diff --git a/Makefile b/Makefile
index 1904c7a..641ac87 100644
--- a/Makefile
+++ b/Makefile
@@ -1,4 +1,4 @@
-# This Makefile was generated using MakeGen v1.1.1 made by Tim Håkansson
+# This Makefile was generated using MakeGen v1.1.2 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++
@@ -32,18 +32,18 @@ $(OUTPUT): $(OBJECTS)
 install: all
 	$(info Installing MakeGen to /usr/bin/)
 	@cp $(OUTPUT) /usr/bin/makegen
-$(OBJPATH)/ConfigFile.o : /home/thraix/Documents/MakeGen/src/ConfigFile.cpp /home/thraix/Documents/MakeGen/src/Common.h /home/thraix/Documents/MakeGen/src/ConfigFile.h /home/thraix/Documents/MakeGen/src/FileUtils.h 
+$(OBJPATH)/ConfigFile.o : src/ConfigFile.cpp src/Common.h src/ConfigFile.h src/FileUtils.h 
 	$(info -[20%]- $<)
 	$(CC) $(CFLAGS) -o $@ $<
-$(OBJPATH)/HFileGen.o : /home/thraix/Documents/MakeGen/src/HFileGen.cpp /home/thraix/Documents/MakeGen/src/FileUtils.h /home/thraix/Documents/MakeGen/src/Common.h /home/thraix/Documents/MakeGen/src/HFileGen.h /home/thraix/Documents/MakeGen/src/ConfigFile.h
+$(OBJPATH)/HFileGen.o : src/HFileGen.cpp src/FileUtils.h src/Common.h src/HFileGen.h src/ConfigFile.h
 	$(info -[40%]- $<)
 	$(CC) $(CFLAGS) -o $@ $<
-$(OBJPATH)/IncludeDeps.o : /home/thraix/Documents/MakeGen/src/IncludeDeps.cpp /home/thraix/Documents/MakeGen/src/Common.h /home/thraix/Documents/MakeGen/src/IncludeDeps.h
+$(OBJPATH)/IncludeDeps.o : src/IncludeDeps.cpp src/Common.h src/IncludeDeps.h src/ConfigFile.h src/FileUtils.h 
 	$(info -[60%]- $<)
 	$(CC) $(CFLAGS) -o $@ $<
-$(OBJPATH)/Makefile.o : /home/thraix/Documents/MakeGen/src/Makefile.cpp /home/thraix/Documents/MakeGen/src/Common.h /home/thraix/Documents/MakeGen/src/FileUtils.h  /home/thraix/Documents/MakeGen/src/IncludeDeps.h /home/thraix/Documents/MakeGen/src/Makefile.h /home/thraix/Documents/MakeGen/src/ConfigFile.h
+$(OBJPATH)/Makefile.o : src/Makefile.cpp src/Common.h src/FileUtils.h  src/IncludeDeps.h src/ConfigFile.h  src/Makefile.h 
 	$(info -[80%]- $<)
 	$(CC) $(CFLAGS) -o $@ $<
-$(OBJPATH)/main.o : /home/thraix/Documents/MakeGen/src/main.cpp /home/thraix/Documents/MakeGen/src/Common.h /home/thraix/Documents/MakeGen/src/ConfigFile.h /home/thraix/Documents/MakeGen/src/HFileGen.h  /home/thraix/Documents/MakeGen/src/IncludeDeps.h /home/thraix/Documents/MakeGen/src/Makefile.h  /home/thraix/Documents/MakeGen/src/Timer.h
+$(OBJPATH)/main.o : src/main.cpp src/Common.h src/ConfigFile.h src/FileUtils.h  src/HFileGen.h  src/IncludeDeps.h   src/Makefile.h  src/Timer.h
 	$(info -[100%]- $<)
 	$(CC) $(CFLAGS) -o $@ $<
diff --git a/src/Common.h b/src/Common.h
index ac81250..8f28e27 100755
--- a/src/Common.h
+++ b/src/Common.h
@@ -1,6 +1,7 @@
 #pragma once
 
 #include <iostream>
+#include <string>
 
 #define BIT(x) (1<<x)
 
@@ -12,7 +13,7 @@
 // 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 1
+#define MAKEGEN_VERSION_MINOR 2
 #define MAKEGEN_VERSION ("v" STR(MAKEGEN_VERSION_MAJOR) "." STR(MAKEGEN_VERSION_RELEASE) "." STR(MAKEGEN_VERSION_MINOR))
 
 const static unsigned int FLAG_HELP = BIT(0);
@@ -37,3 +38,16 @@ void Log(const T& var, const Ts& ...vars)
   Log(vars...);
 }
 
+inline std::string CommonPrefix(const std::string& s1, const std::string& s2)
+{
+  size_t n = 0;
+  for(size_t i = 0; i<s1.size() && i<s2.size();++i)
+  {
+    if(s1[i] != s2[i])
+    {
+      n = i;
+      break;
+    }
+  }
+  return s1.substr(0, n);
+}
diff --git a/src/ConfigFile.cpp b/src/ConfigFile.cpp
index d17954e..4f61fd0 100755
--- a/src/ConfigFile.cpp
+++ b/src/ConfigFile.cpp
@@ -119,8 +119,8 @@ ConfigFile ConfigFile::Load(const std::string& filepath)
   // Create dependency config files.
   for(size_t i = 0; i < conf.dependencies.size();++i)
   {
+    conf.dependencyConfigs.push_back(ConfigFile::Load(conf.configPath + conf.dependencies[i]));
     conf.dependencies[i] = FileUtils::GetRealPath(conf.dependencies[i]);
-    conf.dependencyConfigs.push_back(ConfigFile::Load(conf.dependencies[i]));
   }
 
