diff --git a/Makefile b/Makefile
index df24277..bc32c18 100644
--- a/Makefile
+++ b/Makefile
@@ -1,4 +1,4 @@
-# This Makefile was generated using MakeGen v1.1.7 made by Tim Håkansson
+# This Makefile was generated using MakeGen v1.1.8 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++
@@ -7,7 +7,7 @@ MKDIR_P=mkdir -p
 BIN=bin/
 OBJPATH=$(BIN)intermediates
 INCLUDES=
-OBJECTS=$(OBJPATH)/ConfigFile.o $(OBJPATH)/HFileGen.o $(OBJPATH)/IncludeDeps.o $(OBJPATH)/Makefile.o $(OBJPATH)/Utils.o $(OBJPATH)/main.o 
+OBJECTS=$(OBJPATH)/ConfigCLI.o $(OBJPATH)/ConfigFile.o $(OBJPATH)/HFileGen.o $(OBJPATH)/IncludeDeps.o $(OBJPATH)/Makefile.o $(OBJPATH)/Utils.o $(OBJPATH)/main.o 
 CFLAGS=$(INCLUDES) -std=c++17 -c -w -g3 -D_DEBUG 
 LIBDIR=
 LDFLAGS=
@@ -33,21 +33,24 @@ $(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 
+	$(info -[14%]- $<)
+	$(CC) $(CFLAGS) -o $@ $<
 $(OBJPATH)/ConfigFile.o : src/ConfigFile.cpp src/ConfigFile.h src/FileUtils.h src/Common.h src/Utils.h 
-	$(info -[16%]- $<)
+	$(info -[28%]- $<)
 	$(CC) $(CFLAGS) -o $@ $<
 $(OBJPATH)/HFileGen.o : src/HFileGen.cpp src/FileUtils.h src/Common.h src/Utils.h src/ConfigFile.h src/HFileGen.h 
-	$(info -[33%]- $<)
+	$(info -[42%]- $<)
 	$(CC) $(CFLAGS) -o $@ $<
 $(OBJPATH)/IncludeDeps.o : src/IncludeDeps.cpp src/Common.h src/IncludeDeps.h src/ConfigFile.h src/FileUtils.h  src/Utils.h 
-	$(info -[50%]- $<)
+	$(info -[57%]- $<)
 	$(CC) $(CFLAGS) -o $@ $<
 $(OBJPATH)/Makefile.o : src/Makefile.cpp src/IncludeDeps.h src/ConfigFile.h src/FileUtils.h src/Common.h src/Utils.h  src/Makefile.h  
-	$(info -[66%]- $<)
+	$(info -[71%]- $<)
 	$(CC) $(CFLAGS) -o $@ $<
 $(OBJPATH)/Utils.o : src/Utils.cpp src/FileUtils.h src/Common.h src/Utils.h src/ConfigFile.h 
-	$(info -[83%]- $<)
+	$(info -[85%]- $<)
 	$(CC) $(CFLAGS) -o $@ $<
-$(OBJPATH)/main.o : src/main.cpp src/Common.h src/ConfigFile.h src/FileUtils.h  src/Utils.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/FileUtils.h  src/Utils.h  src/HFileGen.h  src/Makefile.h  src/Timer.h
 	$(info -[100%]- $<)
 	$(CC) $(CFLAGS) -o $@ $<
diff --git a/README.md b/README.md
index 05d245d..fc2715a 100644
--- a/README.md
+++ b/README.md
@@ -29,13 +29,20 @@ This will install MakeGen into `/usr/bin/makegen`.
 If you want it to be installed in another place just run `make` and copy the file to where you want it.
 
 ## Usage
+### Config file
 In order to create a MakeGen configuration file use the following command:
 
-    makegen --conf
+    makegen conf gen prompt
 
 This will prompt you with all the needed configurations in order to create a Makefile which will compile your code.
 When this is done it will create a file called `makegen.conf` which contains all relevant data for MakeGen to create a Makefile.
 
+If you want to change your config you can modify the makegen.conf file or use makegens config command line interface.
