diff --git a/browser/bookmarks/urls b/browser/bookmarks/urls
deleted file mode 100644
index e69de29..0000000
diff --git a/browser/qutebrowser/bookmarks/urls b/browser/qutebrowser/bookmarks/urls
new file mode 100644
index 0000000..c6fd96e
--- /dev/null
+++ b/browser/qutebrowser/bookmarks/urls
@@ -0,0 +1 @@
+https://security.google.com/settings/security/apppasswords?pli=1 App passwords - Account Settings
diff --git a/browser/keys.conf b/browser/qutebrowser/keys.conf
similarity index 100%
rename from browser/keys.conf
rename to browser/qutebrowser/keys.conf
diff --git a/browser/link.bash b/browser/qutebrowser/link.bash
similarity index 100%
rename from browser/link.bash
rename to browser/qutebrowser/link.bash
diff --git a/browser/quickmarks b/browser/qutebrowser/quickmarks
similarity index 100%
rename from browser/quickmarks
rename to browser/qutebrowser/quickmarks
diff --git a/browser/qutebrowser.conf b/browser/qutebrowser/qutebrowser.conf
similarity index 100%
rename from browser/qutebrowser.conf
rename to browser/qutebrowser/qutebrowser.conf
diff --git a/irc/link.bash b/chat/irc/link.bash
similarity index 100%
rename from irc/link.bash
rename to chat/irc/link.bash
diff --git a/irc/weechat.conf b/chat/irc/weechat.conf
similarity index 100%
rename from irc/weechat.conf
rename to chat/irc/weechat.conf
diff --git a/colors/link.bash b/colors/link.bash
index 1b95b7a..1961ebe 100755
--- a/colors/link.bash
+++ b/colors/link.bash
@@ -4,9 +4,9 @@ DIR=$(cd "$(dirname "${BASH_SOURCE[0]}" )/.." && pwd)
 source "$DIR/variables.bash"
 
 rm -f ~/.Xresources.colors
-rm -f "$DOTFILES_PATH/vim/config/colors/current.vim"
+rm -f "$DOTFILES_PATH/editor/nvim/config/colors/current.vim"
 ln -s "$DOTFILES_PATH/colors/xresources" "$HOME/.Xresources.colors"
-ln -s "$DOTFILES_PATH/colors/vim" "$DOTFILES_PATH/vim/config/colors/current.vim"
+ln -s "$DOTFILES_PATH/colors/vim" "$DOTFILES_PATH/editor/nvim/config/colors/current.vim"
 
-source "$DOTFILES_PATH/x/xloadresources"
+source "$DOTFILES_PATH/env/x/xloadresources"
 
diff --git a/vim/config/init.vim b/editor/nvim/config/init.vim
similarity index 100%
rename from vim/config/init.vim
rename to editor/nvim/config/init.vim
diff --git a/editor/nvim/link.bash b/editor/nvim/link.bash
new file mode 100755
index 0000000..3479c2f
--- /dev/null
+++ b/editor/nvim/link.bash
@@ -0,0 +1,10 @@
+#!/usr/bin/env bash
+
+DIR=$(cd "$(dirname "${BASH_SOURCE[0]}" )/../.." && pwd)
+source "$DIR/variables.bash"
+
+rm -rf "$HOME/.config/nvim"
+ln -s "$DOTFILES_PATH/editor/nvim/config" "$HOME/.config/nvim"
+
+nvim +PlugInstal +qall
+
diff --git a/sh/bash_profile b/env/sh/bash_profile
similarity index 100%
rename from sh/bash_profile
rename to env/sh/bash_profile
diff --git a/sh/bashrc b/env/sh/bashrc
similarity index 100%
rename from sh/bashrc
rename to env/sh/bashrc
diff --git a/sh/inputrc b/env/sh/inputrc
