Fix upgraded package not being cleared

This commit fixes out-dated files in root directory of unpacked packages
not being cleared due to skipped files in sub-directories causing ENOTEMPTY
exception, when removing top-level directories.

Example:

/dir1/dir2/file    <- if this is ignored and /dir1/ only contains dirs
/plugin.py         <- this wouldn't be deleted as /dir1 was not added
                      to ignored_dirs and removing fails as not being empty

Thus ignore non-empty directories.

package_control/clear_directory.py

@@ -1,3 +1,4 @@
+import errno
 import os
 import stat
 import sys
@@ -53,21 +54,13 @@ def clear_directory(directory, ignored_files=None, ignore_errors=True):
  trash_dir = sys_path.trash_path()
  os.makedirs(trash_dir, exist_ok=True)
 
- ignored_dirs = set()
  was_exception = False
 
  for root, dirs, files in os.walk(directory, topdown=False):
  try:
- for d in dirs:
- path = os.path.join(root, d)
- if path not in ignored_dirs:
- os.rmdir(path)
-
  for f in files:
  path = os.path.normcase(os.path.join(root, f))
  if ignored_files and path in ignored_files:
- # also ignore parent folder from being removed
- ignored_dirs.add(root)
  continue
 
  try:
@@ -85,7 +78,15 @@ def clear_directory(directory, ignored_files=None, ignore_errors=True):
  )
  os.rename(path, trash_path)
 
- except OSError:
+ for d in dirs:
+ try:
+ os.rmdir(os.path.join(root, d))
+ except OSError as e:
+ if e.errno == errno.ENOTEMPTY:
+ continue
+ raise
+
+ except OSError as e:
  if not ignore_errors:
  raise
  was_exception = True