diff --git a/Makefile b/Makefile
index 11ad938..260c62f 100644
--- a/Makefile
+++ b/Makefile
@@ -1,4 +1,4 @@
-# This Makefile was generated using MakeGen v1.3.5 made by Tim Håkansson
+# This Makefile was generated using MakeGen v1.3.6 made by Tim Håkansson
 # and is licensed under MIT. Full source of the project can be found at
 # https://github.com/Thraix/MakeGen
 CC=@g++
@@ -33,28 +33,28 @@ $(OUTPUT): $(OBJECTS)
 install: all
 	$(info Installing MakeGen to /usr/bin/)
 	@cp $(OUTPUT) /usr/bin/makegen
-$(OBJPATH)/ConfigCLI.o : src/ConfigCLI.cpp src/Common.h src/ConfigCLI.h src/ConfigFile.h src/ConfigUtils.h src/FileUtils.h src/Utils.h src/xml/XMLObject.h
+$(OBJPATH)/ConfigCLI.o : src/ConfigCLI.cpp src/Common.h src/ConfigCLI.h src/ConfigFile.h src/ConfigUtils.h src/FileUtils.h src/Utils.h src/FlagData.h src/xml/XMLObject.h
 	$(info -[10%]- $<)
 	$(CC) $(CFLAGS) -o $@ $<
-$(OBJPATH)/ConfigFile.o : src/ConfigFile.cpp src/ConfigFile.h src/ConfigUtils.h src/Common.h src/FileUtils.h src/Utils.h src/xml/XMLObject.h src/compatibility/ConfigFileConf.h src/xml/XML.h
+$(OBJPATH)/ConfigFile.o : src/ConfigFile.cpp src/ConfigFile.h src/ConfigUtils.h src/Common.h src/FileUtils.h src/Utils.h src/FlagData.h src/xml/XMLObject.h src/compatibility/ConfigFileConf.h src/xml/XML.h
 	$(info -[20%]- $<)
 	$(CC) $(CFLAGS) -o $@ $<
-$(OBJPATH)/HFileGen.o : src/HFileGen.cpp src/FileUtils.h src/Common.h src/Utils.h src/HFileGen.h src/ConfigFile.h src/ConfigUtils.h src/xml/XMLObject.h
+$(OBJPATH)/HFileGen.o : src/HFileGen.cpp src/FileUtils.h src/Common.h src/Utils.h src/HFileGen.h src/ConfigFile.h src/ConfigUtils.h src/FlagData.h src/xml/XMLObject.h
 	$(info -[30%]- $<)
 	$(CC) $(CFLAGS) -o $@ $<
-$(OBJPATH)/IncludeDeps.o : src/IncludeDeps.cpp src/Common.h src/IncludeDeps.h src/ConfigFile.h src/ConfigUtils.h src/FileUtils.h src/Utils.h src/xml/XMLObject.h
+$(OBJPATH)/IncludeDeps.o : src/IncludeDeps.cpp src/Common.h src/IncludeDeps.h src/ConfigFile.h src/ConfigUtils.h src/FileUtils.h src/Utils.h src/FlagData.h src/xml/XMLObject.h
 	$(info -[40%]- $<)
 	$(CC) $(CFLAGS) -o $@ $<
