diff --git a/bench/app.py b/bench/app.py
index 763446826..d8f559074 100755
--- a/bench/app.py
+++ b/bench/app.py
@@ -228,7 +228,7 @@ def pull_apps(apps=None, bench_path='.', reset=False):
 	rebase = '--rebase' if get_config(bench_path).get('rebase_on_pull') else ''
 
 	apps = apps or get_apps(bench_path=bench_path)
-	# chech for local changes
+	# check for local changes
 	if not reset:
 		for app in apps:
 			excluded_apps = get_excluded_apps()
@@ -271,9 +271,10 @@ def pull_apps(apps=None, bench_path='.', reset=False):
 				reset_cmd = "git reset --hard {remote}/{branch}".format(
 					remote=remote, branch=get_current_branch(app,bench_path=bench_path))
 				if get_config(bench_path).get('shallow_clone'):
-					exec_cmd("git fetch --depth 1 --no-tags", cwd=app_dir)
+					exec_cmd("git fetch --depth=1 --no-tags", cwd=app_dir)
 					exec_cmd(reset_cmd, cwd=app_dir)
-					exec_cmd("git clean -dfx", cwd=app_dir)
+					exec_cmd("git reflog expire --all", cwd=app_dir)
+					exec_cmd("git gc --prune=all", cwd=app_dir)
 				else:
 					exec_cmd("git fetch --all", cwd=app_dir)
 					exec_cmd(reset_cmd, cwd=app_dir)
@@ -284,20 +285,15 @@ def pull_apps(apps=None, bench_path='.', reset=False):
 
 
 def is_version_upgrade(app='frappe', bench_path='.', branch=None):
-	try:
-		fetch_upstream(app, bench_path=bench_path)
-	except CommandFailedError:
-		raise InvalidRemoteException("No remote named upstream for {0}".format(app))
-
 	upstream_version = get_upstream_version(app=app, branch=branch, bench_path=bench_path)
 
 	if not upstream_version:
-		raise InvalidBranchException("Specified branch of app {0} is not in upstream".format(app))
+		raise InvalidBranchException('Specified branch of app {0} is not in upstream remote'.format(app))
 
 	local_version = get_major_version(get_current_version(app, bench_path=bench_path))
 	upstream_version = get_major_version(upstream_version)
 
-	if upstream_version - local_version > 0:
+	if upstream_version > local_version:
 		return (True, local_version, upstream_version)
 
 	return (False, local_version, upstream_version)
@@ -330,10 +326,6 @@ def use_rq(bench_path):
 	celery_app = os.path.join(bench_path, 'apps', 'frappe', 'frappe', 'celery_app.py')
 	return not os.path.exists(celery_app)
 
-def fetch_upstream(app, bench_path='.'):
-	repo_dir = get_repo_dir(app, bench_path=bench_path)
-	return subprocess.call(["git", "fetch", "upstream"], cwd=repo_dir)
-
 def get_current_version(app, bench_path='.'):
 	repo_dir = get_repo_dir(app, bench_path=bench_path)
 	try:
@@ -352,10 +344,16 @@ def get_develop_version(app, bench_path='.'):
 
 def get_upstream_version(app, branch=None, bench_path='.'):
 	repo_dir = get_repo_dir(app, bench_path=bench_path)
+	try:
+		subprocess.call('git fetch --depth=1 --no-tags upstream', shell=True, cwd=repo_dir)
+	except CommandFailedError:
+		raise InvalidRemoteException('Failed to fetch from remote named upstream for {0}'.format(app))
+
 	if not branch:
 		branch = get_current_branch(app, bench_path=bench_path)
 	try:
-		contents = subprocess.check_output(['git', 'show', 'upstream/{branch}:{app}/__init__.py'.format(branch=branch, app=app)], cwd=repo_dir, stderr=subprocess.STDOUT)
+		contents = subprocess.check_output('git show upstream/{branch}:{app}/__init__.py'.format(branch=branch, app=app),
+			shell=True, cwd=repo_dir, stderr=subprocess.STDOUT)
 		contents = contents.decode('utf-8')
 	except subprocess.CalledProcessError as e:
 		if b"Invalid object" in e.output: