diff --git a/config.example.toml b/config.example.toml
index fb8c5096..247d87d9 100644
--- a/config.example.toml
+++ b/config.example.toml
@@ -2,188 +2,239 @@
 # [include] sections are processed in the order you write them
 # Files in $CONFIG_DIR/topgrade.d/ are automatically included before this file
 [include]
-#paths = ["/etc/topgrade.toml"]
+# paths = ["/etc/topgrade.toml"]
+
 
 [misc]
-# Don't ask for confirmations
-#assume_yes = true
-
-# Disable specific steps - same options as the command line flag
-#disable = ["system", "emacs"]
-
-# Ignore failures for these steps
-#ignore_failures = ["powershell"]
-
-# Run specific steps - same options as the command line flag
-#only = ["system", "emacs"]
-
-# Do not ask to retry failed steps (default: false)
-#no_retry = true
-
-# Sudo command to be used
-#sudo_command = "sudo"
-
 # Run `sudo -v` to cache credentials at the start of the run
 # This avoids a blocking password prompt in the middle of an unattended run
-#pre_sudo = false
+# (default: false)
+# pre_sudo = false
 
-# Run inside tmux
-#run_in_tmux = true
+# Sudo command to be used
+# sudo_command = "sudo"
+
+# Disable specific steps - same options as the command line flag
+# disable = ["system", "emacs"]
+
+# Ignore failures for these steps
+# ignore_failures = ["powershell"]
 
 # List of remote machines with Topgrade installed on them
-#remote_topgrades = ["toothless", "pi", "parnas"]
-
-# Arguments to pass to SSH when upgrading remote systems
-#ssh_arguments = "-o ConnectTimeout=2"
+# remote_topgrades = ["toothless", "pi", "parnas"]
 
 # Path to Topgrade executable on remote machines
-#remote_topgrade_path = ".cargo/bin/topgrade"
+# remote_topgrade_path = ".cargo/bin/topgrade"
+
+# Arguments to pass to SSH when upgrading remote systems
+# ssh_arguments = "-o ConnectTimeout=2"
 
 # Arguments to pass tmux when pulling Repositories
-#tmux_arguments = "-S /var/tmux.sock"
+# tmux_arguments = "-S /var/tmux.sock"
 
-# Do not set the terminal title
-#set_title = false
+# Do not set the terminal title (dfault: true)
+# set_title = true
 
-# Display the time in step titles
+# Display the time in step titles (default: true)
 # display_time = true
 
-# Cleanup temporary or old files
-#cleanup = true
+# Don't ask for confirmations (no default value)
+# assume_yes = true
 
-# Skip sending a notification at the end of a run
-#skip_notify = true
+# Do not ask to retry failed steps (default: false)
+# no_retry = true
 
-# Whether to self update (this is ignored if the binary has been built without self update support, available also via setting the environment variable TOPGRADE_NO_SELF_UPGRADE)
-#no_self_update = true
+# Run inside tmux (default: false)
+# run_in_tmux = true
 
-# Extra Home Manager arguments
-#home_manager_arguments = ["--flake", "file"]
+# Cleanup temporary or old files (default: false)
+# cleanup = true
+
+# Send a notification for every step (default: false)
+# notify_each_step = false
+
+# Skip sending a notification at the end of a run (default: false)
+# skip_notify = true
+
+# The Bash-it branch to update (default: "stable")
+# bashit_branch = "stable"
+
+# Run specific steps - same options as the command line flag
+# only = ["system", "emacs"]
+
+# Whether to self update
+#
+# this will be ignored if the binary is built without self update support
+#
+# available also via setting the environment variable TOPGRADE_NO_SELF_UPGRADE)
+# no_self_update = true
 
 # Extra tracing filter directives
 # These are prepended to the `--log-filter` argument
 # See: https://docs.rs/tracing-subscriber/latest/tracing_subscriber/filter/struct.EnvFilter.html#directives
-#log_filters = ["topgrade::command=debug", "warn"]
+# log_filters = ["topgrade::command=debug", "warn"]
+
 