+To see the possible changes you can do see the help file by entering:
+
+    makegen conf
+
+### Compiling
 After that simply compile your code with:
 
     makegen
@@ -52,4 +59,4 @@ If multiple options are given to MakeGen it will execute them in the following o
     clean all install run
 
 Since MakeGen generates include dependencies in your Makefile it can cause the Makefile to get very cluttered.
-In order to make it less cluttered you can run `makegen --simple` which will generate (and run) a Makefile without header file dependencies.
+In order to make it less cluttered you can run `makegen --simple` which will generate (and run) a Makefile without header file dependencies.
\ No newline at end of file
diff --git a/makegen.conf b/makegen.conf
index 89366d7..e445d05 100644
--- a/makegen.conf
+++ b/makegen.conf
@@ -1,18 +1,19 @@
 #libs
 #libdirs
 #includedirs
-#srcdir
-src
 #defines
 _DEBUG
 #compileflags
+#dependencies
+#srcdir
+src/
 #outputdir
-bin
+bin/
 #projectname
 MakeGen
 #outputname
 makegen
 #executable
 true
-#dependencies
-
+#generatehfile
+false
diff --git a/src/Common.h b/src/Common.h
index cec2180..6b5af40 100755
--- a/src/Common.h
+++ b/src/Common.h
@@ -12,20 +12,20 @@
 // Release , should be backwards compatible with any minor version
 #define MAKEGEN_VERSION_RELEASE 1
 // Minor changes, should be compatible with any other minor version with same major and release.
-#define MAKEGEN_VERSION_MINOR 7
+#define MAKEGEN_VERSION_MINOR 8
 #define MAKEGEN_VERSION ("v" STR(MAKEGEN_VERSION_MAJOR) "." STR(MAKEGEN_VERSION_RELEASE) "." STR(MAKEGEN_VERSION_MINOR))
 
 const static unsigned int FLAG_HELP = BIT(0);
-const static unsigned int FLAG_GEN = BIT(1);
-const static unsigned int FLAG_VERSION = BIT(2);
-const static unsigned int FLAG_CLEAN = BIT(3);
-const static unsigned int FLAG_MAKE = BIT(4);
-const static unsigned int FLAG_RUN = BIT(5);
-const static unsigned int FLAG_INSTALL = BIT(6);
-const static unsigned int FLAG_REBUILD = BIT(7);
-const static unsigned int FLAG_SINGLE_THREAD = BIT(8);
-const static unsigned int FLAG_DEPENDENCY = BIT(9);
-const static unsigned int FLAG_SIMPLE = BIT(10);
+const static unsigned int FLAG_VERSION = BIT(1);
+const static unsigned int FLAG_CLEAN = BIT(2);
+const static unsigned int FLAG_MAKE = BIT(3);
+const static unsigned int FLAG_RUN = BIT(4);
+const static unsigned int FLAG_INSTALL = BIT(5);
+const static unsigned int FLAG_REBUILD = BIT(6);
+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);
 
 
 #define LOG_INFO(...) Log(__VA_ARGS__); std::cout << std::endl
diff --git a/src/ConfigCLI.cpp b/src/ConfigCLI.cpp
new file mode 100644
index 0000000..d8d8796
--- /dev/null
+++ b/src/ConfigCLI.cpp
@@ -0,0 +1,367 @@
+#include "ConfigCLI.h"
+
+#include "Common.h"
+#include "ConfigFile.h"
+
+#include <set>
+
+void ConfigCLI::DisplayCLIHelp()
+{
+  LOG_INFO("MakeGen conf is used to create, modify and query the makegen.conf file.");
+  LOG_INFO("");
+  LOG_INFO("Usage: makegen conf <command> [<args>] [--help] ");
+  LOG_INFO("");
+  LOG_INFO("Generating config files");
+  LOG_INFO("  gen             Prompt the user to enter information to create config");
+  LOG_INFO("");
+
+  LOG_INFO("Modifying config settings");
+  LOG_INFO("  add             Add values to config settings which support multiple arguments");
+  LOG_INFO("  remove          Remove values to config settings which support multiple");
