diff --git a/src/check.sh b/src/check.sh
index b0df8ff..598802a 100644
--- a/src/check.sh
+++ b/src/check.sh
@@ -6,4 +6,5 @@ check() {
   log debug "collected bkp files:\n$bkp_files"
 
   scan_packages
+  merge_base "$base_files"
 }
diff --git a/src/configuration.sh b/src/configuration.sh
index 71a3d5a..0a9faf3 100644
--- a/src/configuration.sh
+++ b/src/configuration.sh
@@ -15,7 +15,7 @@ scan_directory() {
     done
   fi
 
-  echo "$files"
+  printf "%b" "$files"
 }
 
 scan_packages() {
diff --git a/src/file/merge_base.sh b/src/file/merge_base.sh
new file mode 100644
index 0000000..42f9d0e
--- /dev/null
+++ b/src/file/merge_base.sh
@@ -0,0 +1,20 @@
+merge_base() {
+  local base_files="$1"
+  local strategy=
+
+  for file in $base_files; do
+    log debug "[merge-base] Processing $file"
+    local absolute_path="$(echo "$file" | sed 's/^base//')"
+    log debug "[merge-base] Absolute path: $absolute_path"
+    local config_path="$CONFIG_ROOT/$file"
+    log debug "[merge-base] Config path: $config_path"
+
+    if diff "$absolute_path" "$config_path" > /dev/null; then
+      log debug "[merge-base] Files match"
+    else
+      log debug "[merge-base] Files differ"
+      strategy="$(ask "Configuration and system files differ" "Overwrite system,Overwrite config,Show difference")"
+      log debug "[merge-base] Chosen strategy: $strategy"
+    fi
+  done
+}
diff --git a/src/index.sh b/src/index.sh
index f168b74..9899f9a 100644
--- a/src/index.sh
+++ b/src/index.sh
@@ -9,3 +9,5 @@
 . "$TORI_ROOT/src/package/validate_input_packages.sh"
 . "$TORI_ROOT/src/package/package_conflict_input_parser.sh"
 . "$TORI_ROOT/src/package/update_package_cache.sh"
+
+. "$TORI_ROOT/src/file/merge_base.sh"