-$(OBJPATH)/Makefile.o : src/Makefile.cpp src/Common.h src/IncludeDeps.h src/ConfigFile.h src/ConfigUtils.h src/FileUtils.h src/Utils.h src/xml/XMLObject.h src/Makefile.h
+$(OBJPATH)/Makefile.o : src/Makefile.cpp src/Common.h src/IncludeDeps.h src/ConfigFile.h src/ConfigUtils.h src/FileUtils.h src/Utils.h src/FlagData.h src/xml/XMLObject.h src/Makefile.h
 	$(info -[50%]- $<)
 	$(CC) $(CFLAGS) -o $@ $<
-$(OBJPATH)/Utils.o : src/Utils.cpp src/ConfigFile.h src/ConfigUtils.h src/Common.h src/FileUtils.h src/Utils.h src/xml/XMLObject.h
+$(OBJPATH)/Utils.o : src/Utils.cpp src/ConfigFile.h src/ConfigUtils.h src/Common.h src/FileUtils.h src/Utils.h src/FlagData.h src/xml/XMLObject.h
 	$(info -[60%]- $<)
 	$(CC) $(CFLAGS) -o $@ $<
-$(OBJPATH)/ConfigFileConf.o : src/compatibility/ConfigFileConf.cpp src/ConfigFile.h src/ConfigUtils.h src/Common.h src/FileUtils.h src/Utils.h src/xml/XMLObject.h src/compatibility/ConfigFileConf.h
+$(OBJPATH)/ConfigFileConf.o : src/compatibility/ConfigFileConf.cpp src/ConfigFile.h src/ConfigUtils.h src/Common.h src/FileUtils.h src/Utils.h src/FlagData.h src/xml/XMLObject.h src/compatibility/ConfigFileConf.h
 	$(info -[70%]- $<)
 	$(CC) $(CFLAGS) -o $@ $<
-$(OBJPATH)/main.o : src/main.cpp src/Common.h src/ConfigCLI.h src/ConfigFile.h src/ConfigUtils.h src/FileUtils.h src/Utils.h src/xml/XMLObject.h src/HFileGen.h src/Makefile.h src/Timer.h
+$(OBJPATH)/main.o : src/main.cpp src/Common.h src/ConfigCLI.h src/ConfigFile.h src/ConfigUtils.h src/FileUtils.h src/Utils.h src/FlagData.h src/xml/XMLObject.h src/HFileGen.h src/Makefile.h src/Timer.h
 	$(info -[80%]- $<)
 	$(CC) $(CFLAGS) -o $@ $<
 $(OBJPATH)/XML.o : src/xml/XML.cpp src/xml/XML.h src/xml/XMLObject.h src/xml/XMLException.h
diff --git a/src/Common.h b/src/Common.h
index b8d88b4..0d51d6e 100755
--- a/src/Common.h
+++ b/src/Common.h
@@ -14,7 +14,7 @@
 // Release, should be backwards compatible with any minor version
 #define MAKEGEN_VERSION_RELEASE 3
 // Minor changes, generally bug fixes
-#define MAKEGEN_VERSION_MINOR 5
+#define MAKEGEN_VERSION_MINOR 6
 
