@@ -112,14 +112,14 @@ def _write_new_config_file(path, output):
         f.write(to_write)
 
 
-def autoupdate(runner, store, tags_only, repos=()):
+def autoupdate(config_file, store, tags_only, repos=()):
     """Auto-update the pre-commit config to the latest versions of repos."""
-    migrate_config(runner, quiet=True)
+    migrate_config(config_file, quiet=True)
     retv = 0
     output_repos = []
     changed = False
 
-    input_config = load_config(runner.config_file_path)
+    input_config = load_config(config_file)
 
     for repo_config in input_config['repos']:
         if (
@@ -152,6 +152,6 @@ def autoupdate(runner, store, tags_only, repos=()):
     if changed:
         output_config = input_config.copy()
         output_config['repos'] = output_repos
-        _write_new_config_file(runner.config_file_path, output_config)
+        _write_new_config_file(config_file, output_config)
 
     return retv
@@ -8,6 +8,7 @@
 
 from pre_commit import git
 from pre_commit import output
+from pre_commit.clientlib import load_config
 from pre_commit.languages import python
 from pre_commit.repository import repositories
 from pre_commit.util import cmd_output
@@ -31,8 +32,8 @@
 TEMPLATE_END = '# end templated\n'
 
 
-def _hook_paths(git_root, hook_type):
-    pth = os.path.join(git.get_git_dir(git_root), 'hooks', hook_type)
+def _hook_paths(hook_type):
+    pth = os.path.join(git.get_git_dir(), 'hooks', hook_type)
     return pth, '{}.legacy'.format(pth)
 
 
@@ -55,7 +56,8 @@ def shebang():
 
 
 def install(
-        runner, store, overwrite=False, hooks=False, hook_type='pre-commit',
+        config_file, store,
+        overwrite=False, hooks=False, hook_type='pre-commit',
         skip_on_missing_conf=False,
 ):
     """Install the pre-commit hooks."""
@@ -66,7 +68,7 @@ def install(
         )
         return 1
 
-    hook_path, legacy_path = _hook_paths(runner.git_root, hook_type)
+    hook_path, legacy_path = _hook_paths(hook_type)
 
     mkdirp(os.path.dirname(hook_path))
 
@@ -84,7 +86,7 @@ def install(
         )
 
     params = {
-        'CONFIG': runner.config_file,
+        'CONFIG': config_file,
         'HOOK_TYPE': hook_type,
         'INSTALL_PYTHON': sys.executable,
         'SKIP_ON_MISSING_CONFIG': skip_on_missing_conf,
@@ -108,19 +110,19 @@ def install(
 
     # If they requested we install all of the hooks, do so.
     if hooks:
-        install_hooks(runner, store)
+        install_hooks(config_file, store)
 
     return 0
 
 
-def install_hooks(runner, store):
-    for repository in repositories(runner.config, store):
+def install_hooks(config_file, store):
+    for repository in repositories(load_config(config_file), store):
         repository.require_installed()
 
 
-def uninstall(runner, hook_type='pre-commit'):
+def uninstall(hook_type='pre-commit'):
     """Uninstall the pre-commit hooks."""
-    hook_path, legacy_path = _hook_paths(runner.git_root, hook_type)
+    hook_path, legacy_path = _hook_paths(hook_type)
 
     # If our file doesn't exist or it isn't ours, gtfo.
     if not os.path.exists(hook_path) or not is_our_script(hook_path):
 
@@ -45,15 +45,15 @@ def _migrate_sha_to_rev(contents):
     return reg.sub(r'\1rev:', contents)
 
 
-def migrate_config(runner, quiet=False):
-    with io.open(runner.config_file_path) as f:
+def migrate_config(config_file, quiet=False):
+    with io.open(config_file) as f:
         orig_contents = contents = f.read()
 
     contents = _migrate_map(contents)
     contents = _migrate_sha_to_rev(contents)
 
     if contents != orig_contents:
-        with io.open(runner.config_file_path, 'w') as f:
+        with io.open(config_file, 'w') as f:
             f.write(contents)
 
         print('Configuration has been migrated.')
 
@@ -11,6 +11,7 @@
 from pre_commit import color
 from pre_commit import git
 from pre_commit import output
+from pre_commit.clientlib import load_config
 from pre_commit.output import get_hook_message
 from pre_commit.repository import repositories
 from pre_commit.staged_files_only import staged_files_only
@@ -214,16 +215,16 @@ def _has_unmerged_paths():
     return bool(stdout.strip())
 
 
-def _has_unstaged_config(runner):
+def _has_unstaged_config(config_file):
     retcode, _, _ = cmd_output(
-        'git', 'diff', '--no-ext-diff', '--exit-code', runner.config_file_path,
+        'git', 'diff', '--no-ext-diff', '--exit-code', config_file,
         retcode=None,
     )
     # be explicit, other git errors don't mean it has an unstaged config.
     return retcode == 1
 
 
-def run(runner, store, args, environ=os.environ):
+def run(config_file, store, args, environ=os.environ):
     no_stash = args.all_files or bool(args.files)
 
     # Check if we have unresolved merge conflict files and fail fast.
@@ -233,10 +234,10 @@ def run(runner, store, args, environ=os.environ):
     if bool(args.source) != bool(args.origin):
         logger.error('Specify both --origin and --source.')
         return 1
-    if _has_unstaged_config(runner) and not no_stash:
+    if _has_unstaged_config(config_file) and not no_stash:
         logger.error(
             'Your pre-commit configuration is unstaged.\n'
-            '`git add {}` to fix this.'.format(runner.config_file),
+            '`git add {}` to fix this.'.format(config_file),
         )
         return 1
 