similarity index 100%
rename from sh/inputrc
rename to env/sh/inputrc
diff --git a/sh/layout_dev.tmux b/env/sh/layout_dev.tmux
similarity index 100%
rename from sh/layout_dev.tmux
rename to env/sh/layout_dev.tmux
diff --git a/env/sh/link.bash b/env/sh/link.bash
new file mode 100755
index 0000000..1cf31c5
--- /dev/null
+++ b/env/sh/link.bash
@@ -0,0 +1,23 @@
+#!/usr/bin/env bash
+
+DIR=$(cd "$(dirname "${BASH_SOURCE[0]}" )/../.." && pwd)
+source $DIR/variables.bash
+
+mkdir -p "$HOME/.tmux/layouts"
+
+MODULE_PATH="$DOTFILES_PATH/env/sh"
+
+rm -f "$HOME/.bashrc"
+rm -f "$HOME/.bash_profile"
+rm -f "$HOME/.tmux.conf"
+rm -f "$HOME/.tmux/layouts/dev.tmux"
+rm -f "$HOME/.inputrc"
+ln -s "$MODULE_PATH/bashrc" "$HOME/.bashrc"
+ln -s "$MODULE_PATH/bash_profile" "$HOME/.bash_profile"
+ln -s "$MODULE_PATH/tmux.conf" "$HOME/.tmux.conf"
+ln -s "$MODULE_PATH/layout_dev.tmux" "$HOME/.tmux/layouts/dev.tmux"
+ln -s "$MODULE_PATH/inputrc" "$HOME/.inputrc"
+
+sed -i "/export DOTFILES_PATH/c export DOTFILES_PATH=\"$DIR\"" "$HOME/.bashrc"
+
+echo "You should re-source ~/.bashrc ;)"
diff --git a/sh/tmux.conf b/env/sh/tmux.conf
similarity index 100%
rename from sh/tmux.conf
rename to env/sh/tmux.conf
diff --git a/wm/bspwm_config b/env/wm/bspwm_config
similarity index 100%
rename from wm/bspwm_config
rename to env/wm/bspwm_config
diff --git a/wm/bspwmrc b/env/wm/bspwmrc
similarity index 100%
rename from wm/bspwmrc
rename to env/wm/bspwmrc
diff --git a/wm/extras/bar/colors.bash b/env/wm/extras/bar/colors.bash
similarity index 100%
rename from wm/extras/bar/colors.bash
rename to env/wm/extras/bar/colors.bash
diff --git a/wm/extras/bar/formatter.bash b/env/wm/extras/bar/formatter.bash
similarity index 100%
rename from wm/extras/bar/formatter.bash
rename to env/wm/extras/bar/formatter.bash
diff --git a/wm/extras/bar/modules/bspwm-bm.bash b/env/wm/extras/bar/modules/bspwm-bm.bash
similarity index 100%
rename from wm/extras/bar/modules/bspwm-bm.bash
rename to env/wm/extras/bar/modules/bspwm-bm.bash
diff --git a/wm/extras/bar/modules/clock-bm.bash b/env/wm/extras/bar/modules/clock-bm.bash
similarity index 100%
rename from wm/extras/bar/modules/clock-bm.bash
rename to env/wm/extras/bar/modules/clock-bm.bash
diff --git a/wm/extras/bar/modules/date-bm.bash b/env/wm/extras/bar/modules/date-bm.bash
similarity index 100%
rename from wm/extras/bar/modules/date-bm.bash
rename to env/wm/extras/bar/modules/date-bm.bash
diff --git a/wm/extras/bar/modules/example.bash b/env/wm/extras/bar/modules/example.bash
similarity index 100%
rename from wm/extras/bar/modules/example.bash
rename to env/wm/extras/bar/modules/example.bash
diff --git a/wm/extras/bar/modules/module.bash b/env/wm/extras/bar/modules/module.bash
similarity index 100%
rename from wm/extras/bar/modules/module.bash
rename to env/wm/extras/bar/modules/module.bash
