diff --git a/README.md b/README.md
index dd9116f..b228628 100644
--- a/README.md
+++ b/README.md
@@ -22,11 +22,17 @@ The current dotfiles are geared toward wayland for which the setup looks similar
 
 The dotfiles use `GNU stow` to link themselves in the home directory. You can clone this repository anywhere (though I have mine in `~/.dotfiles` as it seemed most logical for me).
 
-I would recommend doing a `git clone --recursive` for this repository, since it contains git [submodules](https://nering.dev/2016/git-submodules-vs-subtrees/), which will then automatically get pulled in as well. Of course, you can do it non-recursively and then just pull those modules selectively which you actually want.
+I would recommend doing an initial `git clone --recursive` for this repository, since it contains git [submodules](https://nering.dev/2016/git-submodules-vs-subtrees/), which will then automatically get pulled in as well.
+Of course, you can do it non-recursively and then just pull those modules selectively which you actually want.
 
 Once in the repository directory, when you then run `./install.sh` it will install many of the packages I use (though they are probably slightly out-of-date) and link the dotfiles into the home directory.
-If you do not want to install any packages, but only link the dotfiles run `stow -S */` from the main repository directory.
-Since dotfiles management is based on `stow`, it will not overwrite anything already in the home directory (though you can force it to if you really want, using `stow --override='.*'` -- I do not recommend this).
+I would mostly recommend this on fresh machines or a test machine first - it *will* link my personal dotfiles and, if you allow it, *will* install quite a few packages.
+By default it will ask your consent for some steps -- use `./install.sh -f` to force yes to everything.
+
+The dotfile installation procedure is based on `stow`, it will *not overwrite* anything already in the home directory (though you can force it to if you really want, using `stow --override='.*'` -- I do not recommend this).
+
+> **NOTE**
+> The same non-destructive installation procedure does *not* apply to the package installation and system setting file linking, where it can potentially overwrite or remove existing files.
 
 After all files are linked and you open a new shell session, the `dotlink` alias will allow you to re-link all dotfiles from anywhere on the system.[^1]
 
diff --git a/bootstrap/install_packages.sh b/bootstrap/install_packages.sh
index 4f812fb..4608b6e 100755
--- a/bootstrap/install_packages.sh
+++ b/bootstrap/install_packages.sh
@@ -7,7 +7,9 @@
 # DESCRIPTION:  Display usage information for this script.
 # PARAMETERS:   see usage function
 #==============================================================================
-packages="${BOOTSTRAP_PACKAGES:-packages.txt}"
+PKG_TSV_FILE=${PKG_TSV_FILE:-bootstrap/packages.tsv}
+packages_repo="${BOOTSTRAP_PACKAGES:-$(grep -e '	R	' "$PKG_TSV_FILE" | cut -f1 -d'	' )}"
+packages_aur="${BOOTSTRAP_PACKAGES_AUR:-$(grep -e '	A	' "$PKG_TSV_FILE" | cut -f1 -d'	' )}"
 
 main() {
     local cmd=""
@@ -60,27 +62,16 @@ update_repos() {
 install_packages() {
     unattended="$1"
     if "$unattended"; then
-        yay -Squ --noconfirm --needed - <"$packages"
+        echo "$packages_repo" "$packages_aur" | yay -Squ --noconfirm --needed -
     else
-        yay -Su --needed - <"$packages"
-    fi
-}
-
-check_consent() {
-    echo "This will take a while and install many packages. Proceed [y/N]?"
-    read -r yes
-    if [[ "$yes" != y* ]]; then
-        echo "Exiting."
-        exit
+        echo "$packages_repo" | yay -Squ --needed -
+        echo "$packages_aur" | yay -S --needed -
     fi
 }
 