 #define MAKEGEN_VERSION ("v" STR(MAKEGEN_VERSION_MAJOR) "." STR(MAKEGEN_VERSION_RELEASE) "." STR(MAKEGEN_VERSION_MINOR))
 
@@ -29,6 +29,7 @@ const static unsigned int FLAG_SINGLE_THREAD = BIT(7);
 const static unsigned int FLAG_DEPENDENCY = BIT(8);
 const static unsigned int FLAG_SIMPLE = BIT(9);
 const static unsigned int FLAG_CONFIG = BIT(10);
+const static unsigned int FLAG_TARGET = BIT(11);
 
 
 #define LOG_INFO(...) LogHelper(__VA_ARGS__)
diff --git a/src/ConfigCLI.cpp b/src/ConfigCLI.cpp
index 6bb5635..38cc37e 100644
--- a/src/ConfigCLI.cpp
+++ b/src/ConfigCLI.cpp
@@ -3,8 +3,6 @@
 #include "Common.h"
 #include "ConfigFile.h"
 
-#include <set>
-
 void ConfigCLI::DisplayCLIHelp()
 {
   LOG_INFO(1+(char*)R"(
@@ -174,12 +172,12 @@ int ConfigCLI::Gen(int argc, char** argv)
   std::string option = argv[1];
   if(option == "prompt")
   {
-    ConfigFile::Gen().Save();
+    ConfigFile::Gen(FlagData{}).Save();
     return 0;
   }
   if(option == "default")
   {
-    ConfigFile{FileUtils::GetRealPath("."),0}.Save();
+    ConfigFile{FileUtils::GetRealPath("."), FlagData{}, 0}.Save();
     return 0;
   }
   else
@@ -324,7 +322,7 @@ int ConfigCLI::Main(int argc, char** argv)
     DisplayCLIHelp();
     return 0;
   }
-  std::optional<ConfigFile> config = ConfigFile::GetConfigFile();
+  std::optional<ConfigFile> config = ConfigFile::GetConfigFile("./", FlagData{});
   std::string command = argv[1];
   if(command == "gen")
   {
@@ -351,7 +349,7 @@ int ConfigCLI::Main(int argc, char** argv)
       return 1;
     }
   }
-  else 
+  else
   {
     LOG_ERROR("There is no config file in the current directory");
     return 1;
diff --git a/src/ConfigCLI.h b/src/ConfigCLI.h
index 4335ae6..597b967 100644
--- a/src/ConfigCLI.h
+++ b/src/ConfigCLI.h
@@ -2,7 +2,7 @@
 
 #include "ConfigFile.h"
 
-struct ConfigCLI 
+struct ConfigCLI
 {
   public:
     static int Main(int argc, char** argv);
diff --git a/src/ConfigFile.cpp b/src/ConfigFile.cpp
index b844f95..b4a25a1 100755
--- a/src/ConfigFile.cpp
+++ b/src/ConfigFile.cpp
@@ -6,7 +6,7 @@
 
 #include <fstream>
 
-ConfigFile::ConfigFile(const std::string& path, int)
+ConfigFile::ConfigFile(const std::string& path, const FlagData& flagData, int)
   : configPath{path}
 {
   // Converts project name (current directory) to lowercase
@@ -16,7 +16,10 @@ ConfigFile::ConfigFile(const std::string& path, int)
 
   // Version, target and configuration is probably going to be used in the future
   makegen.AddXMLObject(XMLObject("version", {}, "v1.3.0"));
-  makegen.AddXMLObject(XMLObject("target", {}, "Release"));
+  if(flagData.flags & FLAG_TARGET)
+    makegen.AddXMLObject(XMLObject("target", {}, flagData.target));
+  else
+    makegen.AddXMLObject(XMLObject("target", {}, "Release"));
 
   XMLObject configuration("configuration", {{"name", "Release"}}, std::map<std::string, std::vector<XMLObject>>{});
   configuration.AddXMLObject(XMLObject("projectname", {}, ConfigUtils::GetDefaultProjectName(configPath)));
@@ -29,35 +32,42 @@ ConfigFile::ConfigFile(const std::string& path, int)
 
   makegen.AddXMLObject(configuration);
   config = makegen;
-  Init();
+  Init(flagData);
 }
 
-ConfigFile::ConfigFile(const std::string& path)
+ConfigFile::ConfigFile(const std::string& path, const FlagData& flagData)
   : config{XML::FromFile(path + CONFIG_FILENAME)}, configPath{path}
 {
-  Init();
+  Init(flagData);
 }
 
-ConfigFile::ConfigFile(XMLObject& config, const std::string& path)
+ConfigFile::ConfigFile(XMLObject& config, const std::string& path, const FlagData& flagData)
   : config{config}, configPath{path}
 {
-  Init();
+  Init(flagData);
 }
 
-void ConfigFile::Init()
+void ConfigFile::Init(const FlagData& flagData)
 {
-  const std::vector<XMLObject>* targetXml = config.GetObjectPtr("target");
-  target = "Release";
-  if(!targetXml || targetXml->size() == 0)
+  if (flagData.flags & FLAG_TARGET)
   {
-    LOG_ERROR("No target found in config file. Using target=", target);
-    return;
+    target = flagData.target;
+  }
+  else
+  {
+    const std::vector<XMLObject>* targetXml = config.GetObjectPtr("target");
+    target = "Release";
+    if(!targetXml || targetXml->size() == 0)
+    {
+      LOG_ERROR("No target found in config file. Using target=", target);
+      return;
+    }
+    if(targetXml->size() > 1)
+      LOG_ERROR("To many targets in config file. Using target=", (*targetXml)[0].GetText());
+    if(targetXml->size() > 0)
+      target = (*targetXml)[0].GetText();
   }
 