diff --git a/wm/extras/bar/modules/pacaur-updates-bm.bash b/env/wm/extras/bar/modules/pacaur-updates-bm.bash
similarity index 100%
rename from wm/extras/bar/modules/pacaur-updates-bm.bash
rename to env/wm/extras/bar/modules/pacaur-updates-bm.bash
diff --git a/wm/extras/bar/run_bar.bash b/env/wm/extras/bar/run_bar.bash
similarity index 100%
rename from wm/extras/bar/run_bar.bash
rename to env/wm/extras/bar/run_bar.bash
diff --git a/wm/extras/bar/start.bash b/env/wm/extras/bar/start.bash
similarity index 100%
rename from wm/extras/bar/start.bash
rename to env/wm/extras/bar/start.bash
diff --git a/env/wm/link.bash b/env/wm/link.bash
new file mode 100755
index 0000000..8a0ec7d
--- /dev/null
+++ b/env/wm/link.bash
@@ -0,0 +1,15 @@
+#!/usr/bin/env bash
+
+DIR=$(cd "$(dirname "${BASH_SOURCE[0]}" )/../.." && pwd)
+source "$DIR/variables.bash"
+
+MODULE_PATH="$DOTFILES_PATH/env/wm"
+
+mkdir -p "$HOME/.config/bspwm"
+mkdir -p "$HOME/.config/sxhkd"
+
+rm -f "$HOME/.config/bspwm/bspwmrc"
+rm -f "$HOME/.config/sxhkd/sxhkdrc"
+ln -s "$MODULE_PATH/bspwmrc" "$HOME/.config/bspwm/bspwmrc"
+ln -s "$MODULE_PATH/sxhkdrc" "$HOME/.config/sxhkd/sxhkdrc"
+
diff --git a/wm/sxhkdrc b/env/wm/sxhkdrc
similarity index 100%
rename from wm/sxhkdrc
rename to env/wm/sxhkdrc
diff --git a/x/gtk2rc b/env/x/gtk2rc
similarity index 100%
rename from x/gtk2rc
rename to env/x/gtk2rc
diff --git a/x/gtk3settings.ini b/env/x/gtk3settings.ini
similarity index 100%
rename from x/gtk3settings.ini
rename to env/x/gtk3settings.ini
diff --git a/env/x/link.bash b/env/x/link.bash
new file mode 100755
index 0000000..d1594f2
--- /dev/null
+++ b/env/x/link.bash
@@ -0,0 +1,31 @@
+#!/usr/bin/env bash
+
+DIR=$(cd "$(dirname "${BASH_SOURCE[0]}" )/../.." && pwd)
+source "$DIR/variables.bash"
+
+MODULE_PATH="$DOTFILES_PATH/env/x"
+
+mkdir -p "$HOME/.config/gtk-3.0"
+rm -f "$HOME/.xinitrc"
+rm -f "$HOME/.Xresources"
+rm -f "$HOME/.gtkrc-2.0"
+rm -f "$HOME/.config/gtk-3.0/settings.ini"
+ln -s "$MODULE_PATH/xinitrc" "$HOME/.xinitrc"
+ln -s "$MODULE_PATH/xresources" "$HOME/.Xresources"
+ln -s "$MODULE_PATH/gtk3settings.ini" "$HOME/.config/gtk-3.0/settings.ini"
+ln -s "$MODULE_PATH/gtk2rc" "$HOME/.gtkrc-2.0"
+
+sudo mkdir -p /root/.gtk-3.0/
+sudo mkdir -p /root/.config/gtk-3.0/
+sudo rm -f "/root/.gtkrc-2.0"
+sudo rm -f "/root/.gtk-3.0/settings.ini"
+sudo rm -f "/root/.config/gtk-3.0/settings.ini"
+sudo ln -s "$MODULE_PATH/gtk2rc" "/root/.gtkrc-2.0"
+sudo ln -s "$MODULE_PATH/gtk3settings.ini" "/root/.gtk-3.0/settings.ini"
+sudo ln -s "$MODULE_PATH/gtk3settings.ini" "/root/.config/gtk-3.0/settings.ini"
+
+sudo rm -f "/etc/udev/rules.d/90-usb-device-plugin.rules"
+sudo ln -s "$MODULE_PATH/udev_rules/90-usb-device-plugin.rules" "/etc/udev/rules.d/90-usb-device-plugin.rules"
+
+source "$MODULE_PATH/xloadresources"
+
diff --git a/x/reset_monitors.bash b/env/x/reset_monitors.bash
