diff --git a/CMakeLists.txt b/CMakeLists.txt
index e8752db3f69e323d9cb07186157b4a56e6d04986..6d8e2b4b493b7670738aa1925406e9a016ba04fa 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,33 +1,33 @@
-/***********************************************************************************
- * Copyright (c) 2016, UT-Battelle
- * All rights reserved.
- *
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions are met:
- *   * Redistributions of source code must retain the above copyright
- *     notice, this list of conditions and the following disclaimer.
- *   * Redistributions in binary form must reproduce the above copyright
- *     notice, this list of conditions and the following disclaimer in the
- *     documentation and/or other materials provided with the distribution.
- *   * Neither the name of the xacc nor the
- *     names of its contributors may be used to endorse or promote products
- *     derived from this software without specific prior written permission.
- *
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
- * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
- * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
- * DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY
- * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
- * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
- * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
- * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
- * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
- *
- * Contributors:
- *   Initial API and implementation - Alex McCaskey
- *
- **********************************************************************************/
+#***********************************************************************************
+# Copyright (c) 2016, UT-Battelle
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#   * Redistributions of source code must retain the above copyright
+#     notice, this list of conditions and the following disclaimer.
+#   * Redistributions in binary form must reproduce the above copyright
+#     notice, this list of conditions and the following disclaimer in the
+#     documentation and/or other materials provided with the distribution.
+#   * Neither the name of the xacc nor the
+#     names of its contributors may be used to endorse or promote products
+#     derived from this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+# DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY
+# DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+#
+# Contributors:
+#   Initial API and implementation - Alex McCaskey
+#
+#**********************************************************************************/
 project(XACC CXX)
 cmake_minimum_required(VERSION 2.8)
 set(CMAKE_DISABLE_IN_SOURCE_BUILDS ON)
@@ -75,4 +75,5 @@ include_directories("${CMAKE_SOURCE_DIR}/tpls/common/exception")
 add_subdirectory(tpls)
 add_subdirectory(xacc)
 add_subdirectory(quantum)
+add_subdirectory(tools)
 add_subdirectory(examples)
diff --git a/examples/CMakeLists.txt b/examples/CMakeLists.txt
index daa9a6f799b5d361b6814eae058d6ef8c3a6a040..b68a57ed8190d99cfd1116ad3721c8977041ee6e 100644
--- a/examples/CMakeLists.txt
+++ b/examples/CMakeLists.txt
@@ -1 +1,31 @@
+#***********************************************************************************
+# Copyright (c) 2016, UT-Battelle
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#   * Redistributions of source code must retain the above copyright
+#     notice, this list of conditions and the following disclaimer.
+#   * Redistributions in binary form must reproduce the above copyright
+#     notice, this list of conditions and the following disclaimer in the
+#     documentation and/or other materials provided with the distribution.
+#   * Neither the name of the xacc nor the
+#     names of its contributors may be used to endorse or promote products
+#     derived from this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+# DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY
+# DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+#
+# Contributors:
+#   Initial API and implementation - Alex McCaskey
+#
+#**********************************************************************************/
 add_subdirectory(quantum)
diff --git a/examples/quantum/CMakeLists.txt b/examples/quantum/CMakeLists.txt
index 00128b095b6a273f23a659c64fe537a91253071d..f4798bd791e14fd9a56ed19c8f8f592674dccd23 100644
--- a/examples/quantum/CMakeLists.txt
+++ b/examples/quantum/CMakeLists.txt
@@ -1 +1,31 @@
+#***********************************************************************************
+# Copyright (c) 2016, UT-Battelle
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#   * Redistributions of source code must retain the above copyright
+#     notice, this list of conditions and the following disclaimer.
+#   * Redistributions in binary form must reproduce the above copyright
+#     notice, this list of conditions and the following disclaimer in the
+#     documentation and/or other materials provided with the distribution.
+#   * Neither the name of the xacc nor the