-  if(targetXml->size() > 1)
-    LOG_ERROR("To many targets in config file. Using target=", (*targetXml)[0].GetText());
-  if(targetXml->size() > 0)
-    target = (*targetXml)[0].GetText();
 }
 
 std::string& ConfigFile::GetSettingString(ConfigSetting setting)
@@ -323,13 +333,13 @@ ConfigFile& ConfigFile::GetDependencyConfig(size_t i)
   return dependencyConfigs[i];
 }
 
-std::optional<ConfigFile> ConfigFile::GetConfigFile(const std::string& filepath)
+std::optional<ConfigFile> ConfigFile::GetConfigFile(const std::string& filepath, const FlagData& flagData)
 {
   std::map<std::string, ConfigFile> loadedConfigs;
-  return GetConfigFile(filepath, loadedConfigs);
+  return GetConfigFile(filepath, loadedConfigs, flagData);
 }
 
-std::optional<ConfigFile> ConfigFile::GetConfigFile(const std::string& filepath, std::map<std::string, ConfigFile>& loadedConfigs)
+std::optional<ConfigFile> ConfigFile::GetConfigFile(const std::string& filepath, std::map<std::string, ConfigFile>& loadedConfigs, const FlagData& flagData)
 {
   std::string realPath = FileUtils::GetRealPath(filepath);
   if(realPath == "")
@@ -354,7 +364,7 @@ std::optional<ConfigFile> ConfigFile::GetConfigFile(const std::string& filepath,
   if(f.good())
   {
     f.close();
-    ConfigFile conf = ConfigFile(filepath);
+    ConfigFile conf = ConfigFile(filepath, flagData);
     if(conf.hasInitError)
       return {};
     loadedConfigs.emplace(realPath, conf);
@@ -363,7 +373,7 @@ std::optional<ConfigFile> ConfigFile::GetConfigFile(const std::string& filepath,
     // Create dependency config files.
     for(size_t i = 0; i < dependencies.size();++i)
     {
-      std::optional<ConfigFile> dep = GetConfigFile(conf.configPath + dependencies[i], loadedConfigs);
+      std::optional<ConfigFile> dep = GetConfigFile(conf.configPath + dependencies[i], loadedConfigs, flagData);
       if(dep)
       {
         conf.dependencyConfigs.push_back(*dep);
@@ -425,7 +435,7 @@ void ConfigFile::InputMultiple(const std::string& inputText, std::vector<std::st
   }
 }
 
-ConfigFile ConfigFile::Gen()
+ConfigFile ConfigFile::Gen(const FlagData& flagData)
 {
   bool executable, shared, generateHFile;
   std::vector<std::string> libs, libdirs, includedirs, defines, compileFlags, linkingFlags, dependencies, excludeSources, excludeHeaders;
@@ -467,7 +477,10 @@ ConfigFile ConfigFile::Gen()
 
   // Version, target and configuration is probably going to be used in the future
   makegen.AddXMLObject(XMLObject("version", {}, "v1.3.0"));
-  makegen.AddXMLObject(XMLObject("target", {}, "Release"));
+  if(flagData.flags & FLAG_TARGET)
+    makegen.AddXMLObject(XMLObject("target", {}, flagData.target));
+  else
+    makegen.AddXMLObject(XMLObject("target", {}, "Release"));
 
   XMLObject configuration("configuration", {{"name", "Release"}}, std::map<std::string, std::vector<XMLObject>>{});
   configuration.AddXMLObject(XMLObject("projectname", {}, projectname));
@@ -493,7 +506,7 @@ ConfigFile ConfigFile::Gen()
     configuration.AddXMLObject({"dependency",{},*it});
 
   makegen.AddXMLObject(configuration);
-  return ConfigFile{makegen, FileUtils::GetRealPath(".")};
+  return ConfigFile{makegen, FileUtils::GetRealPath("."), flagData};
 }
 
 void ConfigFile::Save() const
diff --git a/src/ConfigFile.h b/src/ConfigFile.h
index e058497..81f8ee7 100755
--- a/src/ConfigFile.h
+++ b/src/ConfigFile.h
@@ -1,6 +1,7 @@
 #pragma once
 