similarity index 100%
rename from x/reset_monitors.bash
rename to env/x/reset_monitors.bash
diff --git a/x/udev_rules/90-usb-device-plugin.rules b/env/x/udev_rules/90-usb-device-plugin.rules
similarity index 100%
rename from x/udev_rules/90-usb-device-plugin.rules
rename to env/x/udev_rules/90-usb-device-plugin.rules
diff --git a/x/xinitrc b/env/x/xinitrc
similarity index 100%
rename from x/xinitrc
rename to env/x/xinitrc
diff --git a/x/xloadresources b/env/x/xloadresources
similarity index 100%
rename from x/xloadresources
rename to env/x/xloadresources
diff --git a/x/xresources b/env/x/xresources
similarity index 100%
rename from x/xresources
rename to env/x/xresources
diff --git a/git/link.bash b/git/link.bash
deleted file mode 100755
index 006891d..0000000
--- a/git/link.bash
+++ /dev/null
@@ -1,8 +0,0 @@
-#!/usr/bin/env bash
-
-DIR=$(cd "$(dirname "${BASH_SOURCE[0]}" )/.." && pwd)
-source "$DIR/variables.bash"
-
-rm -f "$HOME/.gitconfig"
-ln -s "$DOTFILES_PATH/git/gitconfig" "$HOME/.gitconfig"
-
diff --git a/link_all.bash b/link_all.bash
index d59634c..b5f0664 100755
--- a/link_all.bash
+++ b/link_all.bash
@@ -3,10 +3,12 @@
 DIR=$(cd "$(dirname "${BASH_SOURCE[0]}" )/" && pwd)
 source "$DIR/variables.bash"
 
+ALERT_AGREEMENT_FILE="$DIR/scripts/agree_to_bootstrap.lock"
+
 # Let user know that this script will delete their current configuration and
 # that they should read this script before running. We'll use a lock file so
 # the user only needs to agree once.
-if [ -f "$DIR/agree_to_bootstrap.lock" ]; then
+if [ -f "$ALERT_AGREEMENT_FILE" ]; then
     # User agreed already - do nothing
     echo "Linking..."
 else
@@ -16,15 +18,15 @@ else
     read -r -p "Are you sure you want to continue? [y/N] " response
     response=${response,,} # to_lower
     if [[ $response =~ ^(yes|y)$ ]]; then
-        touch "$DIR/agree_to_bootstrap.lock"
+        echo "agreed" > "$ALERT_AGREEMENT_FILE"
     else
         exit 1
     fi
 fi
 
 source "$DOTFILES_PATH/colors/link.bash"
-source "$DOTFILES_PATH/git/link.bash"
-source "$DOTFILES_PATH/vim/link.bash"
-source "$DOTFILES_PATH/sh/link.bash"
-source "$DOTFILES_PATH/x/link.bash"
-source "$DOTFILES_PATH/wm/link.bash"
+source "$DOTFILES_PATH/misc/git/link.bash"
+source "$DOTFILES_PATH/editor/nvim/link.bash"
+source "$DOTFILES_PATH/env/sh/link.bash"
+source "$DOTFILES_PATH/env/x/link.bash"
+source "$DOTFILES_PATH/env/wm/link.bash"
diff --git a/git/gitconfig b/misc/git/gitconfig
similarity index 100%
rename from git/gitconfig
rename to misc/git/gitconfig
diff --git a/misc/git/link.bash b/misc/git/link.bash
new file mode 100755
index 0000000..faf3dc1
--- /dev/null
+++ b/misc/git/link.bash
@@ -0,0 +1,8 @@
+#!/usr/bin/env bash
+
+DIR=$(cd "$(dirname "${BASH_SOURCE[0]}" )/../.." && pwd)
+source "$DIR/variables.bash"
+
+rm -f "$HOME/.gitconfig"
