diff --git a/.gitignore b/.gitignore
index 59b6e00e4..ec24b8187 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,9 +1,12 @@
+# Build files
 build
 cbuild
 dist
 openql.egg-info
 lab
+env
 
+# Temp files
 *.dot
 *.qc
 *.dat
@@ -14,8 +17,9 @@ lab
 *.pyd
 *.pyc
 *.cache
-openql/openql.py
-*/test_output/*
-tests/cc/test_output
+swig/openql.py
+swig/openql/openql.py
+
+# Test files
+test_output
 .ipynb_checkpoints
-doc/notebooks/test_output
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 1830cdb93..2468d8928 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -41,9 +41,9 @@ SET(CLI11_INCLUDE_DIRS
 
 ## These are the include directories used by the compiler.
 INCLUDE_DIRECTORIES(
-  ${PROJECT_SOURCE_DIR}
   ${LEMON_INCLUDE_DIRS}
   ${CLI11_INCLUDE_DIRS}
+  ${PROJECT_SOURCE_DIR}/src
 )
 
 IF(CMAKE_COMPILER_IS_GNUCXX)
@@ -52,7 +52,7 @@ IF(CMAKE_COMPILER_IS_GNUCXX)
 ENDIF(CMAKE_COMPILER_IS_GNUCXX)
 
 IF(MSVC)
-SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /std:c++11 /MP  /D_USE_MATH_DEFINES")
+  SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /std:c++11 /MP /D_USE_MATH_DEFINES")
 ENDIF(MSVC)
 
 IF("${CMAKE_CXX_COMPILER_ID}" MATCHES "Clang")
@@ -60,6 +60,6 @@ IF("${CMAKE_CXX_COMPILER_ID}" MATCHES "Clang")
   SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O3 -std=c++11 -Wall -Wfatal-errors -Wno-unused-local-typedef -ggdb")
 ENDIF("${CMAKE_CXX_COMPILER_ID}" MATCHES "Clang")
 
-ADD_SUBDIRECTORY(programs)
+ADD_SUBDIRECTORY(examples)
 ADD_SUBDIRECTORY(tests)
-ADD_SUBDIRECTORY(openql)
+ADD_SUBDIRECTORY(swig)
diff --git a/Jenkinsfile-master b/Jenkinsfile-master
index 25e984a8f..3c33493ac 100644
--- a/Jenkinsfile-master
+++ b/Jenkinsfile-master
@@ -1,11 +1,11 @@
 pipeline {
     agent any
     environment {
-       PERSIST_WORKSPACE = ""
-   }
+        PERSIST_WORKSPACE = ""
+    }
 
     stages {
-        stage('Checkout eQASM_Assembler'){
+        stage('Checkout eQASM_Assembler') {
             steps {
                 script {
                     PERSIST_WORKSPACE = WORKSPACE
@@ -15,7 +15,7 @@ pipeline {
                 sh 'GIT_SSH_COMMAND="ssh -i /var/jenkins_home/.ssh/jenkins_eqasm_assembler_deploy" git clone git@github.com:QE-Lab/eQASM_Assembler.git'
             }
         }
-        stage('Checkout libqasm'){
+        stage('Checkout libqasm') {
             steps {
                 script {
                     PERSIST_WORKSPACE = WORKSPACE
@@ -35,10 +35,10 @@ pipeline {
             steps {
                 dir(PERSIST_WORKSPACE) {
                     sh 'pwd'
-                    sh 'rm -Rf cbuild'
+                    sh 'rm -rf cbuild'
                     sh 'mkdir cbuild'
                     sh 'cd cbuild/ && cmake .. && make'
-                    sh 'rm -Rf env'
+                    sh 'rm -rf env'
                     sh 'python3 -m venv env'
                     sh '''
                             . ./env/bin/activate &&
diff --git a/Jenkinsfile-v2.2.0 b/Jenkinsfile-v2.2.0
index 0df1fd4f8..92458a2dd 100644
--- a/Jenkinsfile-v2.2.0
+++ b/Jenkinsfile-v2.2.0
@@ -1,11 +1,11 @@
 pipeline {
     agent any
     environment {
-       PERSIST_WORKSPACE = ""
-   }
+        PERSIST_WORKSPACE = ""
+    }
 
     stages {
-        stage('Checkout eQASM_Assembler'){
+        stage('Checkout eQASM_Assembler') {
             steps {
                 script {
                     PERSIST_WORKSPACE = WORKSPACE
@@ -15,7 +15,7 @@ pipeline {
                 sh 'GIT_SSH_COMMAND="ssh -i /var/jenkins_home/.ssh/jenkins_eqasm_assembler_deploy" git clone --branch v2.2.0 git@github.com:QE-Lab/eQASM_Assembler.git'
             }
         }
-        stage('Checkout libqasm'){
+        stage('Checkout libqasm') {
             steps {
                 script {
                     PERSIST_WORKSPACE = WORKSPACE
@@ -35,10 +35,10 @@ pipeline {
             steps {
                 dir(PERSIST_WORKSPACE) {
                     sh 'pwd'
-                    sh 'rm -Rf cbuild'
+                    sh 'rm -rf cbuild'
                     sh 'mkdir cbuild'
                     sh 'cd cbuild/ && cmake .. && make'
-                    sh 'rm -Rf env'
+                    sh 'rm -rf env'
                     sh 'python3 -m venv env'
                     sh '''
                             . ./env/bin/activate &&
diff --git a/license b/LICENSE
similarity index 100%
rename from license
rename to LICENSE
diff --git a/MANIFEST.in b/MANIFEST.in
index 0ea53bd6c..c3a534399 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,3 +1,3 @@
 include README.md
-include programs/*.py
-include tests/*.py
\ No newline at end of file
+include examples/*.py
+include tests/*.py
diff --git a/README.md b/README.md
index f5e2e9b4c..b0dbb943d 100644
--- a/README.md
+++ b/README.md
@@ -50,7 +50,7 @@ In all the instructions below, `python` refers to `Python 3` and `pip` refers to
 
