diff --git a/xml_converter/integration_tests/test_cases/proto_and_xml_input_no_duplicates/testcase.yaml b/xml_converter/integration_tests/test_cases/proto_and_xml_input_no_duplicates/testcase.yaml
index d36081b1..9f5d0f93 100644
--- a/xml_converter/integration_tests/test_cases/proto_and_xml_input_no_duplicates/testcase.yaml
+++ b/xml_converter/integration_tests/test_cases/proto_and_xml_input_no_duplicates/testcase.yaml
@@ -8,9 +8,9 @@ expected_stdout: |
     Please remove one of the packs or edit the name of the packs' top level category before running the program again.
     If you want to bypass this stop, use '--allow-duplicates'.
     The following top level categories were found in more than one pack:
-    mycategory in files
-    pack/xml_file.xml
-    pack3/xml_file.xml
-    pack2/markers.bin
+        "mycategory" in files:
+            pack/xml_file.xml
+            pack2/markers.bin
+            pack3/xml_file.xml
 expected_stderr: |
 expected_returncode: 0
\ No newline at end of file
diff --git a/xml_converter/src/xml_converter.cpp b/xml_converter/src/xml_converter.cpp
index 2392d950..18f88ddd 100644
--- a/xml_converter/src/xml_converter.cpp
+++ b/xml_converter/src/xml_converter.cpp
@@ -36,6 +36,7 @@ bool filename_comp(string a, string b) {
     return lowercase(a) < lowercase(b);
 }
 
+// Searchs for files within a directory with a suffix and returns their relative paths.
 vector<string> get_files_by_suffix(string directory, string suffix) {
     vector<string> files;
     DIR* dir = opendir(directory.c_str());
@@ -49,11 +50,11 @@ vector<string> get_files_by_suffix(string directory, string suffix) {
                 // Default: markerpacks have all xml files in the first directory
                 for (string subfile : subfiles) {
                     cout << subfile << " found in subfolder" << endl;
-                    files.push_back(subfile);
+                    files.push_back(join_file_paths(filename, subfile));
                 }
             }
             else if (has_suffix(filename, suffix)) {
-                files.push_back(path);
+                files.push_back(filename);
             }
         }
     }
@@ -66,7 +67,7 @@ map<string, vector<string>> read_taco_directory(
     string input_path,
     map<string, Category>* marker_categories,
     vector<Parseable*>* parsed_pois) {
-    map<string, vector<string>> category_to_filepath;
+    map<string, vector<string>> top_level_category_file_locations;
     if (!filesystem::exists(input_path)) {
         cout << "Error: " << input_path << " is not an existing directory or file" << endl;
     }
@@ -74,28 +75,28 @@ map<string, vector<string>> read_taco_directory(
         string directory_name = filesystem::path(input_path).filename();
         vector<string> xml_files = get_files_by_suffix(input_path, ".xml");
         for (const string& path : xml_files) {
-            set<string> category_names = (parse_xml_file(path, input_path, marker_categories, parsed_pois));
-            string relative_path = directory_name + path.substr(input_path.size());
-            for (set<string>::iterator it = category_names.begin(); it != category_names.end(); it++) {
-                category_to_filepath[*it].push_back(relative_path);
+            set<string> top_level_category_names = parse_xml_file(join_file_paths(input_path, path), input_path, marker_categories, parsed_pois);
+            string relative_path = join_file_paths(directory_name, path);
+            for (set<string>::iterator it = top_level_category_names.begin(); it != top_level_category_names.end(); it++) {
+                top_level_category_file_locations[*it].push_back(relative_path);
             }
         }
     }
     else if (filesystem::is_regular_file(input_path)) {
-        set<string> category_names = parse_xml_file(input_path, get_base_dir(input_path), marker_categories, parsed_pois);
+        set<string> top_level_category_names = parse_xml_file(input_path, get_base_dir(input_path), marker_categories, parsed_pois);
         string filename = filesystem::path(input_path).filename();
-        for (set<string>::iterator it = category_names.begin(); it != category_names.end(); it++) {
-            category_to_filepath[*it].push_back(filename);
+        for (set<string>::iterator it = top_level_category_names.begin(); it != top_level_category_names.end(); it++) {
+            top_level_category_file_locations[*it].push_back(filename);
         }
     }
-    return category_to_filepath;
+    return top_level_category_file_locations;
 }
 
