This script creates symlinks for the ATOM configuration files into your ownCloud/Dropbox/Box/OneDrive/GoogleDrive folder.

atom-update-links.py

# Copyright (c) 2016  Niklas Rosenstein
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.

import argparse
import errno
import os
import sys

if sys.version_info[0] == 3:
  raw_input = input

# http://stackoverflow.com/a/28382515/791713
if os.name == "nt":
  def symlink_ms(source, link_name):
    import ctypes
    is_admin = ctypes.windll.shell32.IsUserAnAdmin()
    if not is_admin:
      raise OSError(errno.EPERM, "only admins can create symlinks")
    csl = ctypes.windll.kernel32.CreateSymbolicLinkW
    csl.argtypes = (ctypes.c_wchar_p, ctypes.c_wchar_p, ctypes.c_uint32)
    csl.restype = ctypes.c_ubyte
    flags = 1 if os.path.isdir(source) else 0
    try:
      if csl(link_name, source.replace('/', '\\'), flags) == 0:
        raise ctypes.WinError()
    except:
        pass
  os.symlink = symlink_ms

def main():
  parser = argparse.ArgumentParser()
  parser.add_argument('atom_dir')
  parser.add_argument('-f', '--force', action='store_true')
  args = parser.parse_args()

  if not os.path.isdir(args.atom_dir):
    print("{0!r}: not a directory".format(args.atom_dir))
    return 1
  source_dir = os.path.abspath(os.path.dirname(__file__))
  for filename in os.listdir(source_dir):
    target = os.path.join(args.atom_dir, filename)
    if os.path.isfile(target) or os.path.islink(target):
      question = "do you really want to overwrite {0!r} (y/N) "
      while not args.force:
        reply = raw_input(question.format(filename)).strip().lower()
        if reply in ('no', 'n'):
          question = None
          break
        elif reply in ('yes', 'y'):
          break
        else:
          print("please reply with yes or no")
      if not question:
        continue
      if os.path.islink(target):
        os.unlink(target)
      else:
        os.remove(target)
    elif os.path.isdir(target):
      print("warning: can not overwrite existing directory {0!r}".format(filename))
      continue

    os.symlink(os.path.join(source_dir, filename), target)
    print("{0!r} linked".format(filename))

if __name__ == "__main__":
  main()

Example:

D:\ownCloud\Prefs\Atom
λ py update-links.py C:\Users\niklas\.atom -f
'config.cson' linked
'init.coffee' linked
'keymap.cson' linked
'snippets.cson' linked
'styles.less' linked
'update-links.py' linked

Note: Windows users require admin privileges!