Bootstrap dotfiles. Keep them symlinked to home directory, but store them elsewhere, without a dot (i.e. not hidden).

dotfiles.py

#!/usr/bin/python

import os
import sys
import subprocess

from stat import *

##############################################################################
# Routine Functions
##############################################################################

def info(msg, prefix="", suffix=""):
    msg = prefix + msg + suffix
    print(msg)

def success(msg):
    msg = "SUCCESS: " + msg
    print(msg)
    sys.exit(0)

def fail(msg):
    msg = "FATAL: " + msg
    print(msg)
    sys.exit(-1)

def print_welcome_banner():
    welcome = "Dotfile installer"
    border = "".join(['-' for x in welcome])

    info(border)
    info(welcome)
    info(border)

##############################################################################
# Logic
##############################################################################

def link_with_home(der, obj, home, link_name):
    """Create symbolic link. Remember, that we have ln -s TARGET LINK_NAME."""

    cmd = "ln -s {}/{} {}/{}".format(der, obj, home, link_name)
    info(cmd, "   * ")
    subprocess.check_call(cmd.split())
    
def remove_existing(name, der):
    """Remove file from directory."""

    filename = "{}/{}".format(der, name)

    if os.path.exists(filename):
        msg = "File exists, removing {}/{}".format(der, name)
        info(msg, "   * ")

        cmd = "rm -rf {}/{}".format(der, name)
        subprocess.check_call(cmd.split())

def set_permissions(name, perms):
    human_perms = oct(perms)
    msg = "Setting permissions on {} to {}".format(name, human_perms)
    info(msg, "   * ")

    os.chmod(name, perms)

##############################################################################
# Main
##############################################################################

def main():
    """Link directories and files with the prefix ~. as a dotfile to the
    user's home directory. If a file or directory does not contain ~. in it's
    filename, then create the link with the same name."""

    print_welcome_banner()
    info("Assuming we're running on a POSIX compliant system", " - ")

    home = os.getenv("HOME")

    os.chdir('../')
    der = os.getcwd()

    ##########################################################################
    # Special files to avoid
    ##########################################################################

    exclude = []
    exclude.append('exclude')
    exclude.append('.git')

    objs = []
    for x in os.listdir():
        for y in exclude:
            if y in x:
                break
        else:
            objs.append(x)

    ##########################################################################
    # Symlink
    ##########################################################################

    info("Performing the following commands:", " - ")

    for obj in objs:
        if os.path.isfile(obj):
            perms = S_IRWXU & (S_IRUSR | S_IWUSR)
        else:
            perms = S_IRWXU & (S_IRUSR | S_IWUSR | S_IXUSR)

        set_permissions(obj, perms)

        new_name = obj.replace('~.', '.')
        remove_existing(new_name, home)
        link_with_home(der, obj, home, new_name)

        print()

    success("Dotfiles ready.")

if __name__ == "__main__":
    main()