+ln -s "$DOTFILES_PATH/misc/git/gitconfig" "$HOME/.gitconfig"
+
diff --git a/arch_linux_init/bar.bash b/os/arch_linux_init/bar.bash
similarity index 100%
rename from arch_linux_init/bar.bash
rename to os/arch_linux_init/bar.bash
diff --git a/arch_linux_init/fonts.bash b/os/arch_linux_init/fonts.bash
similarity index 100%
rename from arch_linux_init/fonts.bash
rename to os/arch_linux_init/fonts.bash
diff --git a/arch_linux_init/git.bash b/os/arch_linux_init/git.bash
similarity index 100%
rename from arch_linux_init/git.bash
rename to os/arch_linux_init/git.bash
diff --git a/arch_linux_init/gmusic.bash b/os/arch_linux_init/gmusic.bash
similarity index 100%
rename from arch_linux_init/gmusic.bash
rename to os/arch_linux_init/gmusic.bash
diff --git a/arch_linux_init/neovim.bash b/os/arch_linux_init/neovim.bash
similarity index 100%
rename from arch_linux_init/neovim.bash
rename to os/arch_linux_init/neovim.bash
diff --git a/arch_linux_init/pacaur.bash b/os/arch_linux_init/pacaur.bash
similarity index 100%
rename from arch_linux_init/pacaur.bash
rename to os/arch_linux_init/pacaur.bash
diff --git a/arch_linux_init/shell.bash b/os/arch_linux_init/shell.bash
similarity index 100%
rename from arch_linux_init/shell.bash
rename to os/arch_linux_init/shell.bash
diff --git a/arch_linux_init/urxvt.bash b/os/arch_linux_init/urxvt.bash
similarity index 100%
rename from arch_linux_init/urxvt.bash
rename to os/arch_linux_init/urxvt.bash
diff --git a/arch_linux_init/utils.bash b/os/arch_linux_init/utils.bash
similarity index 100%
rename from arch_linux_init/utils.bash
rename to os/arch_linux_init/utils.bash
diff --git a/arch_linux_init/wm.bash b/os/arch_linux_init/wm.bash
similarity index 100%
rename from arch_linux_init/wm.bash
rename to os/arch_linux_init/wm.bash
diff --git a/arch_linux_init/xorg.bash b/os/arch_linux_init/xorg.bash
similarity index 100%
rename from arch_linux_init/xorg.bash
rename to os/arch_linux_init/xorg.bash
diff --git a/sh/link.bash b/sh/link.bash
deleted file mode 100755
index 9a8ca6b..0000000
--- a/sh/link.bash
+++ /dev/null
@@ -1,22 +0,0 @@
-#!/usr/bin/env bash
-
-DIR=$(cd "$(dirname "${BASH_SOURCE[0]}" )/.." && pwd)
-source $DIR/variables.bash
-
-mkdir -p "$HOME/.tmux/layouts"
-
-rm -f "$HOME/.bashrc"
-rm -f "$HOME/.bash_profile"
-rm -f "$HOME/.tmux.conf"
-rm -f "$HOME/.tmux/layouts/dev.tmux"
-rm -f "$HOME/.inputrc"
-ln -s "$DOTFILES_PATH/sh/bashrc" "$HOME/.bashrc"
-ln -s "$DOTFILES_PATH/sh/bash_profile" "$HOME/.bash_profile"
-ln -s "$DOTFILES_PATH/sh/tmux.conf" "$HOME/.tmux.conf"
-ln -s "$DOTFILES_PATH/sh/layout_dev.tmux" "$HOME/.tmux/layouts/dev.tmux"
-ln -s "$DOTFILES_PATH/sh/inputrc" "$HOME/.inputrc"
-
-sed -i "/export DOTFILES_PATH/c export DOTFILES_PATH=\"$DIR\"" "$HOME/.bashrc"
-
-echo "You should re-source ~/.bashrc ;)"
-
diff --git a/variables.bash b/variables.bash
