diff --git a/src/prodir/cpp/tree_structurer.cpp b/src/prodir/cpp/tree_structurer.cpp
index 2302cce..fe31f25 100644
--- a/src/prodir/cpp/tree_structurer.cpp
+++ b/src/prodir/cpp/tree_structurer.cpp
@@ -1,5 +1,5 @@
 #include "tree_structurer.hpp"
-
+#include <map>
 #include <algorithm>
 #include <filesystem>
 #include <fstream>
@@ -123,62 +123,166 @@ std::vector<fs::path> TreeStructurer::get_filtered_paths(const fs::path& start)
 
 std::vector<std::string> TreeStructurer::get_directory_structure(const std::string& startpath) {
     std::vector<std::string> result;
-    
     // Normalize the input path by removing ./ or .\ prefix if present
     std::string normalized_path = startpath;
-    if (startpath.substr(0, 2) == ".\\" || startpath.substr(0, 2) == "./") {
-        normalized_path = startpath.substr(2);
+    if (normalized_path.size() >= 2 && 
+        (normalized_path.substr(0, 2) == ".\\" || normalized_path.substr(0, 2) == "./")) {
+        normalized_path = normalized_path.substr(2);
     }
-    
     fs::path start = normalized_path.empty() ? fs::current_path() : fs::path(normalized_path);
-
+    
     try {
-        auto paths = get_filtered_paths(start);
-        if (paths.empty()) {
-            throw std::runtime_error("No valid files or directories found in: " + start.string());
+        if (!fs::exists(start)) {
+            throw std::runtime_error("Directory does not exist: " + start.string());
         }
-        std::vector<bool> is_last_at_level(256, false);
         
-        for (size_t i = 1; i < paths.size(); ++i) {
-            const auto& path = paths[i];
+        if (!fs::is_directory(start)) {
+            throw std::runtime_error("Path is not a directory: " + start.string());
+        }
+        
+        // Start with the root node
+        std::string root_name = start.filename().string();
+        result.push_back(root_name + "/");
+        
+        // First, collect all paths and organize them by their parent directories
+        std::map<std::string, std::vector<fs::path>> dir_contents;
+        std::vector<std::string> dir_paths;  // To maintain order of directories
+        
+        // Add root directory
+        dir_contents["/"] = {};
+        dir_paths.push_back("/");
+        
+        // Collect files and directories
+        for (const auto& entry : fs::recursive_directory_iterator(start)) {
+            const auto& path = entry.path();
             std::string rel_path = get_relative_path(path, start);
             