 Openql can be installed as a conda package (currently on Linux and Windows) by:
 
-```
+```sh
 conda install -c imran.ashraf openql 
 ```
 
@@ -58,13 +58,13 @@ conda install -c imran.ashraf openql
 
 conda packages can also be built locally by using the recipie available in `conda-recipe` directory, by running the following command:
 
-```
+```sh
 conda build conda-recipe/.
 ```
 
 The generated package can then be installed by:
 
-```
+```sh
 conda install openql --use-local
 ```
 
@@ -73,7 +73,7 @@ conda install openql --use-local
 
 N.B. the instructions below will compile the C++ files the first time you try to install OpenQL package. If you are updating an existing installation you should first clean and recompile the C++ files using the following command. 
 
-```
+```sh
 python cleanme.py
 ```
 
@@ -81,19 +81,19 @@ python cleanme.py
 
 Running the following command in Terminal/Power Shell should install the openql package:
 
-```
+```sh
 python setup.py install  --user
 ```
 
 Or
 
-```
+```sh
 pip install  -e .
 ```
 
 By defining NPROCS=N environment variable, multiple processos can be created for faster compilation. For example, the following command will create 4 processes for compilation:
 
-```
+```sh
 NPROCS=4 python setup.py install  --user
 ```
 
@@ -102,13 +102,13 @@ NPROCS=4 python setup.py install  --user
 
 In order to pass all the tests, `qisa-as` and `libqasm` should be installed first. Follow [qisa-as](https://github.com/QE-Lab/eQASM_Assembler) and [libqasm](https://github.com/QE-Lab/libqasm) instructions to install python interfaces of these modules. Once `qisa-as` and `libqasm` are installed, you can run all the tests by:
 
-```
+```sh
 py.test -v
 ```
 
 Or
 
-```
+```sh
 python -m pytest
 ```
 
@@ -120,18 +120,18 @@ Existing tests and programs can be compiled by the following instructions. You c
 
 ## Linux/OSX
 
-```
-mkdir cbuild 
-cd OpenQL/cbuild 
+```sh
+mkdir cbuild
+cd cbuild 
 cmake ..   # generates the make file based on CMakeLists.txt in the OpenQL directory
 make       # compiles the source code into the current directory. 
 ```
 
-To execute an example program go to e.g., `OpenQL/cbuild/programs` and execute one of the files e.g.,  `./simple`. The output will be saved to the output directory next to the file.
+To execute an example program go to e.g., `OpenQL/cbuild/examples` and execute one of the files e.g.,  `./simple`. The output will be saved to the output directory next to the file.
 
 If one wants to compile and run a single file, e.g., `example.cc`, to compile it one can run : 
 
-```
+```sh
 mkdir output           # create an output directory if it does not exist
 g++ -std=c++11 example.cc -o example.exe -I OpenQL/   # compile the file
 ./example.exe                                         # execute the file
@@ -140,25 +140,26 @@ g++ -std=c++11 example.cc -o example.exe -I OpenQL/   # compile the file
 ## Windows
 
 ```
-cd OpenQL/cbuild
+mkdir cbuild
+cd cbuild
 cmake -G "NMake Makefiles" ..
 nmake
 ```
 
 ## Usage
 
-Example C++ tests and programs can be found in 'tests' and 'programs'
-directories. Executables for these will be generated in 'build/tests' and 'build/programs'
+Example C++ tests and programs can be found in 'tests' and 'examples'
+directories. Executables for these will be generated in 'build/tests' and 'build/examples'
 directory.
 
-Example python tests and programs can be found in the 'tests' and 'programs' directories.
+Example python tests and programs can be found in the 'tests' and 'examples' directories.
 These can be executed as 'python tests/simplePyTest.py'.
 
 # Getting started 
 
 After installing OpenQL a good place to get started is by looking at the files
 in the "tests" directory. Here you can find commented examples on how to use OpenQL.
-For instance, `programs/getting_started.py` could be a good starting point.
+For instance, `examples/getting_started.py` could be a good starting point.
 `doc` directory as well as the Wiki page documents various aspects.
 
 N.B. gates in OpenQL are *case insensitive*. 
diff --git a/conda-recipe/meta.yaml b/conda-recipe/meta.yaml
index fb4552fd4..1dc3eba60 100644
--- a/conda-recipe/meta.yaml
+++ b/conda-recipe/meta.yaml
@@ -3,7 +3,7 @@ package:
   version: "0.7.0"
 
 source:
-  # use the following path for the source if this recipie is inside the repo
+  # use the following path for the source if this recipe is inside the repo
   path: ../.
 