+  LOG_INFO("                   arguments");
+  LOG_INFO("  set             Set value to config settings which support only one argument");
+  LOG_INFO("");
+
+  LOG_INFO("Querying config settings");
+  LOG_INFO("  get             Get value of the config setting");
+}
+
+void ConfigCLI::DisplayGenHelp()
+{
+  LOG_INFO("Generate a config file from prompts");
+  LOG_INFO("");
+  LOG_INFO("Usage: makegen conf gen <option>");
+  LOG_INFO("");
+  LOG_INFO("options:");
+  LOG_INFO("  prompt           Prompt the user for all needed settings");
+}
+
+void ConfigCLI::DisplayAddHelp()
+{
+  LOG_INFO("Add values to config settings which support multiple arguments");
+  LOG_INFO("");
+  LOG_INFO("Usage: makegen conf add <setting> <value> [<values>]");
+  LOG_INFO("");
+  LOG_INFO("Valid settings are:");
+  LOG_INFO("  library       Library");
+  LOG_INFO("  libdir        Library directory");
+  LOG_INFO("  includedir    Include directory");
+  LOG_INFO("  define        Preprocessor define");
+  LOG_INFO("  cflag         g++ compiler flags");
+  LOG_INFO("  dependency    Project which current project depends on");
+}
+
+void ConfigCLI::DisplayRemoveHelp()
+{
+  LOG_INFO("Remove values to config settings which support multiple arguments");
+  LOG_INFO("");
+  LOG_INFO("Usage: makegen conf remove <setting> <value> [<values>]");
+  LOG_INFO("");
+  LOG_INFO("Valid settings are:");
+  LOG_INFO("  library       Library name");
+  LOG_INFO("  libdir        Library directory");
+  LOG_INFO("  includedir    Include directory");
+  LOG_INFO("  define        Preprocessor define");
+  LOG_INFO("  cflag         g++ compiler flags");
+  LOG_INFO("  dependency    Project which current project depends on");
+}
+
+void ConfigCLI::DisplaySetHelp()
+{
+  LOG_INFO("Set value to config settings which only support one argument");
+  LOG_INFO("");
+  LOG_INFO("Usage: makegen conf set <setting> <value>");
+  LOG_INFO("");
+  LOG_INFO("Valid string settings are:");
+  LOG_INFO("  outputdir     Directory of the compiled output");
+  LOG_INFO("  output        Name of the output executable/library");
+  LOG_INFO("  name          Name of the project");
+  LOG_INFO("  hfile         Name of the generated project h-file");
+  LOG_INFO("");
+  LOG_INFO("Valid boolean settings are:");
+  LOG_INFO("  executable    Specifies if the project be compiled as executable or library");
+  LOG_INFO("  shared        Specifies if the library should be compiled as shared.");
+  LOG_INFO("  genhfile      Specifies if MakeGen should generate a project h-file");
+  LOG_INFO("");
+  LOG_INFO("Boolean values can be set to either true/t/yes/y or false/f/no/n");
+}
+
+void ConfigCLI::DisplayGetHelp()
+{
+  LOG_INFO("Get value of the config setting");
+  LOG_INFO("");
+  LOG_INFO("Usage: makegen conf get <setting>");
+  LOG_INFO("");
+  LOG_INFO("Valid settings are:");
+  LOG_INFO("  library       Library name");
+  LOG_INFO("  libdir        Library directory");
+  LOG_INFO("  includedir    Include directory");
+  LOG_INFO("  define        Preprocessor define");
+  LOG_INFO("  cflag         g++ compiler flags");
+  LOG_INFO("  dependency    Project which current project depends on");
+  LOG_INFO("  outputdir     Directory of the compiled output");
+  LOG_INFO("  output        Name of the output executable/library");
+  LOG_INFO("  name          Name of the project");