-            int level = std::count(rel_path.begin(), rel_path.end(), fs::path::preferred_separator);
-
-            bool is_last = true;
-            for (size_t j = i + 1; j < paths.size(); ++j) {
-                std::string next_rel_path = get_relative_path(paths[j], start);
-                int next_level = std::count(next_rel_path.begin(), next_rel_path.end(), fs::path::preferred_separator);
-                if (next_level == level) {
-                    is_last = false;
-                    break;
-                }
-                if (next_level < level) {
+            // Replace backslashes with forward slashes
+            std::replace(rel_path.begin(), rel_path.end(), '\\', '/');
+            
+            // Skip if it should be ignored
+            bool should_skip = false;
+            for (const auto& component : path) {
+                if (should_ignore_dir(component.string())) {
+                    should_skip = true;
                     break;
                 }
             }
-
-            is_last_at_level[level] = is_last;
-
-            std::string line;
-            for (int j = 0; j < level; ++j) {
-                if (j == level - 1) {
-                    line += is_last ? "└── " : "├── ";
-                } else {
-                    line += is_last_at_level[j] ? "    " : "│   ";
+            if (should_skip) continue;
+            
+            if (entry.is_directory()) {
+                if (should_ignore_dir(path.filename().string())) {
+                    continue;
                 }
+                
+                // Add directory to its parent
+                std::string parent_path = "/";
+                size_t last_slash = rel_path.find_last_of('/');
+                if (last_slash != std::string::npos) {
+                    parent_path = rel_path.substr(0, last_slash);
+                    if (parent_path.empty()) {
+                        parent_path = "/";
+                    }
+                }
+                
+                // Create parent directory entry if it doesn't exist
+                if (dir_contents.find(parent_path) == dir_contents.end()) {
+                    dir_contents[parent_path] = {};
+                    dir_paths.push_back(parent_path);
+                }
+                
+                // Create directory entry
+                dir_contents[parent_path].push_back(path);
+                
+                // Create entry for this directory's contents
+                dir_contents[rel_path] = {};
+                dir_paths.push_back(rel_path);
+            } else {
+                if (should_ignore_file(path.filename().string())) {
+                    continue;
+                }
+                
+                // Add file to its parent
+                std::string parent_path = "/";
+                size_t last_slash = rel_path.find_last_of('/');
+                if (last_slash != std::string::npos) {
+                    parent_path = rel_path.substr(0, last_slash);
+                    if (parent_path.empty()) {
+                        parent_path = "/";
+                    }
+                }
+                
+                // Create parent directory entry if it doesn't exist
+                if (dir_contents.find(parent_path) == dir_contents.end()) {
+                    dir_contents[parent_path] = {};
+                    dir_paths.push_back(parent_path);
+                }
+                
+                dir_contents[parent_path].push_back(path);
             }
-
-            line += path.filename().string();
-            if (fs::is_directory(path)) {
-                line += "/";
-            }
-            result.push_back(line);
         }
+        
+        // Now create the tree structure
+        std::function<void(const std::string&, const std::string&, std::vector<bool>&)> 
+        build_tree = [&](const std::string& dir_path, const std::string& prefix, std::vector<bool>& is_last_stack) {
+            // Sort paths - directories first, then files
+            std::vector<fs::path>& paths = dir_contents[dir_path];
+            std::sort(paths.begin(), paths.end(), [](const fs::path& a, const fs::path& b) {
+                bool a_is_dir = fs::is_directory(a);
+                bool b_is_dir = fs::is_directory(b);
+                if (a_is_dir != b_is_dir) {
+                    return a_is_dir > b_is_dir;  // Directories before files
+                }
+                return a.filename() < b.filename();  // Alphabetical order
+            });
+            
+            // Add entries for this directory
+            for (size_t i = 0; i < paths.size(); ++i) {
+                const auto& path = paths[i];
+                bool is_last = (i == paths.size() - 1);
+                
+                // Build the line prefix
+                std::string line_prefix = prefix;
+                if (!prefix.empty()) {
+                    line_prefix += is_last ? "└── " : "├── ";
+                }
+                
+                // Add the file/directory name
+                std::string name = path.filename().string();
+                std::string line = line_prefix + name;
+                
+                if (fs::is_directory(path)) {
+                    line += "/";
+                }
+                
+                result.push_back(line);
+                
+                // If it's a directory, process its contents with updated prefix
+                if (fs::is_directory(path)) {
+                    std::string rel_path = get_relative_path(path, start);
+                    std::replace(rel_path.begin(), rel_path.end(), '\\', '/');
+                    
+                    std::string next_prefix = prefix;
+                    if (!prefix.empty()) {
+                        next_prefix += is_last ? "    " : "│   ";
+                    }
+                    
+                    std::vector<bool> next_is_last_stack = is_last_stack;
+                    next_is_last_stack.push_back(is_last);
+                    
+                    build_tree(rel_path, next_prefix, next_is_last_stack);
+                }
+            }
+        };
+        
+        // Start building the tree from the root
+        std::vector<bool> is_last_stack;
+        build_tree("/", "", is_last_stack);
+        
     } catch (const fs::filesystem_error& e) {
         throw std::runtime_error("Failed to access directory: " + std::string(e.what()));
     }
-
+    
     return result;
 }
 
@@ -406,7 +510,7 @@ void TreeStructurer::create_file(const fs::path& path) {
     }
 }
 
-// Reads a structure file into a vector of non-empty lines.
+// Reads a structure file into a vector of non-empty lines, ignoring comments.
 std::vector<std::string> TreeStructurer::read_structure_file(const std::string& filepath) {
     std::vector<std::string> lines;
     // Open file in binary mode to avoid Windows CRLF conversion
@@ -416,16 +520,45 @@ std::vector<std::string> TreeStructurer::read_structure_file(const std::string&
     }
 
     std::string line;
+
     while (std::getline(file, line)) {
         // Remove carriage return if present (Windows files)
         if (!line.empty() && line.back() == '\r') {
             line.pop_back();
         }
-        
+
+        std::cout << "Processing line: " << line << std::endl;
+
+        size_t hash_pos = line.find('#');
+        size_t single_line_comment_pos = line.find("//");
+        size_t multi_line_comment_start_pos = line.find("/*");
+
+        if (hash_pos != std::string::npos) {
+            // Trim the line at the hash comment
+            line = line.substr(0, hash_pos);
+            std::cout << "Trimmed line at hash comment position: " << hash_pos << std::endl;
+        } else if (single_line_comment_pos != std::string::npos) {
+            // Trim the line at the single-line comment
+            line = line.substr(0, single_line_comment_pos);
+            std::cout << "Trimmed line at single-line comment position: " << single_line_comment_pos << std::endl;
+        } else if (multi_line_comment_start_pos != std::string::npos) {
+            // Trim the line at the multi-line comment start
+            line = line.substr(0, multi_line_comment_start_pos);
+            std::cout << "Trimmed line at multi-line comment start position: " << multi_line_comment_start_pos << std::endl;
+        }
+
+        // Remove leading and trailing whitespace
+        line.erase(0, line.find_first_not_of(" \t\n\r\f\v"));
+        line.erase(line.find_last_not_of(" \t\n\r\f\v") + 1);
+
         if (!line.empty()) {
             lines.push_back(line);
+            std::cout << "Added non-empty line: " << line << std::endl;
+        } else {
+            std::cout << "Skipped empty or commented-out line." << std::endl;
         }
     }
+
     return lines;
 }
 // Checks the structure for obvious mistakes (e.g. a jump in indentation).