   # otherwise, use the following to get source
diff --git a/programs/CMakeLists.txt b/examples/CMakeLists.txt
similarity index 75%
rename from programs/CMakeLists.txt
rename to examples/CMakeLists.txt
index 732b51147..a61267022 100644
--- a/programs/CMakeLists.txt
+++ b/examples/CMakeLists.txt
@@ -1,6 +1,6 @@
 INCLUDE_DIRECTORIES(
-  ${PROJECT_SOURCE_DIR}
-  ${PROJECT_SOURCE_DIR}/programs
+  ${PROJECT_SOURCE_DIR}/src
+  ${PROJECT_SOURCE_DIR}/examples
   ${PROJECT_SOURCE_DIR}/tests
 )
 
@@ -20,15 +20,15 @@ INCLUDE_DIRECTORIES(
 # TARGET_LINK_LIBRARIES(multi_qubits_randomized_benchmarking ${LEMON_LIBRARIES} )
 
 # create output directory for test outputs
-ADD_CUSTOM_TARGET(programs-output-directory ALL
+ADD_CUSTOM_TARGET(examples-output-directory ALL
     COMMAND ${CMAKE_COMMAND} -E make_directory test_output)
 
 # copy configuration files
-CONFIGURE_FILE(${PROJECT_SOURCE_DIR}/tests/test_cfg_cbox.json 
-	test_cfg_cbox.json COPYONLY)
+CONFIGURE_FILE(${PROJECT_SOURCE_DIR}/tests/test_cfg_cbox.json
+    test_cfg_cbox.json COPYONLY)
 
-CONFIGURE_FILE(${PROJECT_SOURCE_DIR}/tests/hardware_config_cc_light.json 
-	hardware_config_cc_light.json COPYONLY)
+CONFIGURE_FILE(${PROJECT_SOURCE_DIR}/tests/hardware_config_cc_light.json
+    hardware_config_cc_light.json COPYONLY)
 
-CONFIGURE_FILE(${PROJECT_SOURCE_DIR}/tests/hardware_config_qx.json 
-	hardware_config_qx.json COPYONLY)
+CONFIGURE_FILE(${PROJECT_SOURCE_DIR}/tests/hardware_config_qx.json
+    hardware_config_qx.json COPYONLY)
diff --git a/programs/getting_started.py b/examples/getting_started.py
similarity index 100%
rename from programs/getting_started.py
rename to examples/getting_started.py
diff --git a/programs/instructions.map b/examples/instructions.map
similarity index 100%
rename from programs/instructions.map
rename to examples/instructions.map
diff --git a/programs/multi_qubits_randomized_benchmarking.cc b/examples/multi_qubits_randomized_benchmarking.cc
similarity index 99%
rename from programs/multi_qubits_randomized_benchmarking.cc
rename to examples/multi_qubits_randomized_benchmarking.cc
index 73fe5f502..b60aa6290 100644
--- a/programs/multi_qubits_randomized_benchmarking.cc
+++ b/examples/multi_qubits_randomized_benchmarking.cc
@@ -8,7 +8,7 @@
 
 #include <time.h>
 
-#include <ql/openql.h>
+#include <openql.h>
 
 // clifford inverse lookup table for grounded state
 const size_t inv_clifford_lut_gs[] = {0, 2, 1, 3, 8, 10, 6, 11, 4, 9, 5, 7, 12, 16, 23, 21, 13, 17, 18, 19, 20, 15, 22, 14};
diff --git a/programs/randomized_benchmarking.cc b/examples/randomized_benchmarking.cc
similarity index 99%
rename from programs/randomized_benchmarking.cc
rename to examples/randomized_benchmarking.cc
index ce1be0e1b..21b24375b 100644
--- a/programs/randomized_benchmarking.cc
+++ b/examples/randomized_benchmarking.cc
@@ -10,7 +10,7 @@
 
 #include <time.h>
 
-#include <ql/openql.h>
+#include <openql.h>
 
 // clifford inverse lookup table for grounded state
 const size_t inv_clifford_lut_gs[] = {0, 2, 1, 3, 8, 10, 6, 11, 4, 9, 5, 7, 12, 16, 23, 21, 13, 17, 18, 19, 20, 15, 22, 14};
diff --git a/programs/rb_single.cc b/examples/rb_single.cc
similarity index 98%
rename from programs/rb_single.cc
rename to examples/rb_single.cc
index e14d1215a..2837d2883 100644
--- a/programs/rb_single.cc
+++ b/examples/rb_single.cc
@@ -10,7 +10,7 @@
 
 #include <time.h>
 
-#include <ql/openql.h>
+#include <openql.h>
 
 // clifford inverse lookup table for grounded state
 const size_t inv_clifford_lut_gs[] = {0, 2, 1, 3, 8, 10, 6, 11, 4, 9, 5, 7, 12, 16, 23, 21, 13, 17, 18, 19, 20, 15, 22, 14};
diff --git a/programs/rb_single.py b/examples/rb_single.py
similarity index 100%
rename from programs/rb_single.py
rename to examples/rb_single.py
diff --git a/programs/scaffCC/square_root.cc b/examples/scaffCC/square_root.cc
similarity index 100%
rename from programs/scaffCC/square_root.cc
rename to examples/scaffCC/square_root.cc
diff --git a/programs/simple.cc b/examples/simple.cc
similarity index 98%
rename from programs/simple.cc
rename to examples/simple.cc
index b67cdb09d..4a23dd7bb 100644
--- a/programs/simple.cc
+++ b/examples/simple.cc
@@ -8,7 +8,7 @@
 
 #include <time.h>
 
-#include <ql/openql.h>
+#include <openql.h>
 
 int main(int argc, char ** argv)
 {
diff --git a/setup.py b/setup.py
index e89c5b7cd..0ca48489d 100644
--- a/setup.py
+++ b/setup.py
@@ -6,13 +6,13 @@
 from sys import platform
 
 rootDir = os.path.dirname(os.path.realpath(__file__))
-srcDir = os.path.join(rootDir, "ql")
+srcDir = os.path.join(rootDir, "src")
 buildDir = os.path.join(rootDir, "cbuild")
-clibDir = os.path.join(buildDir, "openql")
+clibDir = os.path.join(buildDir, "swig")
 
 nprocs = 1
 env_var_nprocs = os.environ.get('NPROCS')
-if(env_var_nprocs != None):
+if (env_var_nprocs != None):
   nprocs = int(env_var_nprocs)
 
 print('Using {} processes for compilation'.format(nprocs))
@@ -59,11 +59,13 @@
 else:
     print('Unknown/Unsupported OS !!!')
 