 # Commands to run before anything
 [pre_commands]
-#"Emacs Snapshot" = "rm -rf ~/.emacs.d/elpa.bak && cp -rl ~/.emacs.d/elpa ~/.emacs.d/elpa.bak"
+# "Emacs Snapshot" = "rm -rf ~/.emacs.d/elpa.bak && cp -rl ~/.emacs.d/elpa ~/.emacs.d/elpa.bak"
+
 
 # Commands to run after anything
 [post_commands]
-#"Emacs Snapshot" = "rm -rf ~/.emacs.d/elpa.bak && cp -rl ~/.emacs.d/elpa ~/.emacs.d/elpa.bak"
+# "Emacs Snapshot" = "rm -rf ~/.emacs.d/elpa.bak && cp -rl ~/.emacs.d/elpa ~/.emacs.d/elpa.bak"
+
 
 # Custom commands
 [commands]
-#"Python Environment" = "~/dev/.env/bin/pip install -i https://pypi.python.org/simple -U --upgrade-strategy eager jupyter"
-#"Custom command using interactive shell (unix)" = "-i vim_upgrade"
+# "Python Environment" = "~/dev/.env/bin/pip install -i https://pypi.python.org/simple -U --upgrade-strategy eager jupyter"
+# "Custom command using interactive shell (unix)" = "-i vim_upgrade"
+
 
 [python]
-#enable_pip_review = true                         ###disabled by default
-#enable_pip_review_local = true                   ###disabled by default
-#enable_pipupgrade = true                         ###disabled by default
-#pipupgrade_arguments = "-y -u --pip-path pip"    ###disabled by default
+# enable_pip_review = true                         ###disabled by default
+# enable_pip_review_local = true                   ###disabled by default
+# enable_pipupgrade = true                         ###disabled by default
+# pipupgrade_arguments = "-y -u --pip-path pip"    ###disabled by default
+
 
 [composer]
-#self_update = true
+# self_update = true
+
 
 [brew]
-#greedy_cask = true
-#autoremove = true
+# greedy_cask = true
+# autoremove = true
+
 
 [linux]
-# Arch Package Manager to use. Allowed values: autodetect, aura, garuda_update, pacman, pamac, paru, pikaur, trizen, yay.
-#arch_package_manager = "pacman"
+# Arch Package Manager to use.
+# Allowed values:
+#   autodetect, aura, garuda_update, pacman, pamac, paru, pikaur, trizen, yay
+# arch_package_manager = "pacman"
+
 # Arguments to pass yay (or paru) when updating packages
-#yay_arguments = "--nodevel"
+# yay_arguments = "--nodevel"
+
 # Arguments to pass dnf when updating packages
-#dnf_arguments = "--refresh"
-#aura_aur_arguments = "-kx"
-#aura_pacman_arguments = ""
-#garuda_update_arguments = ""
-#show_arch_news = true
-#trizen_arguments = "--devel"
-#pikaur_arguments = ""
-#pamac_arguments = "--no-devel"
-#enable_tlmgr = true
-#emerge_sync_flags = "-q"
-#emerge_update_flags = "-uDNa --with-bdeps=y world"
-#redhat_distro_sync = false
-#suse_dup = false
-#rpm_ostree = false
-#nix_arguments = "--flake"
-#nix_env_arguments = "--prebuilt-only"
+# dnf_arguments = "--refresh"
+
+# aura_aur_arguments = "-kx"
+
+# aura_pacman_arguments = ""
+# garuda_update_arguments = ""
+
+# show_arch_news = true
+
+# trizen_arguments = "--devel"
+
+# pikaur_arguments = ""
+
+# pamac_arguments = "--no-devel"
+
+# enable_tlmgr = true
+
+# emerge_sync_flags = "-q"
+
+# emerge_update_flags = "-uDNa --with-bdeps=y world"
+
+# redhat_distro_sync = false
+
+# suse_dup = false
+
+# rpm_ostree = false
+
+# nix_arguments = "--flake"
+
+# nix_env_arguments = "--prebuilt-only"
+
+# Extra Home Manager arguments
+# home_manager_arguments = ["--flake", "file"]
+
 