 install() {
     unattended=$1
     echo "Beginning package bootstrap ..............................................."
-    if ! "$unattended"; then
-        check_consent
-    fi
     echo "Installing yay ............................................................"
     install_yay
     echo "Installing apps ..........................................................."
diff --git a/bootstrap/system-packages/etc/pacman.conf b/bootstrap/system-packages/etc/pacman.conf
new file mode 100644
index 0000000..922ac08
--- /dev/null
+++ b/bootstrap/system-packages/etc/pacman.conf
@@ -0,0 +1,100 @@
+#
+# /etc/pacman.conf
+#
+# See the pacman.conf(5) manpage for option and repository directives
+
+#
+# GENERAL OPTIONS
+#
+[options]
+# The following paths are commented out with their default values listed.
+# If you wish to use different paths, uncomment and update the paths.
+#RootDir     = /
+#DBPath      = /var/lib/pacman/
+#CacheDir    = /var/cache/pacman/pkg/
+#LogFile     = /var/log/pacman.log
+#GPGDir      = /etc/pacman.d/gnupg/
+#HookDir     = /etc/pacman.d/hooks/
+HoldPkg     = pacman glibc
+#XferCommand = /usr/bin/curl -L -C - -f -o %o %u
+#XferCommand = /usr/bin/wget --passive-ftp -c -O %o %u
+#CleanMethod = KeepInstalled
+Architecture = auto
+
+# Pacman won't upgrade packages listed in IgnorePkg and members of IgnoreGroup
+#IgnorePkg   =
+#IgnoreGroup =
+
+#NoUpgrade   =
+#NoExtract   =
+
+# Misc options
+UseSyslog
+Color
+#NoProgressBar
+CheckSpace
+VerbosePkgLists
+ParallelDownloads = 5
+
+# By default, pacman accepts packages signed by keys that its local keyring
+# trusts (see pacman-key and its man page), as well as unsigned packages.
+SigLevel    = Required DatabaseOptional
+LocalFileSigLevel = Optional
+#RemoteFileSigLevel = Required
+
+# NOTE: You must run `pacman-key --init` before first using pacman; the local
+# keyring can then be populated with the keys of all official Arch Linux
+# packagers with `pacman-key --populate archlinux`.
+
+#
+# REPOSITORIES
+#   - can be defined here or included from another file
+#   - pacman will search repositories in the order defined here
+#   - local/custom mirrors can be added here or in separate files
+#   - repositories listed first will take precedence when packages
+#     have identical names, regardless of version number
+#   - URLs will have $repo replaced by the name of the current repo
+#   - URLs will have $arch replaced by the name of the architecture
+#
+# Repository entries are of the format:
+#       [repo-name]
+#       Server = ServerName
+#       Include = IncludePath
+#
+# The header [repo-name] is crucial - it must be present and
+# uncommented to enable the repo.
+#
+
+# The testing repositories are disabled by default. To enable, uncomment the
+# repo name header and Include lines. You can add preferred servers immediately
+# after the header, and they will be used before the default mirrors.
+
+#[testing]
+#Include = /etc/pacman.d/mirrorlist
+
+[core]
+Include = /etc/pacman.d/mirrorlist
+
+[extra]
+Include = /etc/pacman.d/mirrorlist
+
+#[community-testing]
+#Include = /etc/pacman.d/mirrorlist
+
+[community]
+Include = /etc/pacman.d/mirrorlist
+
+# If you want to run 32 bit applications on your x86_64 system,
+# enable the multilib repositories as required here.
+
+#[multilib-testing]
+#Include = /etc/pacman.d/mirrorlist
+
+[multilib]
+Include = /etc/pacman.d/mirrorlist
+
+# An example of a custom package repository.  See the pacman manpage for
+# tips on creating your own repositories.
+#[custom]
+#SigLevel = Optional TrustAll
+#Server = file:///home/custompkgs
diff --git a/install.sh b/install.sh
index 0dad27e..273981a 100755
--- a/install.sh
+++ b/install.sh
@@ -43,13 +43,12 @@ check_consent() {
         true
     else
         [[ "$1" == "y" ]] && default_consent="[Y/n]" || default_consent="[y/N]"
-        printf "%s %s " "$2" "$default_consent"
+        printf "%b %b " "$2" "$default_consent"
         read -r answer
         if [[ "$1" == "n" ]] && [[ "$answer" != y* ]]; then
             printf "%s\n" "$3"
             false
         elif [[ "$1" == "y" ]] && [[ "$answer" == n* ]]; then
-            echo second
             printf "%s\n" "$3"
             false
         else
@@ -59,7 +58,7 @@ check_consent() {
 }
 
 entry_question() {
-    check_consent n "This will take a while, install many packages and link dotfiles all over the place. Proceed?" "Aborting." || exit
+    check_consent n "This will take a while and install many packages and link dotfiles all over the place depending on your selections.\nYou need to be in the base directory of the dotfiles repository.\nProceed?" "Aborting." || exit
 }
 
 enable_git_hooks() {
@@ -80,21 +79,30 @@ stow_dotfiles() {
     echo "Linked dotfiles."
 }
 
+run_elevated() {
+    if command -v doas >/dev/null 2>&1; then
+        doas "$@"
+    elif command -v sudo >/dev/null 2>&1; then
+        sudo "$@"
+    fi
+}
+
 stow_system_packages() {
-    check_consent n "Link system settings as well? This will require sudo access." "Not touching system files." || return
-    sudo stow --dir="$bootstrap_dir" --target="/" -R system-packages/
+    check_consent n "Link system settings files? This will require sudo access and may overwrite existing files." "Not touching system files." || return
+    if [ -e "/etc/pacman.conf" ]; then
+        check_consent n "Found an existing pacman.conf file, installation will error if it exists. Remove file?" && run_elevated rm "/etc/pacman.conf"
+    fi
+    run_elevated stow --dir="$bootstrap_dir" --target="/" -R system-packages/
     echo "Linked system files."
 }
 
 install_packages() {
-    check_consent n "Install pre-designated packages? This will take a while." "Not installing packages." || return
-    export BOOTSTRAP_PACKAGES="bootstrap/packages.txt"
+    check_consent n "Install pre-designated packages? This will take a while, install a lot of packages and require super user privileges." "Not installing packages." || return
     if ! "$UNATTENDED"; then
         "$bootstrap_dir"/install_packages.sh
     else
         "$bootstrap_dir"/install_packages.sh -f
     fi
-    unset BOOTSTRAP_PACKAGES
     echo "Installed packages."
 }
 
@@ -104,12 +112,14 @@ install() {
         entry_question
     fi
 
-    echo "====================== BEGINNING INSTALLATION ============================="
+    echo "====================== BEGINNING SYSTEM FILE MANAGEMENT ============================="
+    stow_system_packages
+
+    echo "====================== BEGINNING PACKAGE INSTALLATION ============================="
     install_packages
 
     echo "=================== BEGINNING DOTFILE MANAGEMENT =========================="
     stow_dotfiles
-    stow_system_packages
 
     echo "================== ENABLING GIT REPOSITORY HOOKS =========================="
     enable_git_hooks