-genclib = os.path.join(clibDir, clibname)
-clib = os.path.join(rootDir, "openql", clibname)
-copyfile(genclib, clib)
+clib = os.path.join(clibDir, clibname)
+swigDir = os.path.join(rootDir, "swig", "openql")
+clibSwig = os.path.join(swigDir, clibname)
+
+copyfile(clib, clibSwig)
 copyfile(os.path.join(clibDir, "openql.py"),
-         os.path.join(rootDir, "openql", "openql.py"))
+         os.path.join(swigDir, "openql.py"))
 os.chdir(rootDir)
 
 
@@ -117,8 +119,9 @@ def read(fname):
       author='Nader Khammassi and Imran Ashraf',
       author_email='nader.khammassi@gmail.com, iimran.aashraf@gmail.com',
       url='https://github.com/QE-Lab/OpenQL',
-      license=read('license'),
+      license=read('LICENSE'),
       packages=['openql'],
+      package_dir={'': 'swig'},
       include_package_data=True,
-      package_data={'openql': [clib]},
+      package_data={'openql': [clibSwig]},
       zip_safe=False)
diff --git a/ql/arch/cbox/allxy.cc b/src/arch/cbox/allxy.cc
similarity index 93%
rename from ql/arch/cbox/allxy.cc
rename to src/arch/cbox/allxy.cc
index ab33ceb53..e06dbca01 100644
--- a/ql/arch/cbox/allxy.cc
+++ b/src/arch/cbox/allxy.cc
@@ -1,7 +1,7 @@
 
-#include <ql/openql.h>
-#include <ql/arch/cbox/cbox_eqasm_compiler.h>
-#include <ql/arch/cbox/instruction_scheduler.h>
+#include <openql.h>
+#include <arch/cbox/cbox_eqasm_compiler.h>
+#include <arch/cbox/instruction_scheduler.h>
 
 
 #define x180(q) kernel.gate("x180",q)
diff --git a/ql/arch/cbox/cbox_eqasm_compiler.cc b/src/arch/cbox/cbox_eqasm_compiler.cc
similarity index 97%
rename from ql/arch/cbox/cbox_eqasm_compiler.cc
rename to src/arch/cbox/cbox_eqasm_compiler.cc
index b9b986fa2..4ecd8f5d2 100644
--- a/ql/arch/cbox/cbox_eqasm_compiler.cc
+++ b/src/arch/cbox/cbox_eqasm_compiler.cc
@@ -1,8 +1,8 @@
 
 
-#include <ql/openql.h>
-#include <ql/arch/cbox/cbox_eqasm_compiler.h>
-#include <ql/arch/cbox/instruction_scheduler.h>
+#include <openql.h>
+#include <arch/cbox/cbox_eqasm_compiler.h>
+#include <arch/cbox/instruction_scheduler.h>
 
 
 
diff --git a/ql/arch/cbox/cbox_eqasm_compiler.h b/src/arch/cbox/cbox_eqasm_compiler.h
similarity index 99%
rename from ql/arch/cbox/cbox_eqasm_compiler.h
rename to src/arch/cbox/cbox_eqasm_compiler.h
index 4d06f72c4..48aaf1cb6 100644
--- a/ql/arch/cbox/cbox_eqasm_compiler.h
+++ b/src/arch/cbox/cbox_eqasm_compiler.h
@@ -8,10 +8,10 @@
 #ifndef QL_CBOX_EQASM_COMPILER_H
 #define QL_CBOX_EQASM_COMPILER_H
 
-#include <ql/platform.h>
-#include <ql/eqasm_compiler.h>
-#include <ql/arch/cbox/qumis.h>
-#include <ql/utils.h>
+#include <platform.h>
+#include <eqasm_compiler.h>
+#include <arch/cbox/qumis.h>
+#include <utils.h>
 
 // eqasm code : set of qumis instructions
 typedef std::vector<ql::arch::qumis_instr_t> eqasm_t;
diff --git a/ql/arch/cbox/hardware_configuration_loader.cc b/src/arch/cbox/hardware_configuration_loader.cc
similarity index 88%
rename from ql/arch/cbox/hardware_configuration_loader.cc
rename to src/arch/cbox/hardware_configuration_loader.cc
index 7d17f01ca..f209e02a1 100644
--- a/ql/arch/cbox/hardware_configuration_loader.cc
+++ b/src/arch/cbox/hardware_configuration_loader.cc
@@ -12,9 +12,9 @@
 
 #include <cmath>
 
-#include <ql/openql.h>
-#include <ql/json.h>
-#include <ql/gate.h>
+#include <openql.h>
+#include <json.h>
+#include <gate.h>
 
 using namespace nlohmann;
 
diff --git a/ql/arch/cbox/instruction_scheduler.h b/src/arch/cbox/instruction_scheduler.h
similarity index 99%
rename from ql/arch/cbox/instruction_scheduler.h
rename to src/arch/cbox/instruction_scheduler.h
index 6c1b5d05d..6208be521 100644
--- a/ql/arch/cbox/instruction_scheduler.h
+++ b/src/arch/cbox/instruction_scheduler.h
@@ -12,7 +12,7 @@
 #include <iomanip>
 #include <sstream>
 