 [git]
-#max_concurrency = 5
+# max_concurrency = 5
+
 # Git repositories that you want to pull and push
-#repos = [
-#    "~/src/*/",
-#    "~/.config/something"
-#]
+# repos = [
+#     "~/src/*/",
+#     "~/.config/something"
+# ]
 
 # Repositories that you only want to pull
-#pull_only_repos = [
-#    "~/.config/something_else"
-#]
+# pull_only_repos = [
+#     "~/.config/something_else"
+# ]
 
 # Repositories that you only want to push
-#push_only_repos = [
-#    "~/src/*/",
-#    "~/.config/something_third"
-#]
+# push_only_repos = [
+#     "~/src/*/",
+#     "~/.config/something_third"
+# ]
 
 # Don't pull the predefined git repos
-#pull_predefined = false
+# pull_predefined = false
 
 # Arguments to pass Git when pulling repositories
-#pull_arguments = "--rebase --autostash"
+# pull_arguments = "--rebase --autostash"
 
 # Arguments to pass Git when pushing repositories
-#push_arguments = "--all"
+# push_arguments = "--all"
+
 
 [windows]
 # Manually select Windows updates
-#accept_all_updates = false
-#open_remotes_in_new_terminal = true
-#wsl_update_pre_release = true
-#wsl_update_use_web_download = true
+# accept_all_updates = false
+
+# open_remotes_in_new_terminal = true
+
+# wsl_update_pre_release = true
+
+# wsl_update_use_web_download = true
 
 # Causes Topgrade to rename itself during the run to allow package managers
 # to upgrade it. Use this only if you installed Topgrade by using a package
 # manager such as Scoop or Cargo
-#self_rename = true
+# self_rename = true
+
 
 [npm]
 # Use sudo if the NPM directory isn't owned by the current user
-#use_sudo = true
+# use_sudo = true
+
 
 [yarn]
 # Run `yarn global upgrade` with `sudo`
-#use_sudo = true
+# use_sudo = true
+
 
 [vim]
 # For `vim-plug`, execute `PlugUpdate!` instead of `PlugUpdate`
-#force_plug_update = true
+# force_plug_update = true
+
 
 [firmware]
 # Offer to update firmware; if false just check for and display available updates
-#upgrade = true
+# upgrade = true
+
 
 [vagrant]
 # Vagrant directories
-#directories = []
+# directories = []
 
 # power on vagrant boxes if needed
-#power_on = true
+# power_on = true
 
 # Always suspend vagrant boxes instead of powering off
-#always_suspend = true
+# always_suspend = true
+
 
 [flatpak]
 # Use sudo for updating the system-wide installation
-#use_sudo = true
+# use_sudo = true
+
 
 [distrobox]
-#use_root = false
-#containers = ["archlinux-latest"]
+# use_root = false
+
+# containers = ["archlinux-latest"]
\ No newline at end of file
diff --git a/src/config.rs b/src/config.rs
index cc176f7b..10ebbbb9 100644
--- a/src/config.rs
+++ b/src/config.rs
@@ -42,57 +42,6 @@ macro_rules! str_value {
     };
 }
 
-macro_rules! check_deprecated {
-    ($config:expr, $old:ident, $section:ident, $new:ident) => {
-        if $config.$old.is_some() {
-            println!(concat!(
-                "'",
-                stringify!($old),
-                "' configuration option is deprecated. Rename it to '",
-                stringify!($new),
-                "' and put it under the section [",
-                stringify!($section),
-                "]",
-            ));
-        }
-    };
-}
-
-/// Get a deprecated option moved from a section to another
-macro_rules! get_deprecated_moved_opt {
-    ($old_section:expr, $old:ident, $new_section:expr, $new:ident) => {{
-        if let Some(old_section) = &$old_section {
-            if old_section.$old.is_some() {
-                return &old_section.$old;
-            }
-        }
-
-        if let Some(new_section) = &$new_section {
-            return &new_section.$new;
-        }
-
-        return &None;
-    }};
-}
-
-macro_rules! get_deprecated_moved_or_default_to {
-    ($old_section:expr, $old:ident, $new_section:expr, $new:ident, $default_ret:ident) => {{
-        if let Some(old_section) = &$old_section {
-            if let Some(old) = old_section.$old {
-                return old;
-            }
-        }
-
-        if let Some(new_section) = &$new_section {
-            if let Some(new) = new_section.$new {
-                return new;
-            }
-        }
-
-        return $default_ret;
-    }};
-}
-
 pub type Commands = BTreeMap<String, String>;
 