@@ -252,7 +253,8 @@ def run(runner, store, args, environ=os.environ):
 
     with ctx:
         repo_hooks = []
-        for repo in repositories(runner.config, store):
+        config = load_config(config_file)
+        for repo in repositories(config, store):
             for _, hook in repo.hooks:
                 if (
                     (not args.hook or hook['id'] == args.hook) and
@@ -267,4 +269,4 @@ def run(runner, store, args, environ=os.environ):
         for repo in {repo for repo, _ in repo_hooks}:
             repo.require_installed()
 
-        return _run_hooks(runner.config, repo_hooks, args, environ)
+        return _run_hooks(config, repo_hooks, args, environ)
@@ -11,7 +11,6 @@
 from pre_commit import output
 from pre_commit.clientlib import load_manifest
 from pre_commit.commands.run import run
-from pre_commit.runner import Runner
 from pre_commit.store import Store
 from pre_commit.util import tmpdir
 
@@ -43,4 +42,4 @@ def try_repo(args):
         output.write(config_s)
         output.write_line('=' * 79)
 
-        return run(Runner('.', config_filename), store, args)
+        return run(config_filename, store, args)
@@ -30,7 +30,7 @@ def get_root():
         )
 
 
-def get_git_dir(git_root):
+def get_git_dir(git_root='.'):
     opts = ('--git-common-dir', '--git-dir')
     _, out, _ = cmd_output('git', 'rev-parse', *opts, cwd=git_root)
     for line, opt in zip(out.splitlines(), opts):
 
@@ -88,12 +88,12 @@ def _install_rbenv(prefix, version='default'):  # pragma: windows no cover
             activate_file.write('export RBENV_VERSION="{}"\n'.format(version))
 
 
-def _install_ruby(runner, version):  # pragma: windows no cover
+def _install_ruby(prefix, version):  # pragma: windows no cover
     try:
-        helpers.run_setup_cmd(runner, ('rbenv', 'download', version))
+        helpers.run_setup_cmd(prefix, ('rbenv', 'download', version))
     except CalledProcessError:  # pragma: no cover (usually find with download)
         # Failed to download from mirror for some reason, build it instead
-        helpers.run_setup_cmd(runner, ('rbenv', 'install', version))
+        helpers.run_setup_cmd(prefix, ('rbenv', 'install', version))
 
 
 def install_environment(
 
@@ -20,7 +20,6 @@
 from pre_commit.commands.try_repo import try_repo
 from pre_commit.error_handler import error_handler
 from pre_commit.logging_handler import add_logging_handler
-from pre_commit.runner import Runner
 from pre_commit.store import Store
 
 
@@ -89,6 +88,20 @@ def _add_run_options(parser):
     )
 
 
+def _adjust_args_and_chdir(args):
+    # `--config` was specified relative to the non-root working directory
+    if os.path.exists(args.config):
+        args.config = os.path.abspath(args.config)
+    if args.command in {'run', 'try-repo'}:
+        args.files = [os.path.abspath(filename) for filename in args.files]
+
+    os.chdir(git.get_root())
+
+    args.config = os.path.relpath(args.config)
+    if args.command in {'run', 'try-repo'}:
+        args.files = [os.path.relpath(filename) for filename in args.files]
+
+
 def main(argv=None):
     argv = argv if argv is not None else sys.argv[1:]
     argv = [five.to_text(arg) for arg in argv]
@@ -222,43 +235,40 @@ def main(argv=None):
         parser.parse_args([args.help_cmd, '--help'])
     elif args.command == 'help':
         parser.parse_args(['--help'])
-    elif args.command in {'run', 'try-repo'}:
-        args.files = [
-            os.path.relpath(os.path.abspath(filename), git.get_root())
-            for filename in args.files
-        ]
 
     with error_handler():
         add_logging_handler(args.color)
-        runner = Runner.create(args.config)
+
+        _adjust_args_and_chdir(args)
+
         store = Store()
         git.check_for_cygwin_mismatch()
 
         if args.command == 'install':
             return install(
-                runner, store,
+                args.config, store,
                 overwrite=args.overwrite, hooks=args.install_hooks,
                 hook_type=args.hook_type,
                 skip_on_missing_conf=args.allow_missing_config,
             )
         elif args.command == 'install-hooks':
-            return install_hooks(runner, store)
+            return install_hooks(args.config, store)
         elif args.command == 'uninstall':
-            return uninstall(runner, hook_type=args.hook_type)
+            return uninstall(hook_type=args.hook_type)
         elif args.command == 'clean':
             return clean(store)
         elif args.command == 'autoupdate':
             if args.tags_only:
                 logger.warning('--tags-only is the default')
             return autoupdate(
-                runner, store,
+                args.config, store,
                 tags_only=not args.bleeding_edge,
                 repos=args.repos,
             )
         elif args.command == 'migrate-config':
-            return migrate_config(runner)
+            return migrate_config(args.config)
         elif args.command == 'run':
-            return run(runner, store, args)
+            return run(args.config, store, args)
         elif args.command == 'sample-config':
             return sample_config()
         elif args.command == 'try-repo':
Original file line number	Diff line number	Diff line change
@@ -30,7 +30,7 @@ def get_root():
30	30	)
31	31
32	32
33		- def get_git_dir(git_root):
	33	+ def get_git_dir(git_root='.'):
34	34	opts = ('--git-common-dir', '--git-dir')
35	35	_, out, _ = cmd_output('git', 'rev-parse', *opts, cwd=git_root)
36	36	for line, opt in zip(out.splitlines(), opts):