diff --git a/bootstrap.sh b/bootstrap.sh
deleted file mode 100755
index cd374845..00000000
--- a/bootstrap.sh
+++ /dev/null
@@ -1,41 +0,0 @@
-#!/usr/bin/env bash
-cd `dirname $BASH_SOURCE` && source resources/bootstrapping.sh
-DOTFILES_DIRECTORY="$(dotfiles_abspath)/dotfiles"
-
-
-function symlink_dotfiles() {
-    cd $DOTFILES_DIRECTORY
-    [ -a ~/.dotfiles-backups ] && mv ~/.dotfiles-backups ~/.dotfiles-backups.old
-    mkdir ~/.dotfiles-backups
-    for filename in *; do
-        local link_destination="$HOME/.$filename"
-        local link_target=$(${readlink_command} -f $filename)
-        echo "linking $link_destination to $link_target"
-        # Using only test -e doesn't work here because it will return
-        # false if the destination of the symbolic link at does not exist.
-        test -e $link_destination || test -L $link_destination && mv $link_destination ~/.dotfiles-backups
-        ln -si $link_target $link_destination
-    done
-    [ -a ~/.dotfiles-backups.old ] && mv ~/.dotfiles-backups.old ~/.dotfiles-backups/.dotfiles-backups
-}
-
-
-function parse_options() {
-    while getopts "f" OPTCHAR; do
-        case $optchar in
-            f)
-                symlink_dotfiles
-                return
-                ;;
-        esac
-    done
-    shift $((OPTIND-1))
-
-    read -p "Symlinking files from $DOTFILES_DIRECTORY. This may overwrite existing files in your home directory. Do you wish to proceed? (y/n) " -n 1
-    if [[ $REPLY =~ ^[Yy]$ ]]; then
-        echo
-	symlink_dotfiles
-    fi
-}
-
-parse_options
diff --git a/dotfiles/lib/shellrc/brew.sh b/dotfiles/lib/shellrc/brew.sh
index a9eef843..fe153be2 100755
--- a/dotfiles/lib/shellrc/brew.sh
+++ b/dotfiles/lib/shellrc/brew.sh
@@ -1,11 +1,13 @@
 function brew_install_items() {
-    echo $@
     for package_install_string in $@;
     do
-        # Horrible hack to induce word splitting.
-        eval "package_args=($package_install_string)"
+        package_args=$package_install_string
+        if is_zsh;
+            then
+            # Horrible hack to induce word splitting.
+            eval "package_args=($package_install_string)"
+        fi
         brew install $package_args;
-        brew link $package_args[1];
     done
 }
 
@@ -18,68 +20,67 @@ function fix_brew_htop() {
 
 function do_the_brew() {
     ESSENTIAL=(
-        "emacs"
-        "git"
-        "tmux"
-        "python --with-brewed-openssl"
-        "htop"
-        "greadlink"
-        "vim --override-system-vi"
-        "zsh"
-        "make"
+        "emacs" \
+        "tmux" \
+        "python --with-brewed-openssl" \
+        "htop" \
+        "greadlink" \
+        "vim --override-system-vi" \
+        "zsh" \
+        "make" \
     )
     # `find`, `locate`, `updatedb`, and `xargs`, g-prefixed
     # core utilities (those that come with OS X are outdated)
     BASICS=(
-        "findutils"
-        "coreutils"
-        "binutils"
-        "diffutils"
-        "ed --default-names"
-        "gawk"
-        "gnu-indent --default-names"
-        "gnu-sed --default-names"
-        "gnu-tar --default-names"
-        "gnu-which --default-names"
-        "gnutls --default-names"
-        "grep --default-names"
-        "gzip"
-        "watch"
-        "wdiff --with-gettext"
-        "wget --enable-iri"
+        "findutils" \
+        "coreutils" \
+        "binutils" \
+        "diffutils" \
+        "ed --default-names" \
+        "gawk" \
+        "gnu-indent --default-names" \
+        "gnu-sed --default-names" \
+        "gnu-tar --default-names" \
+        "gnu-which --default-names" \
+        "gnutls --default-names" \
+        "grep --default-names" \
+        "gzip" \
+        "watch" \
+        "wdiff --with-gettext" \
+        "wget --enable-iri" \
     )
     SHOULD_INSTALL=(
-        "nmap"
-        "readline"
-        "netcat"
-        "reattach-to-user-namespace"
-        "daemonize"
-        "ngrep"
-        "gist"
-        "gawk"
-        "pstree"
-        "ack"
-        "hub"
-        "tig"
-        "heroku"
-        "scala"
-        "sbt"
-        "node"
-        "npm"
+        "nmap" \
+        "readline" \
+        "netcat" \
+        "reattach-to-user-namespace" \
+        "daemonize" \
+        "ngrep" \
+        "gist" \
+        "gawk" \
+        "pstree" \
+        "ack" \
+        "hub" \
+        "tig" \
+        "heroku" \
+        "scala" \
+        "sbt" \
+        "node" \
+        "npm" \
     )
-    MISC=(
-        "file-formula"
-        "git"
-        "less"
-        "openssh --with-brewed-openssl"
-        "perl518"
-        "rsync"
-        "svn"
-        "unzip"
-        "macvim --override-system-vim --custom-system-icons"
+    MISC=("file-formula" \
+        "less" \
+        "openssh --with-brewed-openssl" \
+        "perl518" \
+        "rsync" \
+        "svn" \
+        "unzip" \
+        "macvim --override-system-vim --custom-system-icons" \
     )
 