 map<string, vector<string>> read_burrito_directory(
     string input_path,
     map<string, Category>* marker_categories,
     vector<Parseable*>* parsed_pois) {
-    map<string, vector<string>> category_to_filepath;
+    map<string, vector<string>> top_level_category_file_locations;
     if (!filesystem::exists(input_path)) {
         cout << "Error: " << input_path << " is not an existing directory or file" << endl;
     }
@@ -103,21 +104,21 @@ map<string, vector<string>> read_burrito_directory(
         string directory_name = filesystem::path(input_path).filename();
         vector<string> burrito_files = get_files_by_suffix(input_path, ".bin");
         for (const string& path : burrito_files) {
-            set<string> category_names = read_protobuf_file(path, input_path, marker_categories, parsed_pois);
-            string relative_path = directory_name + path.substr(input_path.size());
-            for (set<string>::iterator it = category_names.begin(); it != category_names.end(); it++) {
-                category_to_filepath[*it].push_back(relative_path);
+            set<string> top_level_category_names = read_protobuf_file(join_file_paths(input_path, path), input_path, marker_categories, parsed_pois);
+            string relative_path = join_file_paths(directory_name, path);
+            for (set<string>::iterator it = top_level_category_names.begin(); it != top_level_category_names.end(); it++) {
+                top_level_category_file_locations[*it].push_back(relative_path);
             }
         }
     }
     else if (filesystem::is_regular_file(input_path)) {
-        set<string> category_names = read_protobuf_file(input_path, get_base_dir(input_path), marker_categories, parsed_pois);
+        set<string> top_level_category_names = read_protobuf_file(input_path, get_base_dir(input_path), marker_categories, parsed_pois);
         string filename = filesystem::path(input_path).filename();
-        for (set<string>::iterator it = category_names.begin(); it != category_names.end(); it++) {
-            category_to_filepath[*it].push_back(filename);
+        for (set<string>::iterator it = top_level_category_names.begin(); it != top_level_category_names.end(); it++) {
+            top_level_category_file_locations[*it].push_back(filename);
         }
     }
-    return category_to_filepath;
+    return top_level_category_file_locations;
 }
 
 void write_taco_directory(
@@ -172,21 +173,20 @@ void process_data(
     // All of the loaded pois and categories
     vector<Parseable*> parsed_pois;
     map<string, Category> marker_categories;
-    map<string, vector<vector<string>>> category_to_marker_pack_names;
-    map<string, vector<string>> duplicate_categories;
+    map<string, vector<vector<string>>> top_level_category_file_locations_by_pack;
+    map<string, set<string>> duplicate_categories;
 
     // Read in all the xml taco markerpacks
     auto begin = chrono::high_resolution_clock::now();
     for (size_t i = 0; i < input_taco_paths.size(); i++) {
         cout << "Loading taco pack " << input_taco_paths[i] << endl;
 
-        // swap this to map <category, set<filenames>>)
-        map<string, vector<string>> category_names = read_taco_directory(
+        map<string, vector<string>> top_level_category_file_locations = read_taco_directory(
             input_taco_paths[i],
             &marker_categories,
             &parsed_pois);
-        for (map<string, vector<string>>::iterator it = category_names.begin(); it != category_names.end(); it++) {
-            category_to_marker_pack_names[it->first].push_back(it->second);
+        for (map<string, vector<string>>::iterator it = top_level_category_file_locations.begin(); it != top_level_category_file_locations.end(); it++) {
+            top_level_category_file_locations_by_pack[it->first].push_back(it->second);
         }
     }
     auto end = chrono::high_resolution_clock::now();
@@ -198,20 +198,20 @@ void process_data(
     for (size_t i = 0; i < input_guildpoint_paths.size(); i++) {
         cout << "Loading guildpoint pack " << input_guildpoint_paths[i] << endl;
 
-        map<string, vector<string>> category_names = read_burrito_directory(
+        map<string, vector<string>> top_level_category_file_locations = read_burrito_directory(
             input_guildpoint_paths[i],
             &marker_categories,
             &parsed_pois);
-        for (map<string, vector<string>>::iterator it = category_names.begin(); it != category_names.end(); it++) {
-            category_to_marker_pack_names[it->first].push_back(it->second);
+        for (map<string, vector<string>>::iterator it = top_level_category_file_locations.begin(); it != top_level_category_file_locations.end(); it++) {
+            top_level_category_file_locations_by_pack[it->first].push_back(it->second);
         }
     }
 
-    for (map<string, vector<vector<string>>>::iterator it = category_to_marker_pack_names.begin(); it != category_to_marker_pack_names.end(); it++) {
+    for (map<string, vector<vector<string>>>::iterator it = top_level_category_file_locations_by_pack.begin(); it != top_level_category_file_locations_by_pack.end(); it++) {
         if (it->second.size() != 1) {
             for (size_t i = 0; i < it->second.size(); i++) {
                 for (size_t j = 0; j < it->second[i].size(); j++) {
-                    duplicate_categories[it->first].push_back(it->second[i][j]);
+                    duplicate_categories[it->first].insert(it->second[i][j]);
                 }
             }
         }
@@ -224,10 +224,10 @@ void process_data(
         cout << "Please remove one of the packs or edit the name of the packs' top level category before running the program again." << endl;
         cout << "If you want to bypass this stop, use '--allow-duplicates'." << endl;
         cout << "The following top level categories were found in more than one pack:" << endl;
-        for (map<string, vector<string>>::iterator it = duplicate_categories.begin(); it != duplicate_categories.end(); it++) {
-            cout << it->first << " in files:" << endl;
+        for (map<string, set<string>>::iterator it = duplicate_categories.begin(); it != duplicate_categories.end(); it++) {
+            cout << "    \"" << it->first << "\" in files:" << endl;
             for (string str : it->second) {
-                cout << str << endl;
+                cout << "        " << str << endl;
             }
         }
         return;