 #include "ConfigUtils.h"
+#include "FlagData.h"
 #include "xml/XMLObject.h"
 
 #include <map>
@@ -26,9 +27,9 @@ class ConfigFile
 
   public:
     // Generates a new default config file
-    ConfigFile(const std::string& path, int);
-    ConfigFile(const std::string& path);
-    ConfigFile(XMLObject& config, const std::string& path);
+    ConfigFile(const std::string& path, const FlagData& flagData, int);
+    ConfigFile(const std::string& path, const FlagData& flagData);
+    ConfigFile(XMLObject& config, const std::string& path, const FlagData& flagData);
 
     void Save() const;
 
@@ -45,13 +46,13 @@ class ConfigFile
     const std::string& GetConfigPath() const;
     ConfigFile& GetDependencyConfig(size_t i);
   private:
-    void Init();
+    void Init(const FlagData& flagData);
 
   public:
-    static ConfigFile Gen();
-    static std::optional<ConfigFile> GetConfigFile(const std::string& filepath = "./");
+    static ConfigFile Gen(const FlagData& flagData);
+    static std::optional<ConfigFile> GetConfigFile(const std::string& filepath, const FlagData& flagData);
   private:
-    static std::optional<ConfigFile> GetConfigFile(const std::string& filepath, std::map<std::string, ConfigFile>& loadedConfigs);
+    static std::optional<ConfigFile> GetConfigFile(const std::string& filepath, std::map<std::string, ConfigFile>& loadedConfigs, const FlagData& flagData);
     static std::optional<ConfigFile> Load(const std::string& filename);
     static void InputBoolean(const std::string& inputText, bool& b);
     static void InputMultiple(const std::string& inputText, std::vector<std::string>& vec, bool needEnding);
diff --git a/src/FlagData.h b/src/FlagData.h
new file mode 100644
index 0000000..f8b34c5
--- /dev/null
+++ b/src/FlagData.h
@@ -0,0 +1,9 @@
+#pragma once
+
+#include <string>
+
+struct FlagData
+{
+  unsigned int flags{0};
+  std::string target{""}; // Only set if flags contain FLAG_TARGET
+};
diff --git a/src/Utils.cpp b/src/Utils.cpp
index 4854340..0ca47bc 100644
--- a/src/Utils.cpp
+++ b/src/Utils.cpp
@@ -32,6 +32,15 @@ bool Utils::IsHeaderFile(const std::string& filepath)
   return extension == "hpp" || extension == "h" || extension == "hxx";
 }
 
+bool Utils::StartsWith(const std::string& str, const std::string& prefix)
+{
+  if (str.size() < prefix.size())
+    return false;
+
+  return str.compare(0, prefix.size(), prefix) == 0;
+}
+
+
 std::string Utils::CommonPrefix(const std::string& s1, const std::string& s2)
 {
   size_t n = 0;
diff --git a/src/Utils.h b/src/Utils.h
index b051f82..b57bc42 100644
--- a/src/Utils.h
+++ b/src/Utils.h
@@ -34,7 +34,9 @@ struct Utils
 {
   static bool IsSourceFile(const std::string& filepath);
   static bool IsHeaderFile(const std::string& filepath);
+
   static std::string CommonPrefix(const std::string& s1, const std::string& s2);
+  static bool StartsWith(const std::string& str, const std::string& prefix);
   static void GetCppFiles(ConfigFile& conf, std::set<std::string>& cppFiles);
   static void GetCppAndHFiles(ConfigFile& conf, std::set<HFile>& hFiles, std::set<std::string>& cppFiles);
   static void GetHFiles(const std::string& dependencyDir, ConfigFile& conf, std::set<HFile>& hFiles);
diff --git a/src/main.cpp b/src/main.cpp
index 55b5310..eb2b49b 100755
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -2,6 +2,7 @@
 #include "ConfigCLI.h"
 #include "ConfigFile.h"
 #include "FileUtils.h"
+#include "FlagData.h"
 #include "HFileGen.h"
 #include "Makefile.h"
 #include "Timer.h"
@@ -25,22 +26,23 @@ By default it always compiles code with parallell jobs.
 Usage: makegen [options]
 