     install_items=()
+    OPTIND=1
+    echo "${MISC[@]}"
     while getopts "uebsmah" OPTCHAR;
     do
         case $OPTCHAR in
@@ -103,7 +104,20 @@ function do_the_brew() {
                 install_items=("${install_items[@]}" "${ESSENTIAL[@]}" "${BASICS[@]}" "${SHOULD_INSTALL[@]}" "${MISC[@]}")
                 ;;
             h)
-                echo "Usage:
+                do_the_brew_help
+                return
+                ;;
+        esac
+    done
+    echo "Installing the following packages:"
+    for package_name in "${install_items[@]}"; do echo $package_name; done;
+    brew update
+    brew_install_items $install_items
+    brew cleanup
+}
+
+function do_the_brew_help() {
+    echo "do_the_brew Usage:
 -a install all packages.
 -u upgrade brew packages.
 -e install essential packages
@@ -112,12 +126,4 @@ function do_the_brew() {
 -m install very non-essential packages.
 -h display this help message.
 "
-                return
-        esac
-    done
-    echo "Installing:"
-    for package_name in $install_items; do echo $package_name; done;
-    brew update
-    brew_install_items $install_items
-    brew cleanup
 }
diff --git a/dotfiles/lib/shellrc/colors.sh b/dotfiles/lib/shellrc/colors.sh
index b73f991c..84b66662 100644
--- a/dotfiles/lib/shellrc/colors.sh
+++ b/dotfiles/lib/shellrc/colors.sh
@@ -1,2 +1,2 @@
-local dircolors_file="$HOME/.dircolors"
+dircolors_file="$HOME/.dircolors"
 test -r $dircolors_files  && eval "$(dircolors $dircolors_file)"
diff --git a/dotfiles/lib/shellrc/functions.sh b/dotfiles/lib/shellrc/functions.sh
index 7877fffb..c748f301 100644
--- a/dotfiles/lib/shellrc/functions.sh
+++ b/dotfiles/lib/shellrc/functions.sh
@@ -1,9 +1,3 @@
-function dotfiles_abspath() {
-    readlink_command='readlink'
-command -v greadlink > /dev/null && readlink_command="greadlink"
-    echo "$(${readlink_command} -f "$BASH_SOURCE" | xargs dirname | xargs dirname)"
-}
-
 function go2dotfiles() {
     cd $(dirname `readlink -f ~/.zshrc | xargs dirname`)
 }
@@ -42,6 +36,7 @@ function confirm() {
 
 function get_cols() {
     FS=' '
+    OPTIND=1
     while getopts "F:" OPTCHAR; do
         case $OPTCHAR in
             F)
@@ -129,6 +124,7 @@ function git_root() {
 function git_diff_replacing() {
     local original_sha='HEAD~1'
     local new_sha='HEAD'
+    OPTIND=1
     while getopts "do:n:" OPTCHAR;
     do
         case $OPTCHAR in
@@ -154,6 +150,7 @@ function git_diff_replacing() {
 function git_reset_author() {
     local should_update_command=''
     local update_command=''
+    OPTIND=1
     while getopts "a:e:A:E:h" OPTCHAR;
     do
         case $OPTCHAR in
diff --git a/dotfiles/lib/shellrc/python.sh b/dotfiles/lib/shellrc/python.sh
index e5e0960b..a2f8d132 100644
--- a/dotfiles/lib/shellrc/python.sh
+++ b/dotfiles/lib/shellrc/python.sh
@@ -1,17 +1,16 @@
-ESSENTIAL=(ipdb ipython virtualenv)
-FOR_EDITOR=(jedi pyflakes)
-USEFUL=(
-    Flask
-    ddg
-    ouimeaux
-    readline
-    simplejson
-    tox
-    numpy
-)
-
 function install_python_packages() {
-    sudo pip install $ESSENTIAL
+    ESSENTIAL=(ipdb ipython virtualenv)
+    FOR_EDITOR=(jedi pyflakes)
+    USEFUL=(
+        Flask
+        ddg
+        ouimeaux
+        readline
+        simplejson
+        tox
+        numpy
+    )
+    OPTIND=1
     while getopts "uea" OPTCHAR;
     do
         case $OPTCHAR in
@@ -24,8 +23,18 @@ function install_python_packages() {
             a)
                 sudo pip install $FOR_EDITOR
                 sudo pip install $USEFUL
+                install_pygame
+                install_powerline
+                ;;
+            h)
+                echo "
+-u Install useful but non essential python.
+-e Install editor python packages.
+-a Install all python utilities."
+                ;;
         esac
     done
+    sudo pip install $ESSENTIAL
 }
 