-#include <ql/arch/cbox/cbox_eqasm_compiler.h>
+#include <arch/cbox/cbox_eqasm_compiler.h>
 
 namespace ql
 {
diff --git a/ql/arch/cbox/qumis.h b/src/arch/cbox/qumis.h
similarity index 99%
rename from ql/arch/cbox/qumis.h
rename to src/arch/cbox/qumis.h
index 444d2320d..c1dc06dce 100644
--- a/ql/arch/cbox/qumis.h
+++ b/src/arch/cbox/qumis.h
@@ -11,7 +11,7 @@
 #include <string>
 #include <bitset>
 
-#include <ql/arch/cbox/instruction_scheduler.h>
+#include <arch/cbox/instruction_scheduler.h>
 
 namespace ql
 {
diff --git a/ql/arch/cc/codegen_cc.h b/src/arch/cc/codegen_cc.h
similarity index 100%
rename from ql/arch/cc/codegen_cc.h
rename to src/arch/cc/codegen_cc.h
diff --git a/ql/arch/cc/eqasm_backend_cc.h b/src/arch/cc/eqasm_backend_cc.h
similarity index 98%
rename from ql/arch/cc/eqasm_backend_cc.h
rename to src/arch/cc/eqasm_backend_cc.h
index 315e26fca..b75cc949d 100644
--- a/ql/arch/cc/eqasm_backend_cc.h
+++ b/src/arch/cc/eqasm_backend_cc.h
@@ -11,13 +11,13 @@
 
 #define OPT_CC_SCHEDULE_RC     0       // 1=use resource constraint scheduler
 
-#include <ql/platform.h>
-#include <ql/ir.h>
-#include <ql/circuit.h>
-#include <ql/scheduler.h>
-#include <ql/eqasm_compiler.h>
+#include <platform.h>
+#include <ir.h>
+#include <circuit.h>
+#include <scheduler.h>
+#include <eqasm_compiler.h>
 #if OPT_CC_SCHEDULE_RC
- #include <ql/arch/cc_light/cc_light_resource_manager.h>
+ #include <arch/cc_light/cc_light_resource_manager.h>
 #endif
 #include "codegen_cc.h"
 
diff --git a/ql/arch/cc_light/cc_light_eqasm.cc b/src/arch/cc_light/cc_light_eqasm.cc
similarity index 95%
rename from ql/arch/cc_light/cc_light_eqasm.cc
rename to src/arch/cc_light/cc_light_eqasm.cc
index 4d8a26cc7..5c32ef440 100644
--- a/ql/arch/cc_light/cc_light_eqasm.cc
+++ b/src/arch/cc_light/cc_light_eqasm.cc
@@ -1,9 +1,9 @@
 
 
-#include <ql/openql.h>
+#include <openql.h>
 
-#include <ql/arch/cc_light/cc_light_eqasm_compiler.h>
-// #include <ql/arch/cc_light_eqasm.h>
+#include <arch/cc_light/cc_light_eqasm_compiler.h>
+// #include <arch/cc_light_eqasm.h>
 
 
 typedef ql::arch::cc_light_eqasm_instruction  ccl_instr;
diff --git a/ql/arch/cc_light/cc_light_eqasm.h b/src/arch/cc_light/cc_light_eqasm.h
similarity index 100%
rename from ql/arch/cc_light/cc_light_eqasm.h
rename to src/arch/cc_light/cc_light_eqasm.h
diff --git a/ql/arch/cc_light/cc_light_eqasm_compiler.h b/src/arch/cc_light/cc_light_eqasm_compiler.h
similarity index 99%
rename from ql/arch/cc_light/cc_light_eqasm_compiler.h
rename to src/arch/cc_light/cc_light_eqasm_compiler.h
index 78b46daf2..5692d80ab 100644
--- a/ql/arch/cc_light/cc_light_eqasm_compiler.h
+++ b/src/arch/cc_light/cc_light_eqasm_compiler.h
@@ -9,14 +9,14 @@
 #ifndef QL_CC_LIGHT_EQASM_COMPILER_H
 #define QL_CC_LIGHT_EQASM_COMPILER_H
 
-#include <ql/utils.h>
-#include <ql/platform.h>
-#include <ql/kernel.h>
-#include <ql/gate.h>
-#include <ql/ir.h>
-#include <ql/eqasm_compiler.h>
-#include <ql/arch/cc_light/cc_light_eqasm.h>
-#include <ql/arch/cc_light/cc_light_scheduler.h>
+#include <utils.h>
+#include <platform.h>
+#include <kernel.h>
+#include <gate.h>
+#include <ir.h>
+#include <eqasm_compiler.h>
+#include <arch/cc_light/cc_light_eqasm.h>
+#include <arch/cc_light/cc_light_scheduler.h>
 