+  LOG_INFO("  hfile         Name of the generated project h-file");
+  LOG_INFO("  executable    Specifies if the project be compiled as executable or library");
+  LOG_INFO("  shared        Specifies if the library should be compiled as shared.");
+  LOG_INFO("  genhfile      Specifies if MakeGen should generate a project h-file");
+}
+
+std::map<std::string, std::vector<std::string>*> ConfigCLI::GetSettingVectorMap(ConfigFile& config)
+{
+  return {
+    {"library",&config.libs},
+      {"libdir",&config.libdirs},
+      {"includedir",&config.includedirs},
+      {"define",&config.defines},
+      {"cflag",&config.flags},
+      {"dependency",&config.dependencies}
+  };
+}
+
+
+std::map<std::string, std::string*> ConfigCLI::GetSettingStringMap(ConfigFile& config) 
+{
+  return {
+    {"outputdir", &config.outputdir},
+      {"output", &config.outputname},
+      {"name", &config.projectname},
+      {"hfile", &config.hFile},
+  };
+}
+
+std::map<std::string, bool*> ConfigCLI::GetSettingBoolMap(ConfigFile& config) 
+{
+  return {
+    {"executable", &config.executable},
+      {"shared", &config.shared},
+      {"genhfile", &config.generateHFile}
+  };
+}
+
+int ConfigCLI::Gen(int argc, char** argv)
+{
+  if(argc < 2 || std::string(argv[1]) == "--help")
+  {
+    DisplayGenHelp();
+    return 0;
+  }
+  if(argc < 2)
+  {
+    LOG_ERROR("gen needs exactly one parameter");
+    return 1;
+  }
+  std::string option = argv[1];
+  if(option == "prompt")
+  {
+    ConfigFile::Gen().Save();
+    return 0;
+  }
+  else
+  {
+    LOG_ERROR("Invalid option: ", option);
+    return 1;
+  }
+}
+
+int ConfigCLI::Add(int argc, char** argv, ConfigFile& config)
+{
+  if(argc < 2 || std::string(argv[1]) == "--help")
+  {
+    DisplayAddHelp();
+    return 0;
+  }
+  if(argc < 3)
+  {
+    LOG_ERROR("add needs at least two parameters");
+    return 1;
+  }
+
+  auto settingMap = GetSettingVectorMap(config);
+  auto it = settingMap.find(argv[1]);
+  if(it == settingMap.end())
+  {
+    LOG_ERROR("Invalid setting: ", argv[1]);
+    return 1;
+  }
+
+  std::vector<std::string>* setting = it->second;
+  std::set<std::string> settingSet{setting->begin(), setting->end()};
+  for(int i = 2; i<argc;++i)
+  {
+    auto res = settingSet.emplace(argv[i]);
+    if(!res.second)
+    {
+      LOG_ERROR("Duplicate value: ", argv[i]);
+    }
+  }
+  *setting = {settingSet.begin(), settingSet.end()};
+
+  config.Save();
+  return 0;
+}
+
+int ConfigCLI::Remove(int argc, char** argv, ConfigFile& config)
+{
+  if(argc < 2 || std::string(argv[1]) == "--help")
+  {
+    DisplayRemoveHelp();
+    return 0;
+  }
+  if(argc < 3)
+  {
+    LOG_ERROR("remove needs at least two parameters");
+    return 1;
+  }
+
+  auto settingMap = GetSettingVectorMap(config);
+  auto it = settingMap.find(argv[1]);
+  if(it == settingMap.end())
+  {
+    LOG_ERROR("Invalid setting: ", argv[1]);
+    return 1;
+  }
+
+  std::vector<std::string>* setting = it->second;
+  std::set<std::string> settingSet{setting->begin(), setting->end()};
+  for(int i = 2; i<argc;++i)
+  {
+    auto it = settingSet.find(argv[i]);
+    if(it == settingSet.end())
+    {
+      LOG_ERROR("No such value in setting: ", argv[i]);
+    }
+    else
+      settingSet.erase(it);
+  }
+  *setting = {settingSet.begin(), settingSet.end()};
+
+  config.Save();
+  return 0;
+}
