diff --git a/src/directories.cc b/src/directories.cc
index 5a761a4..cbda763 100644
--- a/src/directories.cc
+++ b/src/directories.cc
@@ -160,7 +160,7 @@ void Directories::select(const boost::filesystem::path &path) {
   if(current_path=="")
     return;
     
-  if(path.string().substr(0, current_path.string().size())!=current_path.string())
+  if(path.generic_string().substr(0, current_path.generic_string().size()+1)!=current_path.generic_string()+'/')
     return;
   
   std::list<boost::filesystem::path> paths;
diff --git a/src/juci.cc b/src/juci.cc
index 67075d2..b4c6b67 100644
--- a/src/juci.cc
+++ b/src/juci.cc
@@ -25,9 +25,9 @@ int app::on_command_line(const Glib::RefPtr<Gio::ApplicationCommandLine> &cmd) {
       if(boost::filesystem::exists(p)) {
         p=boost::filesystem::canonical(p);
         if(boost::filesystem::is_regular_file(p))
-          files.emplace_back(p.string());
+          files.emplace_back(p);
         else if(boost::filesystem::is_directory(p))
-          directories.emplace_back(p.string());
+          directories.emplace_back(p);
       }
       else
         std::cerr << "Path " << p << " does not exist." << std::endl;
@@ -49,16 +49,17 @@ void app::on_activate() {
     }
     else {
       std::string files_in_directory;
-      for(size_t c=0;c<files.size();c++) {
-        if(files[c].substr(0, directory.size())==directory) {
-          files_in_directory+=" "+files[c];
-          files.erase(files.begin()+c);
-          c--;
+      for(auto it=files.begin();it!=files.end();) {
+        if(it->generic_string().substr(0, directory.generic_string().size()+1)==directory.generic_string()+'/') {
+          files_in_directory+=" "+it->string();
+          it=files.erase(it);
         }
+        else
+          it++;
       }
       std::thread another_juci_app([this, directory, files_in_directory](){
-        Singleton::terminal()->async_print("Executing: juci "+directory+files_in_directory);
-        Singleton::terminal()->execute("juci "+directory+files_in_directory, ""); //TODO: do not open pipes here, doing this after Juci compiles on Windows
+        Singleton::terminal()->async_print("Executing: juci "+directory.string()+files_in_directory);
+        Singleton::terminal()->execute("juci "+directory.string()+files_in_directory, ""); //TODO: do not open pipes here, doing this after Juci compiles on Windows
       });
       another_juci_app.detach();
     }
diff --git a/src/juci.h b/src/juci.h
index 0f9043b..551a352 100644
--- a/src/juci.h
+++ b/src/juci.h
@@ -3,6 +3,7 @@
 
 #include "window.h"
 #include "logging.h"
+
 class app : public Gtk::Application {
  public:
   app();
@@ -11,8 +12,8 @@ class app : public Gtk::Application {
 
  private:
   std::unique_ptr<Window> window;
-  std::vector<std::string> directories;
-  std::vector<std::string> files;
+  std::vector<boost::filesystem::path> directories;
+  std::vector<boost::filesystem::path> files;
 };
 
 #endif // JUCI_JUCI_H_
diff --git a/src/notebook.cc b/src/notebook.cc
index 40b9874..facb803 100644
--- a/src/notebook.cc
+++ b/src/notebook.cc
@@ -67,7 +67,7 @@ void Notebook::open(const boost::filesystem::path &file_path) {
   auto language=Source::guess_language(file_path);
   if(language && (language->get_id()=="chdr" || language->get_id()=="c" || language->get_id()=="cpp" || language->get_id()=="objc")) {
     boost::filesystem::path project_path;
-    if(directories.cmake && directories.cmake->project_path!="" && file_path.string().substr(0, directories.cmake->project_path.string().size())==directories.cmake->project_path.string())
+    if(directories.cmake && directories.cmake->project_path!="" && file_path.generic_string().substr(0, directories.cmake->project_path.generic_string().size()+1)==directories.cmake->project_path.generic_string()+'/')
       project_path=directories.cmake->project_path;
     else {
       project_path=file_path.parent_path();
@@ -153,7 +153,7 @@ bool Notebook::save(int page, bool reparse_needed) {
       //If CMakeLists.txt have been modified:
       //TODO: recreate cmake even without directories open?
       if(view->file_path.filename()=="CMakeLists.txt") {
-        if(directories.cmake && directories.cmake->project_path!="" && view->file_path.string().substr(0, directories.cmake->project_path.string().size())==directories.cmake->project_path.string() && CMake::create_compile_commands(directories.cmake->project_path)) {
+        if(directories.cmake && directories.cmake->project_path!="" && view->file_path.generic_string().substr(0, directories.cmake->project_path.generic_string().size()+1)==directories.cmake->project_path.generic_string()+'/' && CMake::create_compile_commands(directories.cmake->project_path)) {
           for(auto source_view: source_views) {
             if(auto source_clang_view=dynamic_cast<Source::ClangView*>(source_view)) {
               if(directories.cmake->project_path.string()==source_clang_view->project_path) {