 // eqasm code : set of cc_light_eqasm instructions
 typedef std::vector<ql::arch::cc_light_eqasm_instr_t> eqasm_t;
diff --git a/ql/arch/cc_light/cc_light_resource_manager.h b/src/arch/cc_light/cc_light_resource_manager.h
similarity index 99%
rename from ql/arch/cc_light/cc_light_resource_manager.h
rename to src/arch/cc_light/cc_light_resource_manager.h
index 9ae978b8f..6cc482d58 100644
--- a/ql/arch/cc_light/cc_light_resource_manager.h
+++ b/src/arch/cc_light/cc_light_resource_manager.h
@@ -13,8 +13,8 @@
 #include <fstream>
 #include <vector>
 #include <string>
-#include <ql/json.h>
-#include <ql/resource_manager.h>
+#include <json.h>
+#include <resource_manager.h>
 
 using json = nlohmann::json;
 
diff --git a/ql/arch/cc_light/cc_light_scheduler.h b/src/arch/cc_light/cc_light_scheduler.h
similarity index 97%
rename from ql/arch/cc_light/cc_light_scheduler.h
rename to src/arch/cc_light/cc_light_scheduler.h
index dcf899a02..f1e4d0579 100644
--- a/ql/arch/cc_light/cc_light_scheduler.h
+++ b/src/arch/cc_light/cc_light_scheduler.h
@@ -14,12 +14,12 @@
 #include <lemon/dijkstra.h>
 #include <lemon/connectivity.h>
 
-#include <ql/utils.h>
-#include <ql/gate.h>
-#include <ql/ir.h>
-#include <ql/circuit.h>
-#include <ql/scheduler.h>
-#include <ql/arch/cc_light/cc_light_resource_manager.h>
+#include <utils.h>
+#include <gate.h>
+#include <ir.h>
+#include <circuit.h>
+#include <scheduler.h>
+#include <arch/cc_light/cc_light_resource_manager.h>
 
 #include <iomanip>
 #include <map>
diff --git a/ql/arch/quantumsim_eqasm_compiler.h b/src/arch/quantumsim_eqasm_compiler.h
similarity index 98%
rename from ql/arch/quantumsim_eqasm_compiler.h
rename to src/arch/quantumsim_eqasm_compiler.h
index 7bfa53a62..d88915211 100644
--- a/ql/arch/quantumsim_eqasm_compiler.h
+++ b/src/arch/quantumsim_eqasm_compiler.h
@@ -8,11 +8,11 @@
 #ifndef QL_QUANTUMSIM_EQASM_COMPILER_H
 #define QL_QUANTUMSIM_EQASM_COMPILER_H
 
-#include <ql/platform.h>
-#include <ql/ir.h>
-#include <ql/circuit.h>
-#include <ql/scheduler.h>
-#include <ql/eqasm_compiler.h>
+#include <platform.h>
+#include <ir.h>
+#include <circuit.h>
+#include <scheduler.h>
+#include <eqasm_compiler.h>
 
 namespace ql
 {
diff --git a/ql/arch/spin_demo_2811.json b/src/arch/spin_demo_2811.json
similarity index 100%
rename from ql/arch/spin_demo_2811.json
rename to src/arch/spin_demo_2811.json
diff --git a/ql/attic/transmon.h b/src/attic/transmon.h
similarity index 100%
rename from ql/attic/transmon.h
rename to src/attic/transmon.h
diff --git a/ql/circuit.h b/src/circuit.h
similarity index 100%
rename from ql/circuit.h
rename to src/circuit.h
diff --git a/ql/classical.h b/src/classical.h
similarity index 98%
rename from ql/classical.h
rename to src/classical.h
index 859a88b69..7183926e7 100644
--- a/ql/classical.h
+++ b/src/classical.h
@@ -17,10 +17,10 @@
 #include <map>
 #include <stack>
 
-#include <ql/utils.h>
-#include <ql/str.h>
-#include <ql/gate.h>
-#include <ql/exception.h>
+#include <utils.h>
+#include <str.h>
+#include <gate.h>
+#include <exception.h>
 
 
 namespace ql
diff --git a/ql/eqasm_compiler.h b/src/eqasm_compiler.h
similarity index 96%
rename from ql/eqasm_compiler.h
rename to src/eqasm_compiler.h
index bbe1f331d..bb11b43aa 100644
--- a/ql/eqasm_compiler.h
+++ b/src/eqasm_compiler.h
@@ -12,9 +12,9 @@
 
 #include <fstream>
 
-#include <ql/circuit.h>
-#include <ql/kernel.h>
-#include <ql/platform.h>
+#include <circuit.h>
+#include <kernel.h>
+#include <platform.h>
 
 typedef std::vector<std::string> eqasm_t;
 
diff --git a/ql/exception.cc b/src/exception.cc
similarity index 100%
rename from ql/exception.cc
rename to src/exception.cc
diff --git a/ql/exception.h b/src/exception.h
similarity index 100%
rename from ql/exception.h
rename to src/exception.h
diff --git a/ql/gate.h b/src/gate.h
similarity index 99%
rename from ql/gate.h
rename to src/gate.h
index d4e74e6fc..a1027450d 100644
--- a/ql/gate.h
+++ b/src/gate.h
@@ -19,11 +19,11 @@
 #include <sstream>
 #include <map>
 
-#include <ql/matrix.h>
-#include <ql/json.h>
+#include <matrix.h>
+#include <json.h>
 
-#include <ql/openql.h>
-#include <ql/exception.h>
+#include <openql.h>
+#include <exception.h>
 
 using json = nlohmann::json;
 
diff --git a/ql/hardware_configuration.h b/src/hardware_configuration.h
similarity index 99%
rename from ql/hardware_configuration.h
rename to src/hardware_configuration.h
index 572262736..f871e0998 100644
--- a/ql/hardware_configuration.h
+++ b/src/hardware_configuration.h
@@ -18,10 +18,10 @@
 #include <iterator>
 #include <regex>
 
