diff --git a/core/__init__.py b/core/__init__.py
index 8e726e48..50b283dd 100644
--- a/core/__init__.py
+++ b/core/__init__.py
@@ -23,20 +23,21 @@ except ImportError:
     if sys.platform == 'win32':
         sys.ext('Please install pywin32')
 
-PROGRAM_DIR = libs.util.module_root()
+APP_ROOT = libs.util.module_path(parent=True)
+SOURCE_ROOT = libs.util.module_path()
 
 # init preliminaries
 SYS_ARGV = sys.argv[1:]
 APP_FILENAME = sys.argv[0]
 APP_NAME = os.path.basename(APP_FILENAME)
-LOG_DIR = os.path.join(PROGRAM_DIR, 'logs')
+LOG_DIR = os.path.join(APP_ROOT, 'logs')
 LOG_FILE = os.path.join(LOG_DIR, 'nzbtomedia.log')
 PID_FILE = os.path.join(LOG_DIR, 'nzbtomedia.pid')
-CONFIG_FILE = os.path.join(PROGRAM_DIR, 'autoProcessMedia.cfg')
-CONFIG_SPEC_FILE = os.path.join(PROGRAM_DIR, 'autoProcessMedia.cfg.spec')
-CONFIG_MOVIE_FILE = os.path.join(PROGRAM_DIR, 'autoProcessMovie.cfg')
-CONFIG_TV_FILE = os.path.join(PROGRAM_DIR, 'autoProcessTv.cfg')
-TEST_FILE = os.path.join(PROGRAM_DIR, 'tests', 'test.mp4')
+CONFIG_FILE = os.path.join(APP_ROOT, 'autoProcessMedia.cfg')
+CONFIG_SPEC_FILE = os.path.join(APP_ROOT, 'autoProcessMedia.cfg.spec')
+CONFIG_MOVIE_FILE = os.path.join(APP_ROOT, 'autoProcessMovie.cfg')
+CONFIG_TV_FILE = os.path.join(APP_ROOT, 'autoProcessTv.cfg')
+TEST_FILE = os.path.join(APP_ROOT, 'tests', 'test.mp4')
 MYAPP = None
 
 import six
@@ -747,7 +748,7 @@ def initialize(section=None):
     if platform.system() == 'Windows':
         FFMPEG = os.path.join(FFMPEG_PATH, 'ffmpeg.exe')
         FFPROBE = os.path.join(FFMPEG_PATH, 'ffprobe.exe')
-        SEVENZIP = os.path.join(PROGRAM_DIR, 'core', 'extractor', 'bin', platform.machine(), '7z.exe')
+        SEVENZIP = os.path.join(APP_ROOT, 'core', 'extractor', 'bin', platform.machine(), '7z.exe')
         SHOWEXTRACT = int(str(CFG["Windows"]["show_extraction"]), 0)
 
         if not (os.path.isfile(FFMPEG)):  # problem
diff --git a/core/extractor/__init__.py b/core/extractor/__init__.py
index 4796bb3e..a1ed8457 100644
--- a/core/extractor/__init__.py
+++ b/core/extractor/__init__.py
@@ -19,7 +19,7 @@ def extract(file_path, output_destination):
             core.logger.error("EXTRACTOR: Could not find 7-zip, Exiting")
             return False
         wscriptlocation = os.path.join(os.environ['WINDIR'], 'system32', 'wscript.exe')
-        invislocation = os.path.join(core.PROGRAM_DIR, 'core', 'extractor', 'bin', 'invisible.vbs')
+        invislocation = os.path.join(core.APP_ROOT, 'core', 'extractor', 'bin', 'invisible.vbs')
         cmd_7zip = [wscriptlocation, invislocation, str(core.SHOWEXTRACT), core.SEVENZIP, "x", "-y"]
         ext_7zip = [".rar", ".zip", ".tar.gz", "tgz", ".tar.bz2", ".tbz", ".tar.lzma", ".tlz", ".7z", ".xz"]
         extract_commands = dict.fromkeys(ext_7zip, cmd_7zip)
diff --git a/core/main_db.py b/core/main_db.py
index 939af5b0..c782e763 100644
--- a/core/main_db.py
+++ b/core/main_db.py
@@ -22,7 +22,7 @@ def db_filename(filename="nzbtomedia.db", suffix=None):
     """
     if suffix:
         filename = "{0}.{1}".format(filename, suffix)
-    return core.os.path.join(core.PROGRAM_DIR, filename)
+    return core.os.path.join(core.APP_ROOT, filename)
 
 
 class DBConnection(object):
diff --git a/core/version_check.py b/core/version_check.py
index 41c3ccb9..b24c9a17 100644
--- a/core/version_check.py
+++ b/core/version_check.py
@@ -15,6 +15,7 @@ from six.moves.urllib.request import urlretrieve
 
 import core
 from core import github_api as github, logger
+import libs.util
 
 
 class CheckVersion(object):
@@ -48,7 +49,7 @@ class CheckVersion(object):
         """
 
         # check if we're a windows build
-        if os.path.isdir(os.path.join(core.PROGRAM_DIR, u'.git')):
+        if os.path.isdir(os.path.join(core.APP_ROOT, u'.git')):
             install_type = 'git'
         else:
             install_type = 'source'
@@ -79,7 +80,23 @@ class CheckVersion(object):
 
     def update(self):
         if self.updater.need_update():
-            return self.updater.update()
+            result = self.updater.update()
+            self.clean()
+            return result
+
+    @staticmethod
+    def clean():
+        # Clean libs
+        result = libs.util.git_clean(
+            remove_directories=True,
+            force=True,
+            ignore_rules=True,
+            paths=[
+                libs.LIB_ROOT,
+                core.SOURCE_ROOT,
+            ],
+        )
+        logger.debug(result)
 
 
 class UpdateManager(object):
@@ -174,9 +191,9 @@ class GitUpdateManager(UpdateManager):
 
         try:
             logger.log(u"Executing {cmd} with your shell in {directory}".format
-                       (cmd=cmd, directory=core.PROGRAM_DIR), logger.DEBUG)
+                       (cmd=cmd, directory=core.APP_ROOT), logger.DEBUG)
             p = subprocess.Popen(cmd, stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.STDOUT,
-                                 shell=True, cwd=core.PROGRAM_DIR)
+                                 shell=True, cwd=core.APP_ROOT)
             output, err = p.communicate()
             exit_status = p.returncode
 
