title: Flake8 config not being applied in git hook
body: <p>I have a <code>pre-commit</code> git hook that is supposed to hinder the commit if the added lines don't follow the specified style-guide.</p>
  
  <p>So in the root folder of my repo I have a <code>.flake8</code> file that looks like: </p>
  
  <pre><code>[flake8]
  
  ########## FORMATTING ##########
  # Print the total number of errors.
  #count =
  ## Print the source code generating the error/warning in question.
  #show-source =
  ## Count the number of occurrences of each error/warning code and print a report.
  #statistics =
  
  ########## OPTIONS ##########
  # Set the maximum length that any line (with some exceptions) may be.
  max-line-length = 90
  # Set the maximum allowed McCabe complexity value for a block of code.
  max-complexity = 10
  
  ########## RULES ##########
  ignore = D102,D103,E265
  
  ########## TARGETS ##########
  # Redirect all output to the specified file.
  #output-file = 
  ## Also print output to stdout if output-file has been configured.
  #tee = 
  </code></pre>
  
  <p>And my git hook that is under <code>.git/hooks/pre-commit</code> with full rights: <code>rwxrwxrwx</code> (I know not the safest).</p>
  
  <pre><code>#!/bin/sh
  #
  # Checks so that the file is correctly linted, before commiting.
  # Using the same linter settings as defined in the repo root .flake8
  #
  
  LINT=$(git diff -- '***.py' | py -3 -m flake8 --diff --config="../../.flake8")
  #LINT=$(git diff -- '***.py' | py -3 -m flake8 --diff --max-line-length=90)
  
  if [ -z "$LINT" ]
  then
          exit 0
  else
          echo "$LINT"
          exit 1
  fi
  </code></pre>
  
  <p>The hook works if I change the <code>LINT</code> variable to the out commented one. Then it marks the row that is to long. But If I specify my config file instead then it does not mark it.</p>
  
  <p>I think that the error is either that the <code>--config="../../.flake8</code> is somehow not correct. I'm running this on a windows machine under cygwin (so the path should be formatted correct, no?).</p>
  
  <p>Or that somehow my config file is wrong and thus it doesn't get applied.</p>