 #[derive(ArgEnum, EnumString, EnumVariantNames, Debug, Clone, PartialEq, Eq, Deserialize, EnumIter, Copy)]
@@ -390,11 +339,6 @@ pub struct Misc {
 
     sudo_command: Option<SudoKind>,
 
-    #[merge(strategy = crate::utils::merge_strategies::vec_prepend_opt)]
-    git_repos: Option<Vec<String>>,
-
-    predefined_git_repos: Option<bool>,
-
     #[merge(strategy = crate::utils::merge_strategies::vec_prepend_opt)]
     disable: Option<Vec<Step>>,
 
@@ -409,9 +353,6 @@ pub struct Misc {
     #[merge(strategy = crate::utils::merge_strategies::string_append_opt)]
     ssh_arguments: Option<String>,
 
-    #[merge(strategy = crate::utils::merge_strategies::string_append_opt)]
-    git_arguments: Option<String>,
-
     #[merge(strategy = crate::utils::merge_strategies::string_append_opt)]
     tmux_arguments: Option<String>,
 
@@ -421,15 +362,6 @@ pub struct Misc {
 
     assume_yes: Option<bool>,
 
-    #[merge(strategy = crate::utils::merge_strategies::string_append_opt)]
-    yay_arguments: Option<String>,
-
-    #[merge(strategy = crate::utils::merge_strategies::string_append_opt)]
-    aura_aur_arguments: Option<String>,
-
-    #[merge(strategy = crate::utils::merge_strategies::string_append_opt)]
-    aura_pacman_arguments: Option<String>,
-
     no_retry: Option<bool>,
 
     run_in_tmux: Option<bool>,
@@ -438,8 +370,6 @@ pub struct Misc {
 
     notify_each_step: Option<bool>,
 
-    accept_all_windows_updates: Option<bool>,
-
     skip_notify: Option<bool>,
 
     bashit_branch: Option<String>,
@@ -677,16 +607,6 @@ impl ConfigFile {
             }
         }
 
-        if let Some(misc) = &mut result.misc {
-            if let Some(ref mut paths) = &mut misc.git_repos {
-                for path in paths.iter_mut() {
-                    let expanded = shellexpand::tilde::<&str>(&path.as_ref()).into_owned();
-                    debug!("Path {} expanded to {}", path, expanded);
-                    *path = expanded;
-                }
-            }
-        }
-
         if let Some(paths) = result.git.as_mut().and_then(|git| git.repos.as_mut()) {
             for path in paths.iter_mut() {
                 let expanded = shellexpand::tilde::<&str>(&path.as_ref()).into_owned();
@@ -909,14 +829,6 @@ impl Config {
             ConfigFile::default()
         };
 
-        if let Some(misc) = &config_file.misc {
-            check_deprecated!(misc, git_arguments, git, arguments);
-            check_deprecated!(misc, git_repos, git, repos);
-            check_deprecated!(misc, predefined_git_repos, git, pull_predefined);
-            check_deprecated!(misc, yay_arguments, linux, yay_arguments);
-            check_deprecated!(misc, accept_all_windows_updates, windows, accept_all_updates);
-        }
-
         let allowed_steps = Self::allowed_steps(&opt, &config_file);
 