   Options:
-    -h,     --help        Displays this information
-    -v,     --version     Displays the version of this program
-    -m,-a,  make, all     Generates a Makefile and runs
-                           make all
-    -i,     install       Generates a Makefile and runs
-                           make all && make install
-    -c,     clean         Generates a Makefile and runs
-                           make clean
-    -r,     rebuild       Generates a Makefile and runs
-                           make clean && make all
-    -e,     run, execute  Generates a Makefile and runs
-                           make all && make run
-    -s,     single        Runs additional makegen options as single thread
-                           (no --jobs=X flag)
-            --simple      Creates a simple Makefile without include dependencies
-                           (no --jobs=X flag)
+    -h,     --help             Displays this information
+    -v,     --version          Displays the version of this program
+    -m,-a,  make, all          Generates a Makefile and runs
+                                make all
+    -i,     install            Generates a Makefile and runs
+                                make all && make install
+    -c,     clean              Generates a Makefile and runs
+                                make clean
+    -r,     rebuild            Generates a Makefile and runs
+                                make clean && make all
+    -e,     run, execute       Generates a Makefile and runs
+                                make all && make run
+    -s,     single             Runs additional makegen options as single thread
+                                (no --jobs=X flag)
+            --simple           Creates a simple Makefile without include dependencies
+                                (no --jobs=X flag)
+            --target=<target>  Run the makegen.xml file with the specified target
 
   If no option is given it will run \"make all\"
 
@@ -55,11 +57,11 @@ void GenMakefile(ConfigFile& conf, unsigned int flags)
   Makefile::Save(conf, flags);
 }
 
-unsigned int ReadFlags(int argc, char** argv)
+FlagData ReadFlags(int argc, char** argv)
 {
   if(argc >= 2 && std::string(argv[1]) == "conf")
-    return FLAG_CONFIG;
-  unsigned int flags = 0;
+    return FlagData{FLAG_CONFIG};
+  FlagData flagData{};
   bool make = true;
   for(int i = 1;i<argc;i++)
   {
@@ -68,52 +70,63 @@ unsigned int ReadFlags(int argc, char** argv)
       std::string flag(argv[i]);
       if(flag == "-h" || flag == "--help")
       {
-        flags |= FLAG_HELP;
+        flagData.flags |= FLAG_HELP;
       }
       else if(flag == "-v" || flag == "--version")
       {
-        flags |= FLAG_VERSION;
+        flagData.flags |= FLAG_VERSION;
       }
       else if(flag == "make" || flag == "-m" || flag == "all" || flag == "-a")
       {
-        flags |= FLAG_MAKE;
+        flagData.flags |= FLAG_MAKE;
       }
       else if(flag == "clean" || flag == "-c")
       {
         make = false;
-        flags |= FLAG_CLEAN;
+        flagData.flags |= FLAG_CLEAN;
       }
       else if(flag == "run" || flag == "-e" || flag == "execute")
       {
-        flags |= FLAG_RUN;
+        flagData.flags |= FLAG_RUN;
       }
       else if(flag == "install" || flag == "-i")
       {
-        flags |= FLAG_INSTALL;
+        flagData.flags |= FLAG_INSTALL;
       }
       else if(flag == "rebuild" || flag == "-r")
       {
-        flags |= FLAG_CLEAN;
-        flags |= FLAG_MAKE;
+        flagData.flags |= FLAG_CLEAN;
+        flagData.flags |= FLAG_MAKE;
       }
       else if(flag == "single" || flag == "-s")
       {
-        flags |= FLAG_SINGLE_THREAD;
+        flagData.flags |= FLAG_SINGLE_THREAD;
       }
       else if(flag == "--simple")
       {
-        flags |= FLAG_SIMPLE;
+        flagData.flags |= FLAG_SIMPLE;
+      }
+      else if(Utils::StartsWith(flag, "--target="))
+      {
+        std::string prefix("--target=");
+        if (flag.size() < prefix.size() + 1)
+        {
+          LOG_ERROR("No target specified in --target=<target>");
+          return FlagData{FLAG_HELP};
+        }
+        flagData.flags |= FLAG_TARGET;
+        flagData.target = flag.substr(std::string("--target=").size());
       }
       else if(flag != "")
       {
         LOG_ERROR("Unknown argument ", flag);
-        return FLAG_HELP;
+        return FlagData{FLAG_HELP};
       }
     }
   }
   if(make)
-    flags |= FLAG_MAKE;
-  return flags;
+    flagData.flags |= FLAG_MAKE;
+  return flagData;
 }
 