@@ -345,7 +362,7 @@ class SourceUpdateManager(UpdateManager):
 
     def _find_installed_version(self):
 
-        version_file = os.path.join(core.PROGRAM_DIR, u'version.txt')
+        version_file = os.path.join(core.APP_ROOT, u'version.txt')
 
         if not os.path.isfile(version_file):
             self._cur_commit_hash = None
@@ -437,11 +454,11 @@ class SourceUpdateManager(UpdateManager):
         """
         tar_download_url = 'https://github.com/{org}/{repo}/tarball/{branch}'.format(
             org=self.github_repo_user, repo=self.github_repo, branch=self.branch)
-        version_path = os.path.join(core.PROGRAM_DIR, u'version.txt')
+        version_path = os.path.join(core.APP_ROOT, u'version.txt')
 
         try:
             # prepare the update dir
-            sb_update_dir = os.path.join(core.PROGRAM_DIR, u'sb-update')
+            sb_update_dir = os.path.join(core.APP_ROOT, u'sb-update')
 
             if os.path.isdir(sb_update_dir):
                 logger.log(u"Clearing out update folder {dir} before extracting".format(dir=sb_update_dir))
@@ -485,12 +502,12 @@ class SourceUpdateManager(UpdateManager):
 
             # walk temp folder and move files to main folder
             logger.log(u"Moving files from {source} to {destination}".format
-                       (source=content_dir, destination=core.PROGRAM_DIR))
+                       (source=content_dir, destination=core.APP_ROOT))
             for dirname, dirnames, filenames in os.walk(content_dir):  # @UnusedVariable
                 dirname = dirname[len(content_dir) + 1:]
                 for curfile in filenames:
                     old_path = os.path.join(content_dir, dirname, curfile)
-                    new_path = os.path.join(core.PROGRAM_DIR, dirname, curfile)
+                    new_path = os.path.join(core.APP_ROOT, dirname, curfile)
 
                     # Avoid DLL access problem on WIN32/64
                     # These files needing to be updated manually
diff --git a/libs/__init__.py b/libs/__init__.py
index ed03df1a..6fab928e 100644
--- a/libs/__init__.py
+++ b/libs/__init__.py
@@ -4,8 +4,7 @@ import sys
 
 import libs.util
 
-ROOT_DIR = libs.util.module_root()
-LIB_DIR = os.path.join(ROOT_DIR, 'libs')
+LIB_ROOT = libs.util.module_path()
 
 COMMON = 'common'
 CUSTOM = 'custom'
@@ -18,7 +17,7 @@ MANDATORY = {
     CUSTOM,
 }
 DIRECTORY = {
-    lib: os.path.join(LIB_DIR, lib)
+    lib: os.path.join(LIB_ROOT, lib)
     for lib in [COMMON, CUSTOM, PY2, WIN]
 }
 
diff --git a/libs/__main__.py b/libs/__main__.py
index f82ad647..767f0d6e 100644
--- a/libs/__main__.py
+++ b/libs/__main__.py
@@ -5,7 +5,7 @@ import time
 import libs
 
 if __name__ == '__main__':
-    os.chdir(libs.LIB_DIR)
+    os.chdir(libs.LIB_ROOT)
     for lib, directory in libs.DIRECTORY.items():
         if lib == 'custom':
             continue
diff --git a/libs/util.py b/libs/util.py
index 3b597d69..cde820f2 100644
--- a/libs/util.py
+++ b/libs/util.py
@@ -4,19 +4,20 @@ import sys
 import os
 
 __all__ = [
-    'module_root',
+    'module_path',
     'add_path',
 ]
 
 
-def module_root(module=__file__):
+def module_path(module=__file__, parent=False):
     try:
         path = module.__file__
     except AttributeError:
         path = module
     directory = os.path.dirname(path)
-    parent = os.path.join(directory, os.pardir)
-    absolute = os.path.abspath(parent)
+    if parent:
+        directory = os.path.join(directory, os.pardir)
+    absolute = os.path.abspath(directory)
     normalized = os.path.normpath(absolute)
     return normalized
 
@@ -58,3 +59,31 @@ def install_requirements(
         args.append(path)
 
     subprocess.call(args)
+
+
+def git_clean(remove_directories=False, force=False, dry_run=False, interactive=False, quiet=False, exclude=None,
+              ignore_rules=False, clean_ignored=False, paths=None):
+    command = ['git', 'clean']
+    if remove_directories:
+        command.append('-d')
+    if force:
+        command.append('--force')
+    if interactive:
+        command.append('--interactive')
+    if quiet:
+        command.append('--quiet')
+    if dry_run:
+        command.append('--dry-run')
+    if exclude:
+        command.append('--exclude={pattern}'.format(pattern=exclude))
+    if ignore_rules:
+        command.append('-x')
+    if clean_ignored:
+        command.append('-X')
+    if paths:
+        try:
+            paths = paths.split(' ')
+        except AttributeError:
+            pass
+        command.extend(paths)
+    return subprocess.check_output(command)