 function install_pygame() {
diff --git a/dotfiles/lib/shellrc/synergy.sh b/dotfiles/lib/shellrc/synergy.sh
index 7d4edc49..0b4d98c9 100644
--- a/dotfiles/lib/shellrc/synergy.sh
+++ b/dotfiles/lib/shellrc/synergy.sh
@@ -1,5 +1,6 @@
 function make_me_synergy() {
     local new_host_name="$(echo $SSH_CONNECTION | get_cols 1)"
+    OPTIND=1
     while getopts "h:" OPTCHAR; do
         case $OPTCHAR in
             h)
diff --git a/dotfiles/lib/zsh.sh b/dotfiles/lib/zsh.sh
index 5f272f6e..3990be48 100644
--- a/dotfiles/lib/zsh.sh
+++ b/dotfiles/lib/zsh.sh
@@ -5,6 +5,6 @@ done
 alias srczsh="source ~/.zshrc"
 
 # Online help.
-unalias run-help
+unalias run-help 2> /dev/null 1>/dev/null
 autoload run-help
 HELPDIR=/usr/local/share/zsh/helpfiles
diff --git a/setup.sh b/setup.sh
index de830b48..808f3998 100755
--- a/setup.sh
+++ b/setup.sh
@@ -1,33 +1,85 @@
 #!/usr/bin/env bash
-function setup() {
-    cd `dirname $BASH_SOURCE` && source resources/bootstrapping.sh
-    source dotfiles/lib/shellrc/functions.sh
-    source dotfiles/lib/shellrc/brew.sh
-    source dotfiles/lib/shellrc/python.sh
+cd `dirname $BASH_SOURCE` && source resources/bootstrapping.sh
+source dotfiles/lib/shellrc/functions.sh
+source dotfiles/lib/shellrc/brew.sh
+source dotfiles/lib/shellrc/python.sh
+DOTFILES_DIRECTORY="$(dotfiles_abspath)/dotfiles"
 
-    case `uname` in
-        'Darwin')          
-            osx_setup
-            ;;
-        'Linux')
-            source resources/apt-get.sh
-            ;;
-    esac
 
-    install_powerline
-    source bootstrap.sh
+function symlink_dotfiles() {
+    cd $DOTFILES_DIRECTORY
+    [ -a ~/.dotfiles-backups ] && mv ~/.dotfiles-backups ~/.dotfiles-backups.old
+    mkdir ~/.dotfiles-backups
+    for filename in *; do
+        local link_destination="$HOME/.$filename"
+        local link_target=$(${readlink_command} -f $filename)
+        echo "linking $link_destination to $link_target"
+        # Using only test -e doesn't work here because it will return
+        # false if the destination of the symbolic link at does not exist.
+        test -e $link_destination || test -L $link_destination && mv $link_destination ~/.dotfiles-backups
+        ln -si $link_target $link_destination
+    done
+    [ -a ~/.dotfiles-backups.old ] && mv ~/.dotfiles-backups.old ~/.dotfiles-backups/.dotfiles-backups
 }
 
 
-function osx_setup() {
-    while getopts "uebsmaho" OPTCHAR;
+function symlink_dotfiles_prompt() {
+    read -p "Symlinking files from $DOTFILES_DIRECTORY. This may overwrite existing files in your home directory. Do you wish to proceed? (y/n) " -n 1
+    if [[ $REPLY =~ ^[Yy]$ ]]; then
+        echo
+	symlink_dotfiles
+    fi
+}
+
+function setup_help() {
+    echo "setup Usage:
+-a Install apt-get packages.
+-o Run OSX configuration commands.
+-s Symlink dotfiles to home directory.
+-b Install brew packages.
+-p Install python packages.
+-h display this help message."
+}
+
+function setup() {
+    if [[ $# -eq 0 ]] ; then
+        setup_help
+        exit 0
+    fi
+    while getopts "aosbp" OPTCHAR;
     do
         case $OPTCHAR in
-            h)
-                echo "brew options:"
-                do_the_brew -h
-                exit
+            a)
+                source resources/apt-get.sh
                 ;;
-    source resources/osx.sh
-    do_the_brew $@
+            b)
+                do_the_brew_help
+                read -p "Enter flags for brew package installation:
+"
+                [[ $REPLY[0] != '-' ]] && REPLY="-$REPLY"
+                do_the_brew $REPLY
+                ;;
+            o)
+                sudo -v
+                source resources/osx.sh
+                ;;
+            s)
+                symlink_dotfiles_prompt
+                ;;
+            p)
+                install_python_packages -h
+                read -p "Enter flags for python package installation"
+                if [[ $REPLY[0] != '-' ]]; then
+                    REPLY="-$REPLY"
+                fi
+                install_python_packages $REPLY
+                ;;
+            h)
+                setup_help
+                return
+                ;;
+        esac
+    done
 }
+
+setup $@