-#include <ql/openql.h>
-#include <ql/exception.h>
-#include <ql/json.h>
-#include <ql/gate.h>
+#include <openql.h>
+#include <exception.h>
+#include <json.h>
+#include <gate.h>
 
 namespace ql
 {
diff --git a/ql/instruction_map.h b/src/instruction_map.h
similarity index 100%
rename from ql/instruction_map.h
rename to src/instruction_map.h
diff --git a/ql/interactionMatrix.h b/src/interactionMatrix.h
similarity index 100%
rename from ql/interactionMatrix.h
rename to src/interactionMatrix.h
diff --git a/ql/ir.h b/src/ir.h
similarity index 100%
rename from ql/ir.h
rename to src/ir.h
diff --git a/ql/json.h b/src/json.h
similarity index 100%
rename from ql/json.h
rename to src/json.h
diff --git a/ql/kernel.h b/src/kernel.h
similarity index 99%
rename from ql/kernel.h
rename to src/kernel.h
index ff5e6f8c6..76c5e29b7 100644
--- a/ql/kernel.h
+++ b/src/kernel.h
@@ -13,13 +13,13 @@
 #include <algorithm>
 #include <iterator>
 
-#include "ql/json.h"
-#include "ql/utils.h"
-#include "ql/options.h"
-#include "ql/gate.h"
-#include "ql/classical.h"
-#include "ql/optimizer.h"
-#include "ql/ir.h"
+#include "json.h"
+#include "utils.h"
+#include "options.h"
+#include "gate.h"
+#include "classical.h"
+#include "optimizer.h"
+#include "ir.h"
 
 #define PI M_PI
 
diff --git a/ql/matrix.h b/src/matrix.h
similarity index 100%
rename from ql/matrix.h
rename to src/matrix.h
diff --git a/ql/openql.h b/src/openql.h
similarity index 100%
rename from ql/openql.h
rename to src/openql.h
diff --git a/ql/optimizer.h b/src/optimizer.h
similarity index 100%
rename from ql/optimizer.h
rename to src/optimizer.h
diff --git a/ql/options.h b/src/options.h
similarity index 99%
rename from ql/options.h
rename to src/options.h
index 8ff7992a4..5494d7911 100644
--- a/ql/options.h
+++ b/src/options.h
@@ -8,7 +8,7 @@
 #ifndef QL_OPTIONS_H
 #define QL_OPTIONS_H
 
-#include <ql/utils.h>
+#include <utils.h>
 #include <CLI/CLI.hpp>
 #include <iostream>
 
diff --git a/ql/platform.h b/src/platform.h
similarity index 98%
rename from ql/platform.h
rename to src/platform.h
index d94dea461..b17b209f6 100644
--- a/ql/platform.h
+++ b/src/platform.h
@@ -10,8 +10,8 @@
 #include <string>
 #include <tuple>
 
-#include <ql/circuit.h>
-#include <ql/hardware_configuration.h>
+#include <circuit.h>
+#include <hardware_configuration.h>
 
 namespace ql
 {
diff --git a/ql/program.h b/src/program.h
similarity index 98%
rename from ql/program.h
rename to src/program.h
index 77a5fe3c0..9695dfde5 100644
--- a/ql/program.h
+++ b/src/program.h
@@ -9,16 +9,16 @@
 #ifndef QL_PROGRAM_H
 #define QL_PROGRAM_H
 
-#include <ql/utils.h>
-#include <ql/options.h>
-#include <ql/platform.h>
-#include <ql/kernel.h>
-#include <ql/interactionMatrix.h>
-#include <ql/eqasm_compiler.h>
-#include <ql/arch/cbox/cbox_eqasm_compiler.h>
-#include <ql/arch/cc_light/cc_light_eqasm_compiler.h>
-#include <ql/arch/quantumsim_eqasm_compiler.h>
-#include <ql/arch/cc/eqasm_backend_cc.h>
+#include <utils.h>
+#include <options.h>
+#include <platform.h>
+#include <kernel.h>
+#include <interactionMatrix.h>
+#include <eqasm_compiler.h>
+#include <arch/cbox/cbox_eqasm_compiler.h>
+#include <arch/cc_light/cc_light_eqasm_compiler.h>
+#include <arch/quantumsim_eqasm_compiler.h>
+#include <arch/cc/eqasm_backend_cc.h>
 
 static unsigned long phi_node_count = 0;
 
diff --git a/ql/qasm_loader.cc b/src/qasm_loader.cc
similarity index 94%
rename from ql/qasm_loader.cc
rename to src/qasm_loader.cc
index 6f2cef69e..0c5728a77 100644
--- a/ql/qasm_loader.cc
+++ b/src/qasm_loader.cc
@@ -6,7 +6,7 @@
  */
 
 
-#include <ql/qasm_loader.h>
+#include <qasm_loader.h>
 
 
 /**
diff --git a/ql/resource_manager.h b/src/resource_manager.h
similarity index 100%
rename from ql/resource_manager.h
rename to src/resource_manager.h
diff --git a/ql/scheduler.h b/src/scheduler.h
similarity index 99%
rename from ql/scheduler.h
rename to src/scheduler.h
index 9bc3ac1b6..b7a9cc130 100644
--- a/ql/scheduler.h
+++ b/src/scheduler.h
@@ -66,11 +66,11 @@
 #include <lemon/dijkstra.h>
 #include <lemon/connectivity.h>
 