+
+int ConfigCLI::Set(int argc, char** argv, ConfigFile& config)
+{
+  if(argc < 2 || std::string(argv[1]) == "--help")
+  {
+    DisplaySetHelp();
+    return 0;
+  }
+  if(argc != 3)
+  {
+    LOG_ERROR("set needs exactly two parameters");
+    return 1;
+  }
+
+  auto settingStringMap = GetSettingStringMap(config);
+  auto it1 = settingStringMap.find(argv[1]);
+  if(it1 == settingStringMap.end())
+  {
+    auto settingBoolMap = GetSettingBoolMap(config);
+    auto it2 = settingBoolMap.find(argv[1]);
+    if(it2 == settingBoolMap.end())
+    {
+      LOG_ERROR("Invalid setting: ", argv[1]);
+      return 1;
+    }
+    std::string b = argv[2];
+    if(b == "true" || b == "t" || b == "yes" || b == "y")
+      *(it2->second) = true;
+    else if(b == "false" || b == "f" || b == "no" || b == "n")
+      *it2->second = false;
+    else
+    {
+      LOG_ERROR("Invalid boolean value: ", argv[2]);
+      return 1;
+    }
+    config.Save();
+    return 0;
+  }
+  *it1->second = argv[2];
+  config.Save();
+  return 0;
+}
+
+int ConfigCLI::Get(int argc, char** argv, ConfigFile& config)
+{
+  if(argc < 2 || std::string(argv[1]) == "--help")
+  {
+    DisplayGetHelp();
+    return 0;
+  }
+  if(argc != 2)
+  {
+    LOG_ERROR("get needs exactly one parameter");
+    return 1;
+  }
+  auto settingVectorMap = GetSettingVectorMap(config);
+  auto itV = settingVectorMap.find(argv[1]);
+  if(itV == settingVectorMap.end())
+  {
+    auto settingStringMap = GetSettingStringMap(config);
+    auto itS = settingStringMap.find(argv[1]);
+    if(itS == settingStringMap.end())
+    {
+      auto settingBoolMap = GetSettingBoolMap(config);
+      auto itB = settingBoolMap.find(argv[1]);
+      if(itB == settingBoolMap.end())
+      {
+        LOG_ERROR("Invalid setting: ", argv[1]);
+        return 1;
+      }
+      bool* t = itB->second;
+      LOG_INFO(*itB->second ? "true" : "false");
+      return 0;
+    }
+    LOG_INFO(*itS->second);
+    return 0;
+  }
+  for(auto it = itV->second->begin(); it != itV->second->end(); ++it)
+  {
+    LOG_INFO(*it);
+  }
+  return 0;
+}
+
+int ConfigCLI::Main(int argc, char** argv)
+{
+  // Do nothing
+  if(argc < 2 || std::string(argv[1]) == "--help")
+  {
+    DisplayCLIHelp();
+    return 0;
+  }
+  std::optional<ConfigFile> config = ConfigFile::GetConfigFile();
+  std::string command = argv[1];
+  if(command == "gen")
+  {
+    if(config)
+    {
+      LOG_ERROR("Config file already exist (makegen.conf)");
+      return 1;
+    }
+    return Gen(argc-1, &argv[1]);
+  }
+  else if(config)
+  {
+    if(command == "add")
+      return Add(argc-1, &argv[1], *config);
+    else if(command == "remove")
+      return Remove(argc-1, &argv[1], *config);
+    else if(command == "set")
+      return Set(argc-1, &argv[1], *config);
+    else if(command == "get")
+      return Get(argc-1, &argv[1], *config);
+    else
+    {
+      LOG_ERROR("Unknown config command: ", command);
+      return 1;
+    }
+  }
+  else 
+  {
+    LOG_ERROR("There is no config file in the current directory");
+    return 1;
+  }
+}
diff --git a/src/ConfigCLI.h b/src/ConfigCLI.h
new file mode 100644
index 0000000..88335a1
--- /dev/null
+++ b/src/ConfigCLI.h
@@ -0,0 +1,27 @@
+#pragma once
+
+#include "ConfigFile.h"
+
+struct ConfigCLI 
+{
+  public:
+    static int Main(int argc, char** argv);
+  private:
+    static void DisplayCLIHelp();