 bool RunMake(const std::string& filepath, unsigned int flags, ConfigFile& conf)
@@ -140,7 +153,7 @@ bool RunMake(const std::string& filepath, unsigned int flags, ConfigFile& conf)
   return true;
 }
 
-bool MakeGen(const std::string& filepath, unsigned int flags, ConfigFile& conf)
+bool MakeGen(const std::string& filepath, const FlagData& flagData, ConfigFile& conf)
 {
   std::vector<std::string>& dependencies = conf.GetSettingVectorString(ConfigSetting::Dependency);
   for(size_t i = 0;i<dependencies.size();++i)
@@ -148,10 +161,10 @@ bool MakeGen(const std::string& filepath, unsigned int flags, ConfigFile& conf)
     std::filesystem::path currentPath = std::filesystem::current_path();
     std::filesystem::current_path(dependencies[i]);
 
-    auto conf = ConfigFile::GetConfigFile();
+    auto conf = ConfigFile::GetConfigFile("./", flagData);
     if(conf)
     {
-      bool success = MakeGen("./", flags, conf.value());
+      bool success = MakeGen("./", flagData, conf.value());
       if(!success)
       {
         std::filesystem::current_path(currentPath);
@@ -164,7 +177,7 @@ bool MakeGen(const std::string& filepath, unsigned int flags, ConfigFile& conf)
   LOG_INFO("Building ", conf.GetSettingString(ConfigSetting::ProjectName));
   LOG_INFO("Generating Makefile...");
   Timer timer;
-  GenMakefile(conf, flags);
+  GenMakefile(conf, flagData.flags);
   LOG_INFO("Took ", round(timer.Elapsed()*1000.0)/1000.0,"s");
   LOG_INFO("Running Makefile...");
 
@@ -176,31 +189,31 @@ bool MakeGen(const std::string& filepath, unsigned int flags, ConfigFile& conf)
     if(!FileUtils::HasPath(intermediatePath ))
       FileUtils::CreateDirectory(intermediatePath );
   }
-  return RunMake(filepath, flags, conf);
+  return RunMake(filepath, flagData.flags, conf);
 }
 
 int main(int argc, char** argv)
 {
-  unsigned int flags = ReadFlags(argc,argv);
-  if(flags & FLAG_HELP)
+  FlagData flagData = ReadFlags(argc,argv);
+  if(flagData.flags & FLAG_HELP)
   {
     PrintHelp();
     return 0;
   }
-  if(flags & FLAG_VERSION)
+  if(flagData.flags & FLAG_VERSION)
   {
     LOG_INFO("MakeGen ", MAKEGEN_VERSION);
     return 0;
   }
-  if(flags & FLAG_CONFIG)
+  if(flagData.flags & FLAG_CONFIG)
   {
     return ConfigCLI::Main(argc-1, &argv[1]);
   }
   std::map<std::string, ConfigFile> files{};
-  auto conf = ConfigFile::GetConfigFile();
+  auto conf = ConfigFile::GetConfigFile("./", flagData);
   if(conf)
   {
-    bool success = MakeGen("./", flags, *conf);
+    bool success = MakeGen("./", flagData, *conf);
     return success ? 0 : 1;
   }
   else