical_line=None):
+        # type: (str, str, int, int, str) -> int
+        """Handle an error reported by a check.
+
+        :param str code:
+            The error code found, e.g., E123.
+        :param str filename:
+            The file in which the error was found.
+        :param int line_number:
+            The line number (where counting starts at 1) at which the error
+            occurs.
+        :param int column_number:
+            The column number (where counting starts at 1) at which the error
+            occurs.
+        :param str text:
+            The text of the error message.
+        :param str physical_line:
+            The actual physical line causing the error.
+        :returns:
+            1 if the error was reported. 0 if it was ignored. This is to allow
+            for counting of the number of errors found that were not ignored.
+        :rtype:
+            int
+        """
+        error = Error(code, filename, line_number, column_number, text,
+                      physical_line)
+        if error.filename is None or error.filename == '-':
+            error = error._replace(filename=self.options.stdin_display_name)
+        error_is_selected = (self.should_report_error(error.code) is
+                             Decision.Selected)
+        is_not_inline_ignored = self.is_inline_ignored(error) is False
+        is_included_in_diff = self.is_in_diff(error)
+        if (error_is_selected and is_not_inline_ignored and
+                is_included_in_diff):
+            self.formatter.handle(error)
+            self.listener.notify(error.code, error)
+            return 1
+        return 0
+
+    def add_diff_ranges(self, diffinfo):
+        """Update the StyleGuide to filter out information not in the diff.
+
+        This provides information to the StyleGuide so that only the errors
+        in the line number ranges are reported.
+
+        :param dict diffinfo:
+            Dictionary mapping filenames to sets of line number ranges.
+        """
+        self._parsed_diff = diffinfo
diff --git a/src/flake8/utils.py b/src/flake8/utils.py
new file mode 100644
index 0000000..597dea6
--- /dev/null
+++ b/src/flake8/utils.py
@@ -0,0 +1,279 @@
+"""Utility methods for flake8."""
+import collections
+import fnmatch as _fnmatch
+import inspect
+import io
+import os
+import re
+import sys
+
+DIFF_HUNK_REGEXP = re.compile(r'^@@ -\d+(?:,\d+)? \+(\d+)(?:,(\d+))? @@.*$')
+
+
+def parse_comma_separated_list(value):
+    # type: (Union[Sequence[str], str]) -> List[str]
+    """Parse a comma-separated list.
+
+    :param value:
+        String or list of strings to be parsed and normalized.
+    :returns:
+        List of values with whitespace stripped.
+    :rtype:
+        list
+    """
+    if not value:
+        return []
+
+    if not isinstance(value, (list, tuple)):
+        value = value.split(',')
+
+    return [item.strip() for item in value]
+
+
+def normalize_paths(paths, parent=os.curdir):
+    # type: (Union[Sequence[str], str], str) -> List[str]
+    """Parse a comma-separated list of paths.
+
+    :returns:
+        The normalized paths.
+    :rtype:
+        [str]
+    """
+    return [normalize_path(p, parent)
+            for p in parse_comma_separated_list(paths)]
+
+
+def normalize_path(path, parent=os.curdir):
+    # type: (str, str) -> str
+    """Normalize a single-path.
+
+    :returns:
+        The normalized path.
+    :rtype:
+        str
+    """
+    # NOTE(sigmavirus24): Using os.path.sep allows for Windows paths to
+    # be specified and work appropriately.
+    separator = os.path.sep
+    if separator in path:
+        path = os.path.abspath(os.path.join(parent, path))
+    return path.rstrip(separator)
+
+
+def stdin_get_value():
+    # type: () -> str
+    """Get and cache it so plugins can use it."""
+    cached_value = getattr(stdin_get_value, 'cached_stdin', None)
+    if cached_value is None:
+        stdin_value = sys.stdin.read()
+        if sys.version_info < (3, 0):
+            cached_type = io.BytesIO
+        else:
+            cached_type = io.StringIO
+        stdin_get_value.cached_stdin = cached_type(stdin_value)
+        cached_value = stdin_get_value.cached_stdin
+    return cached_value.getvalue()
+
+
+def parse_unified_diff(diff=None):
+    # type: (str) -> List[str]
+    """Parse the unified diff passed on stdin.
+
+    :returns:
+        dictionary mapping file names to sets of line numbers
+    :rtype:
+        dict
+    """
+    # Allow us to not have to patch out stdin_get_value
+    if diff is None:
+        diff = stdin_get_value()
+
+    number_of_rows = None
+    current_path = None
+    parsed_paths = collections.defaultdict(set)
+    for line in diff.splitlines():
+        if number_of_rows:
+            # NOTE(sigmavirus24): Below we use a slice because stdin may be
+            # bytes instead of text on Python 3.
+            if line[:1] != '-':
+                number_of_rows -= 1
+            # We're in the part of the diff that has lines starting with +, -,
+            # and ' ' to show context and the changes made. We skip these
+            # because the information we care about is the filename and the
+            # range within it.
+            # When number_of_rows reaches 0, we will once again start
+            # searching for filenames and ranges.
+            continue
+
+        # NOTE(sigmavirus24): Diffs that we support look roughly like:
+        #    diff a/file.py b/file.py
+        #    ...