+    static void DisplayGenHelp();
+    static void DisplayAddHelp();
+    static void DisplayRemoveHelp();
+    static void DisplaySetHelp();
+    static void DisplayGetHelp();
+
+    static std::map<std::string, std::vector<std::string>*> GetSettingVectorMap(ConfigFile& config); 
+    static std::map<std::string, std::string*> GetSettingStringMap(ConfigFile& config); 
+    static std::map<std::string, bool*> GetSettingBoolMap(ConfigFile& config); 
+
+    static int Gen(int argc, char** argv);
+    static int Add(int argc, char** argv, ConfigFile& config);
+    static int Remove(int argc, char** argv, ConfigFile& config);
+    static int Set(int argc, char** argv, ConfigFile& config);
+    static int Get(int argc, char** argv, ConfigFile& config);
+
+};
diff --git a/src/ConfigFile.cpp b/src/ConfigFile.cpp
index 78cbe05..46c7887 100755
--- a/src/ConfigFile.cpp
+++ b/src/ConfigFile.cpp
@@ -234,10 +234,10 @@ ConfigFile ConfigFile::Gen()
   else
   {
     InputBoolean("Should it be compiled as a shared library? (y/n)", conf.shared);
-    InputBoolean("Should it compile a single h file? (y/n):", conf.generateHFile);
+    InputBoolean("Should it compile a project h-file? (y/n):", conf.generateHFile);
     if(conf.generateHFile)
     {
-      InputString("Enter the h file name (and path): ", conf.hFile, false, false);
+      InputString("Enter the project h-file name (relative to source directory): ", conf.hFile, false, false);
     }
   }
   InputMultiple("Enter include directory:", conf.includedirs, true);
diff --git a/src/main.cpp b/src/main.cpp
index a8a5799..dcb043e 100755
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -1,4 +1,5 @@
 #include "Common.h"
+#include "ConfigCLI.h"
 #include "ConfigFile.h"
 #include "FileUtils.h"
 #include "HFileGen.h"
@@ -22,8 +23,6 @@ void PrintHelp()
   LOG_INFO("");
   LOG_INFO("  Options:");
   LOG_INFO("    -h,     --help        Displays this information");
-  LOG_INFO("            --conf        Prompt the user to enter information to create config");
-  LOG_INFO("                           file");
   LOG_INFO("    -v,     --version     Displays the version of this program");
   LOG_INFO("    -m,-a,  make, all     Generates a Makefile and runs");
   LOG_INFO("                           make all");
@@ -55,6 +54,8 @@ void GenMakefile(const ConfigFile& conf, unsigned int flags)
 
 unsigned int ReadFlags(int argc, char** argv)
 {
+  if(argc >= 2 && std::string(argv[1]) == "conf")
+    return FLAG_CONFIG;
   unsigned int flags = 0;
   bool make = true;
   for(int i = 1;i<argc;i++)
@@ -66,10 +67,6 @@ unsigned int ReadFlags(int argc, char** argv)
       {
         flags |= FLAG_HELP;
       }
-      else if(flag == "--conf")
-      {
-        flags |= FLAG_GEN;
-      }
       else if(flag == "-v" || flag == "--version")
       {
         flags |= FLAG_VERSION;
@@ -177,10 +174,9 @@ int main(int argc, char** argv)
     LOG_INFO("MakeGen ",MAKEGEN_VERSION);
     return 0;
   }
-  if(flags & FLAG_GEN)
+  if(flags & FLAG_CONFIG)
   {
-    ConfigFile::Gen().Save();
-    return 0;
+    return ConfigCLI::Main(argc-1, &argv[1]);
   }
   std::map<std::string, ConfigFile> files{};
   auto conf = ConfigFile::GetConfigFile();
@@ -192,6 +188,5 @@ int main(int argc, char** argv)
   else
   {
     LOG_ERROR("No ", CONFIG_FILENAME, " or Makefile found.");
-    PrintHelp();
   }
 }