index 31c91d2..bbf6535 100755
--- a/variables.bash
+++ b/variables.bash
@@ -40,3 +40,5 @@ if [ -a "$HOME/.bashrc_env" ]; then
   . "$HOME/.bashrc_env"
 fi
 
+# various paths that are used in the dotfiles
+
diff --git a/vim/config/.gitignore b/vim/config/.gitignore
deleted file mode 100644
index 9780597..0000000
--- a/vim/config/.gitignore
+++ /dev/null
@@ -1,3 +0,0 @@
-*
-!init.vim
-!./colors/*.vim
diff --git a/vim/config/colors/current.vim b/vim/config/colors/current.vim
deleted file mode 120000
index 286c0d2..0000000
--- a/vim/config/colors/current.vim
+++ /dev/null
@@ -1 +0,0 @@
-/home/daniel/.dotfiles/colors/vim
\ No newline at end of file
diff --git a/vim/link.bash b/vim/link.bash
deleted file mode 100755
index 80bd647..0000000
--- a/vim/link.bash
+++ /dev/null
@@ -1,10 +0,0 @@
-#!/usr/bin/env bash
-
-DIR=$(cd "$(dirname "${BASH_SOURCE[0]}" )/.." && pwd)
-source "$DIR/variables.bash"
-
-rm -rf "$HOME/.config/nvim"
-ln -s "$DOTFILES_PATH/vim/config" "$HOME/.config/nvim"
-
-nvim +PlugInstal +qall
-
diff --git a/wm/link.bash b/wm/link.bash
deleted file mode 100755
index 7d166c9..0000000
--- a/wm/link.bash
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/usr/bin/env bash
-
-DIR=$(cd "$(dirname "${BASH_SOURCE[0]}" )/.." && pwd)
-source "$DIR/variables.bash"
-
-mkdir -p "$HOME/.config/bspwm"
-mkdir -p "$HOME/.config/sxhkd"
-
-rm -f "$HOME/.config/bspwm/bspwmrc"
-rm -f "$HOME/.config/sxhkd/sxhkdrc"
-ln -s "$DOTFILES_PATH/wm/bspwmrc" "$HOME/.config/bspwm/bspwmrc"
-ln -s "$DOTFILES_PATH/wm/sxhkdrc" "$HOME/.config/sxhkd/sxhkdrc"
-
diff --git a/x/link.bash b/x/link.bash
deleted file mode 100755
index 3667180..0000000
--- a/x/link.bash
+++ /dev/null
@@ -1,29 +0,0 @@
-#!/usr/bin/env bash
-
-DIR=$(cd "$(dirname "${BASH_SOURCE[0]}" )/.." && pwd)
-source "$DIR/variables.bash"
-
-mkdir -p "$HOME/.config/gtk-3.0"
-rm -f "$HOME/.xinitrc"
-rm -f "$HOME/.Xresources"
-rm -f "$HOME/.gtkrc-2.0"
-rm -f "$HOME/.config/gtk-3.0/settings.ini"
-ln -s "$DOTFILES_PATH/x/xinitrc" "$HOME/.xinitrc"
-ln -s "$DOTFILES_PATH/x/xresources" "$HOME/.Xresources"
-ln -s "$DOTFILES_PATH/x/gtk3settings.ini" "$HOME/.config/gtk-3.0/settings.ini"
-ln -s "$DOTFILES_PATH/x/gtk2rc" "$HOME/.gtkrc-2.0"
-
-sudo mkdir -p /root/.gtk-3.0/
-sudo mkdir -p /root/.config/gtk-3.0/
-sudo rm -f "/root/.gtkrc-2.0"
-sudo rm -f "/root/.gtk-3.0/settings.ini"
-sudo rm -f "/root/.config/gtk-3.0/settings.ini"
-sudo ln -s "$DOTFILES_PATH/x/gtk2rc" "/root/.gtkrc-2.0"
-sudo ln -s "$DOTFILES_PATH/x/gtk3settings.ini" "/root/.gtk-3.0/settings.ini"
-sudo ln -s "$DOTFILES_PATH/x/gtk3settings.ini" "/root/.config/gtk-3.0/settings.ini"
-
-sudo rm -f "/etc/udev/rules.d/90-usb-device-plugin.rules"
-sudo ln -s "$DOTFILES_PATH/x/udev_rules/90-usb-device-plugin.rules" "/etc/udev/rules.d/90-usb-device-plugin.rules"
-
-source "$DOTFILES_PATH/x/xloadresources"
-