         Ok(Self {
@@ -947,8 +859,8 @@ impl Config {
     }
 
     /// The list of git repositories to push and pull.
-    pub fn git_repos(&self) -> &Option<Vec<String>> {
-        get_deprecated_moved_opt!(&self.config_file.misc, git_repos, &self.config_file.git, repos)
+    pub fn git_repos(&self) -> Option<&Vec<String>> {
+        self.config_file.git.as_ref().and_then(|git| git.repos.as_ref())
     }
     /// The list of additional git repositories to pull.
     pub fn git_pull_only_repos(&self) -> Option<&Vec<String>> {
@@ -1158,13 +1070,11 @@ impl Config {
 
     /// Whether to accept all Windows updates
     pub fn accept_all_windows_updates(&self) -> bool {
-        get_deprecated_moved_or_default_to!(
-            &self.config_file.misc,
-            accept_all_windows_updates,
-            &self.config_file.windows,
-            accept_all_updates,
-            true
-        )
+        self.config_file
+            .windows
+            .as_ref()
+            .and_then(|windows| windows.accept_all_updates)
+            .unwrap_or(true)
     }
 
     /// Whether to self rename the Topgrade executable during the run
@@ -1447,13 +1357,12 @@ impl Config {
 
     pub fn use_predefined_git_repos(&self) -> bool {
         !self.opt.disable_predefined_git_repos
-            && get_deprecated_moved_or_default_to!(
-                &self.config_file.misc,
-                predefined_git_repos,
-                &self.config_file.git,
-                pull_predefined,
-                true
-            )
+            && self
+                .config_file
+                .git
+                .as_ref()
+                .and_then(|git| git.pull_predefined)
+                .unwrap_or(true)
     }
 
     pub fn verbose(&self) -> bool {
diff --git a/src/steps/git.rs b/src/steps/git.rs
index 1ac964db..d80a1c53 100644
--- a/src/steps/git.rs
+++ b/src/steps/git.rs
@@ -33,6 +33,7 @@ pub enum GitAction {
     Pull,
 }
 
+#[derive(Debug)]
 pub struct Repositories<'a> {
     git: &'a Git,
     pull_repositories: HashSet<String>,
@@ -387,14 +388,27 @@ impl<'a> Repositories<'a> {
         }
     }
 
+    /// Return true if `pull_repos` and `push_repos` are both empty.
     pub fn is_empty(&self) -> bool {
         self.pull_repositories.is_empty() && self.push_repositories.is_empty()
     }
 
+    // The following 2 functions are `#[cfg(unix)]` because they are only used in
+    // the `oh-my-zsh` step, which is UNIX-only.
+
     #[cfg(unix)]
-    pub fn remove(&mut self, path: &str) {
+    /// Return true if `pull_repos` is empty.
+    pub fn pull_is_empty(&self) -> bool {
+        self.pull_repositories.is_empty()
+    }
+
+    #[cfg(unix)]
+    /// Remove `path` from `pull_repos`
+    ///
+    /// # Panic
+    /// Will panic if `path` is not in the `pull_repos` under a debug build.
+    pub fn remove_from_pull(&mut self, path: &str) {
         let _removed = self.pull_repositories.remove(path);
-        let _removed = self.push_repositories.remove(path);
         debug_assert!(_removed);
     }
 }
diff --git a/src/steps/zsh.rs b/src/steps/zsh.rs
index 8274bd72..8cba9ef6 100644
--- a/src/steps/zsh.rs
+++ b/src/steps/zsh.rs
@@ -230,8 +230,8 @@ pub fn run_oh_my_zsh(ctx: &ExecutionContext) -> Result<()> {
         custom_repos.insert_if_repo(entry.path(), crate::steps::git::GitAction::Pull);
     }
 
-    custom_repos.remove(&oh_my_zsh.to_string_lossy());
-    if !custom_repos.is_empty() {
+    custom_repos.remove_from_pull(&oh_my_zsh.to_string_lossy());
+    if !custom_repos.pull_is_empty() {
         println!("Pulling custom plugins and themes");
         ctx.git().multi_pull(&custom_repos, ctx)?;
     }