diff --git a/.dotter/global.toml b/.dotter/global.toml
index 8df8a65..ff38ee2 100644
--- a/.dotter/global.toml
+++ b/.dotter/global.toml
@@ -32,7 +32,7 @@ depends = []
 "fish/fish_plugins" = "~/.config/fish/fish_plugins"
 "fish/completions" = "~/.config/fish/completions"
 "fish/conf.d" = "~/.config/fish/conf.d"
-"fish/functions" = "~/.config/fish/functions"
+# Note: fish/functions is managed directly as a directory symlink in setup.sh
 
 [fish.variables]
 
diff --git a/CLAUDE.md b/CLAUDE.md
index 94114ee..f558455 100644
--- a/CLAUDE.md
+++ b/CLAUDE.md
@@ -10,3 +10,7 @@ Dotter automatically treats files with `{{` as templates. For files that contain
 target = "~/.config/nvim/lua/plugins/hop.lua"
 type = "symbolic"
 ```
+
+## Directory Symlinks in setup.sh
+
+For directories where programs create new files that should be tracked (e.g., fish's `funcsave` command), use the `ensure_dir_symlink` function in `setup.sh` instead of Dotter. This symlinks the entire directory so dynamically created files are automatically tracked in the repository.
diff --git a/fish/functions/ls.fish b/fish/functions/ls.fish
new file mode 100644
index 0000000..cf6cab1
--- /dev/null
+++ b/fish/functions/ls.fish
@@ -0,0 +1,3 @@
+function ls --wraps=eza --description 'alias ls eza'
+    eza $argv
+end
diff --git a/setup.sh b/setup.sh
index 89328bb..8dad085 100755
--- a/setup.sh
+++ b/setup.sh
@@ -2,6 +2,68 @@
 
 set -eo pipefail
 
+# Function to manage directory symlinks
+# Usage: ensure_dir_symlink <source_dir> <target_link> <force_flag>
+# Args:
+#   source_dir: The actual directory to symlink to (must be absolute path)
+#   target_link: The symlink location to create
+#   force_flag: true/false - whether to force replacement if exists
+ensure_dir_symlink() {
+    local source_dir="$1"
+    local target_link="$2"
+    local force_flag="$3"
+
+    # Expand tilde in paths
+    target_link="${target_link/#\~/$HOME}"
+    source_dir="${source_dir/#\~/$HOME}"
+
+    # Check if target exists
+    if [[ -e "$target_link" || -L "$target_link" ]]; then
+        # Check if it's already a symlink pointing to the right place
+        if [[ -L "$target_link" ]]; then
+            local current_target
+            current_target="$(readlink "$target_link")"
+            if [[ "$current_target" == "$source_dir" ]]; then
+                echo "✓ $target_link already symlinked correctly"
+                return 0
+            else
+                # Symlink exists but points to wrong location
+                if [[ "$force_flag" == true ]]; then
+                    echo "Replacing symlink $target_link (currently points to $current_target)"
+                    rm "$target_link"
+                else
+                    echo "⚠ Warning: $target_link exists but points to $current_target (expected $source_dir)"
+                    echo "  Run with --force-deploy to replace it"
+                    return 0
+                fi
+            fi
+        else
+            # Path exists but is not a symlink
+            if [[ "$force_flag" == true ]]; then
+                echo "Replacing $target_link with symlink (was a regular file/directory)"
+                rm -rf "$target_link"
+            else
+                echo "⚠ Warning: $target_link exists but is not a symlink"
+                echo "  Run with --force-deploy to replace it"
+                return 0
+            fi
+        fi
+    fi
+
+    # Create parent directory if needed
+    local parent_dir
+    parent_dir="$(dirname "$target_link")"
+    if [[ ! -d "$parent_dir" ]]; then
+        echo "Creating parent directory: $parent_dir"
+        mkdir -p "$parent_dir"
+    fi
+
+    # Create the symlink
+    echo "Creating symlink: $target_link -> $source_dir"
+    ln -s "$source_dir" "$target_link"
+    echo "✓ Successfully created symlink"
+}
+
 # Parse command line arguments
 RESET_CONFIG=false
 FORCE_DEPLOY=false
@@ -192,6 +254,12 @@ else
     fi
 fi
 
+# Manage directory symlinks (not handled by Dotter)
+echo ""
+echo "Setting up directory symlinks..."
+DOTFILES_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+ensure_dir_symlink "$DOTFILES_DIR/fish/functions" "~/.config/fish/functions" "$FORCE_DEPLOY"
+
 echo ""
 echo "✓ Setup complete!"
 echo ""