   return conf;
diff --git a/src/FileUtils.h b/src/FileUtils.h
index 2b17838..3232f29 100644
--- a/src/FileUtils.h
+++ b/src/FileUtils.h
@@ -6,6 +6,7 @@
 #include "Common.h"
 #include <cstring>
 #include <vector>
+#include <algorithm>
 #include <stdlib.h>
 
 struct FileUtils
@@ -23,6 +24,60 @@ struct FileUtils
     return filename;
   }
 
+  static std::string GetRelativePath(std::string from, std::string to)
+  {
+    std::string result;
+    if(to[to.size()-1] == '/')
+      to.pop_back();
+    if(from[from.size()-1] == '/')
+      from.pop_back();
+
+    // Check if the directory is inside 'from'
+    if(strncmp(to.c_str(), from.c_str(), from.size()) == 0)
+    {
+      // Same directory
+      if(to.size() == from.size())
+        return "";
+      // Remove the 'from' path
+      return to.substr(from.size()+1);
+    }
+    // Check if the directory is a child of from 
+    else if(strncmp(from.c_str(), to.c_str(), to.size()) == 0)
+    {
+      std::string sub = from.substr(to.size());
+      size_t n = std::count(sub.begin(), sub.end(), '/');
+      for(int i = 0;i<n;i++)
+      {
+        result+="..";
+        if(i != n-1)
+          result+="/";
+      }
+      return result;
+    }
+    // Otherwise it's a path in another directory
+    else
+    {
+      // Find the most common directory
+      std::string commonPath = CommonPrefix(from,to);
+      while(commonPath.back() != '/')
+        commonPath.pop_back();
+      commonPath.pop_back();
+
+      // Go back to the common directory
+      std::string sub = from.substr(commonPath.size());
+      size_t n = std::count(sub.begin(), sub.end(), '/');
+      for(int i = 0;i<n;i++)
+      {
+        result+="..";
+        if(i != n-1)
+          result+="/";
+      }
+      // Add the path which diverges
+      result += to.substr(commonPath.size());
+      return result;
+    }
+  }
+
   static void GetAllFiles(const std::string& folder, std::vector<std::string>& files)
   {
     DIR* dp;
diff --git a/src/IncludeDeps.h b/src/IncludeDeps.h
index 9e11c4b..9d8d039 100755
--- a/src/IncludeDeps.h
+++ b/src/IncludeDeps.h
@@ -6,6 +6,8 @@
 #include <string>
 #include <fstream>
 #include <exception>
+#include "ConfigFile.h"
+#include "FileUtils.h"
 
 struct CompareIncludeDeps;
 
@@ -21,22 +23,24 @@ class IncludeDeps
 
     std::string GetIncludeFile(const std::string& line, size_t pos, const std::string& filename);
 
-    friend std::ostream& operator<<(std::ostream& stream, const IncludeDeps& deps)
+    std::ostream& Output(std::ostream& stream, const ConfigFile& conf)
     {
-      if(printSet.find(deps.filepath) != printSet.end())
+      if(printSet.find(filepath) != printSet.end())
         return stream;
       printCounter++; 
-      printSet.emplace(deps.filepath);
-      stream << deps.filepath;
-      for(auto it = deps.dependencies.begin();it!=deps.dependencies.end();++it)
+      printSet.emplace(filepath);
+      stream << FileUtils::GetRelativePath(conf.configPath, filepath);
+      for(auto it = dependencies.begin();it!=dependencies.end();++it)
       {
-        stream << " " << *(it->second);
+        stream << " ";
+        (it->second)->Output(stream, conf);
       }
       printCounter--;
       if(printCounter == 0)
         printSet.clear();
       return stream;
     }
+
     IncludeDeps(const std::string& filename, const std::string& dir)
       : filepath(dir+filename){}
 
diff --git a/src/Makefile.cpp b/src/Makefile.cpp
index 11acadd..1b5d8ba 100755
--- a/src/Makefile.cpp
+++ b/src/Makefile.cpp
@@ -139,7 +139,9 @@ void Makefile::Save(const ConfigFile& conf)
       size_t extensionPos = it->find_last_of(".");
       size_t slash = it->find_last_of("/")+1;
       std::string oFile = it->substr(slash, extensionPos - slash)+".o ";
-      outputFile << "$(OBJPATH)/" << oFile << ": " << *deps << std::endl;
+      outputFile << "$(OBJPATH)/" << oFile << ": ";
+      deps->Output(outputFile, conf);
+      outputFile << std::endl;
       outputFile << "\t$(info -[" << (int)(i / (float)cppFiles.size() * 100) << "%]- $<)" << std::endl;
       outputFile << "\t$(CC) $(CFLAGS) -o $@ $<" << std::endl;
       //std::cout << *deps << std::endl;
diff --git a/src/main.cpp b/src/main.cpp
index e007557..24ff04f 100755
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -80,7 +80,7 @@ bool MakeGen(const std::string& filepath, const std::string& args, const ConfigF
     if(!success)
       return success;
   }
-  LOG_INFO("---------------------------");
+  LOG_INFO("-----------------------------------");
   LOG_INFO("Building ", conf.projectname);
   LOG_INFO("Generating Makefile...");
   Timer timer;
@@ -91,6 +91,8 @@ bool MakeGen(const std::string& filepath, const std::string& args, const ConfigF
   return system(std::string("make --no-print-directory -C " + filepath + " " + args).c_str()) == 0;
 }
 
+#include "FileUtils.h"
+
 int main(int argc, char** argv)
 {
   unsigned int flags = ReadFlags(argc,argv);