cygwin python checking should happen after setup code
Regressed as part of #436

Before:

```
$ ./pre-commit/venv_cygwin_python/bin/pre-commit clean
An error has occurred: FatalError: git failed. Is it installed, and are you in a Git repository directory?
Check the log at ~/.pre-commit/pre-commit.log
```

Current master:

```
$ ./pre-commit/venv_cygwin_python/bin/pre-commit clean
An unexpected error has occurred: CalledProcessError: Command: ('/usr/bin/git', 'rev-parse', '--show-toplevel')
Return code: 128
Expected return code: 0
Output: (none)
Errors:
    fatal: Not a git repository (or any of the parent directories): .git


Check the log at ~/.pre-commit/pre-commit.log
```
diff --git a/pre_commit/main.py b/pre_commit/main.py
index 4bcd153..9d9329a 100644
--- a/pre_commit/main.py
+++ b/pre_commit/main.py
@@ -152,8 +152,8 @@ def main(argv=None):
 
     with error_handler():
         add_logging_handler(args.color)
-        git.check_for_cygwin_mismatch()
         runner = Runner.create()
+        git.check_for_cygwin_mismatch()
 
         if args.command == 'install':
             return install(
diff --git a/tests/main_test.py b/tests/main_test.py
index 537ff23..86b6dcd 100644
--- a/tests/main_test.py
+++ b/tests/main_test.py
@@ -7,6 +7,7 @@ import mock
 import pytest
 
 from pre_commit import main
+from pre_commit.error_handler import PreCommitSystemExit
 from pre_commit.util import cwd
 from testing.auto_namedtuple import auto_namedtuple
 
@@ -142,3 +143,16 @@ def test_help_cmd_in_empty_directory(
         mock.call(['help', 'run']),
         mock.call(['run', '--help']),
     ])
+
+
+def test_expected_fatal_error_no_git_repo(
+        tempdir_factory, cap_out, mock_out_store_directory,
+):
+    with cwd(tempdir_factory.get()):
+        with pytest.raises(PreCommitSystemExit):
+            main.main([])
+    assert cap_out.get() == (
+        'An error has occurred: FatalError: git failed. '
+        'Is it installed, and are you in a Git repository directory?\\n'
+        'Check the log at ~/.pre-commit/pre-commit.log\\n'
+    )
['pre_commit/main.py', 'tests/main_test.py']