-#include "ql/utils.h"
-#include "ql/gate.h"
-#include "ql/circuit.h"
-#include "ql/ir.h"
-#include "ql/resource_manager.h"
+#include "utils.h"
+#include "gate.h"
+#include "circuit.h"
+#include "ir.h"
+#include "resource_manager.h"
 
 using namespace std;
 using namespace lemon;
diff --git a/ql/str.h b/src/str.h
similarity index 100%
rename from ql/str.h
rename to src/str.h
diff --git a/ql/utils.h b/src/utils.h
similarity index 100%
rename from ql/utils.h
rename to src/utils.h
diff --git a/ql/version.h b/src/version.h
similarity index 100%
rename from ql/version.h
rename to src/version.h
diff --git a/openql/CMakeLists.txt b/swig/CMakeLists.txt
similarity index 97%
rename from openql/CMakeLists.txt
rename to swig/CMakeLists.txt
index 25e7a99cf..ff5386b55 100644
--- a/openql/CMakeLists.txt
+++ b/swig/CMakeLists.txt
@@ -3,10 +3,10 @@ INCLUDE(${SWIG_USE_FILE})
 
 FIND_PACKAGE(PythonLibs)
 INCLUDE_DIRECTORIES(
-    ${PROJECT_SOURCE_DIR}
     ${PYTHON_INCLUDE_PATH}
-    ${CMAKE_CURRENT_SOURCE_DIR}
     ${LEMON_INCLUDE_DIRS}
+    ${CMAKE_CURRENT_SOURCE_DIR}
+    ${PROJECT_SOURCE_DIR}/src
 )
 
 # SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O3 -std=c++11 -Wall -Wfatal-errors")
diff --git a/openql/openql.i b/swig/openql.i
similarity index 99%
rename from openql/openql.i
rename to swig/openql.i
index 561b34171..9826dc598 100644
--- a/openql/openql.i
+++ b/swig/openql.i
@@ -21,7 +21,7 @@ namespace std {
 };
 
 %{
-#include "openql.h"
+#include "openql_i.h"
 %}
 
 
@@ -42,7 +42,7 @@ def set_output_dir(path):
 
 %exception
 {
-try
+    try
     {
         $action
         if (PyErr_Occurred()) SWIG_fail;
@@ -87,8 +87,6 @@ str
     'scheduler_commute' : 'no'   : 'yes/no'
     'scheduler_post179' : 'yes'  : 'yes/no'
     'cz_mode' : 'manual'         : 'auto/manual'
-    
-
 
 Parameters
 ----------
@@ -764,4 +762,4 @@ str
 
 
 // Include the header file with above prototypes
-%include "openql.h"
+%include "openql_i.h"
diff --git a/openql/__init__.py b/swig/openql/__init__.py
similarity index 100%
rename from openql/__init__.py
rename to swig/openql/__init__.py
diff --git a/openql/openql.h b/swig/openql_i.h
similarity index 99%
rename from openql/openql.h
rename to swig/openql_i.h
index 180be6c70..2472cfb94 100644
--- a/openql/openql.h
+++ b/swig/openql_i.h
@@ -15,9 +15,9 @@
 #include <cassert>
 #include <time.h>
 
-#include <ql/version.h>
-#include <ql/openql.h>
-#include <ql/classical.h>
+#include <version.h>
+#include <openql.h>
+#include <classical.h>
 
 static std::string get_version()
 {
diff --git a/openql/quick_feature_test.cc b/swig/quick_feature_test.cc
similarity index 98%
rename from openql/quick_feature_test.cc
rename to swig/quick_feature_test.cc
index 853811d60..2e91f3688 100644
--- a/openql/quick_feature_test.cc
+++ b/swig/quick_feature_test.cc
@@ -11,7 +11,7 @@
 // enable optimizations
 // #define ql_optimize
 
-#include <ql/openql.h>
+#include <openql.h>
 
 int main(int argc, char ** argv)
 {
diff --git a/openql/quick_feature_test.makefile b/swig/quick_feature_test.makefile
similarity index 100%
rename from openql/quick_feature_test.makefile
rename to swig/quick_feature_test.makefile
diff --git a/openql/quick_feature_test.py b/swig/quick_feature_test.py
similarity index 100%
rename from openql/quick_feature_test.py
rename to swig/quick_feature_test.py
diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt
index 130b791d2..6063c027b 100644
--- a/tests/CMakeLists.txt
+++ b/tests/CMakeLists.txt
@@ -1,6 +1,6 @@
 INCLUDE_DIRECTORIES(
-  ${PROJECT_SOURCE_DIR}
-  ${PROJECT_SOURCE_DIR}/programs
+  ${PROJECT_SOURCE_DIR}/src
+  ${PROJECT_SOURCE_DIR}/examples
   ${PROJECT_SOURCE_DIR}/tests
 )
 
diff --git a/tests/cc/test_cc.cc b/tests/cc/test_cc.cc
index 77648aa3b..f1b12e384 100644
--- a/tests/cc/test_cc.cc
+++ b/tests/cc/test_cc.cc
@@ -15,9 +15,8 @@
 
 #include <time.h>
 
-#include "ql/openql.h"
-#include "ql/utils.h"
-
+#include <openql.h>
+#include <utils.h>
 
 #define CFG_FILE_JSON   "test_cfg_cc.json"
 
diff --git a/tests/program_test.cc b/tests/program_test.cc
index c82bda1ac..3cdc64d8f 100644
--- a/tests/program_test.cc
+++ b/tests/program_test.cc
@@ -8,7 +8,7 @@
 
 #include <time.h>
 
-#include <ql/openql.h>
+#include <openql.h>
 
 int main(int argc, char ** argv)
 {
diff --git a/tests/test_179.cc b/tests/test_179.cc
index c21b84c58..f788608f5 100644
--- a/tests/test_179.cc
+++ b/tests/test_179.cc
@@ -8,7 +8,7 @@
 
 #include <time.h>
 
-#include <ql/openql.h>
+#include <openql.h>
 
 
 // all tests below should be run with scheduler_post179 yes and no