+        #    --- a/file.py
+        #    +++ b/file.py
+        # Below we're looking for that last line. Every diff tool that
+        # gives us this output may have additional information after
+        # ``b/file.py`` which it will separate with a \t, e.g.,
+        #    +++ b/file.py\t100644
+        # Which is an example that has the new file permissions/mode.
+        # In this case we only care about the file name.
+        if line[:3] == '+++':
+            current_path = line[4:].split('\t', 1)[0]
+            # NOTE(sigmavirus24): This check is for diff output from git.
+            if current_path[:2] == 'b/':
+                current_path = current_path[2:]
+            # We don't need to do anything else. We have set up our local
+            # ``current_path`` variable. We can skip the rest of this loop.
+            # The next line we will see will give us the hung information
+            # which is in the next section of logic.
+            continue
+
+        hunk_match = DIFF_HUNK_REGEXP.match(line)
+        # NOTE(sigmavirus24): pep8/pycodestyle check for:
+        #    line[:3] == '@@ '
+        # But the DIFF_HUNK_REGEXP enforces that the line start with that
+        # So we can more simply check for a match instead of slicing and
+        # comparing.
+        if hunk_match:
+            (row, number_of_rows) = [
+                1 if not group else int(group)
+                for group in hunk_match.groups()
+            ]
+            parsed_paths[current_path].update(
+                range(row, row + number_of_rows)
+            )
+
+    # We have now parsed our diff into a dictionary that looks like:
+    #    {'file.py': set(range(10, 16), range(18, 20)), ...}
+    return parsed_paths
+
+
+def is_windows():
+    # type: () -> bool
+    """Determine if we're running on Windows.
+
+    :returns:
+        True if running on Windows, otherwise False
+    :rtype:
+        bool
+    """
+    return os.name == 'nt'
+
+
+def can_run_multiprocessing_on_windows():
+    # type: () -> bool
+    """Determine if we can use multiprocessing on Windows.
+
+    :returns:
+        True if the version of Python is modern enough, otherwise False
+    :rtype:
+        bool
+    """
+    is_new_enough_python27 = sys.version_info >= (2, 7, 11)
+    is_new_enough_python3 = sys.version_info > (3, 2)
+    return is_new_enough_python27 or is_new_enough_python3
+
+
+def is_using_stdin(paths):
+    # type: (List[str]) -> bool
+    """Determine if we're going to read from stdin.
+
+    :param list paths:
+        The paths that we're going to check.
+    :returns:
+        True if stdin (-) is in the path, otherwise False
+    :rtype:
+        bool
+    """
+    return '-' in paths
+
+
+def _default_predicate(*args):
+    return False
+
+
+def filenames_from(arg, predicate=None):
+    # type: (str, callable) -> Generator
+    """Generate filenames from an argument.
+
+    :param str arg:
+        Parameter from the command-line.
+    :param callable predicate:
+        Predicate to use to filter out filenames. If the predicate
+        returns ``True`` we will exclude the filename, otherwise we
+        will yield it. By default, we include every filename
+        generated.
+    :returns:
+        Generator of paths
+    """
+    if predicate is None:
+        predicate = _default_predicate
+    if os.path.isdir(arg):
+        for root, sub_directories, files in os.walk(arg):
+            for filename in files:
+                joined = os.path.join(root, filename)
+                if predicate(joined):
+                    continue
+                yield joined
+            # NOTE(sigmavirus24): os.walk() will skip a directory if you
+            # remove it from the list of sub-directories.
+            for directory in sub_directories:
+                if predicate(directory):
+                    sub_directories.remove(directory)
+    else:
+        yield arg
+
+
+def fnmatch(filename, patterns, default=True):
+    # type: (str, List[str], bool) -> bool
+    """Wrap :func:`fnmatch.fnmatch` to add some functionality.
+
+    :param str filename:
+        Name of the file we're trying to match.
+    :param list patterns:
+        Patterns we're using to try to match the filename.
+    :param bool default:
+        The default value if patterns is empty
+    :returns:
+        True if a pattern matches the filename, False if it doesn't.
+        ``default`` if patterns is empty.
+    """
+    if not patterns:
+        return default
+    return any(_fnmatch.fnmatch(filename, pattern) for pattern in patterns)
+
+
+def parameters_for(plugin):
+    # type: (flake8.plugins.manager.Plugin) -> List[str]
+    """Return the parameters for the plugin.
+
+    This will inspect the plugin and return either the function parameters
+    if the plugin is a function or the parameters for ``__init__`` after
+    ``self`` if the plugin is a class.
+
+    :param plugin:
+        The internal plugin object.
+    :type plugin:
+        flake8.plugins.manager.Plugin
+    :returns:
+        Parameters to the plugin.
+    :rtype:
+        list(str)
+    """
+    func = plugin.plugin
+    is_class = not inspect.isfunction(func)
+    if is_class:  # The plugin is a class
+        func = plugin.plugin.__init__
+
+    if sys.version_info < (3, 3):
+        parameters = inspect.getargspec(func)[0]
+    else:
+        parameters = [
+            parameter.name
+            for parameter in inspect.signature(func).parameters.values()
+            if parameter.kind == parameter.POSITIONAL_OR_KEYWORD
+        ]
+
+    if is_class:
+        parameters.remove('self')
+
+    return parameters