+#     names of its contributors may be used to endorse or promote products
+#     derived from this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+# DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY
+# DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+#
+# Contributors:
+#   Initial API and implementation - Alex McCaskey
+#
+#**********************************************************************************/
 add_subdirectory(gate)
diff --git a/examples/quantum/gate/CMakeLists.txt b/examples/quantum/gate/CMakeLists.txt
index 1ec8a7aea0b5d3bc188d1abad9e04fd78f018bc6..b99f593102659446b3fcb36d8ef674956e0cac65 100644
--- a/examples/quantum/gate/CMakeLists.txt
+++ b/examples/quantum/gate/CMakeLists.txt
@@ -1,33 +1,32 @@
-/***********************************************************************************
- * Copyright (c) 2016, UT-Battelle
- * All rights reserved.
- *
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions are met:
- *   * Redistributions of source code must retain the above copyright
- *     notice, this list of conditions and the following disclaimer.
- *   * Redistributions in binary form must reproduce the above copyright
- *     notice, this list of conditions and the following disclaimer in the
- *     documentation and/or other materials provided with the distribution.
- *   * Neither the name of the xacc nor the
- *     names of its contributors may be used to endorse or promote products
- *     derived from this software without specific prior written permission.
- *
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
- * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
- * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
- * DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY
- * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
- * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
- * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
- * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
- * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
- *
- * Contributors:
- *   Initial API and implementation - Alex McCaskey
- *
- **********************************************************************************/
-
+#***********************************************************************************
+# Copyright (c) 2016, UT-Battelle
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#   * Redistributions of source code must retain the above copyright
+#     notice, this list of conditions and the following disclaimer.
+#   * Redistributions in binary form must reproduce the above copyright
+#     notice, this list of conditions and the following disclaimer in the
+#     documentation and/or other materials provided with the distribution.
+#   * Neither the name of the xacc nor the
+#     names of its contributors may be used to endorse or promote products
+#     derived from this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+# DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY
+# DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+#
+# Contributors:
+#   Initial API and implementation - Alex McCaskey
+#
+#**********************************************************************************/
 add_executable(teleport_scaffold teleport_scaffold.cpp)
 target_link_libraries(teleport_scaffold xacc-scaffold ${Boost_LIBRARIES})
\ No newline at end of file
diff --git a/examples/quantum/gate/teleport_scaffold.cpp b/examples/quantum/gate/teleport_scaffold.cpp
index ac496ed6327bdd1278e8636ff3e6b9a49d676ef1..8510e05d4b032ca677004585e1d348358f8d04b7 100644
--- a/examples/quantum/gate/teleport_scaffold.cpp
+++ b/examples/quantum/gate/teleport_scaffold.cpp
@@ -70,7 +70,7 @@ int main (int argc, char** argv) {
 
 	auto ibm_qpu = std::make_shared<IBM5Qubit>();
 	xacc::Program quantumProgram(ibm_qpu, src);
-	quantumProgram.build("--compiler scaffold --writeIR teleport.xaccir");
+	quantumProgram.build("--compiler scaffold --writeIR teleport.xir");
 
 	// FIXME Get Kernel, execute, get result
 
diff --git a/quantum/CMakeLists.txt b/quantum/CMakeLists.txt
index 00128b095b6a273f23a659c64fe537a91253071d..f4798bd791e14fd9a56ed19c8f8f592674dccd23 100644
--- a/quantum/CMakeLists.txt
+++ b/quantum/CMakeLists.txt
@@ -1 +1,31 @@
+#***********************************************************************************
+# Copyright (c) 2016, UT-Battelle
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#   * Redistributions of source code must retain the above copyright
+#     notice, this list of conditions and the following disclaimer.
+#   * Redistributions in binary form must reproduce the above copyright
+#     notice, this list of conditions and the following disclaimer in the
+#     documentation and/or other materials provided with the distribution.
+#   * Neither the name of the xacc nor the
+#     names of its contributors may be used to endorse or promote products
+#     derived from this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+# DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY
+# DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+#
+# Contributors:
+#   Initial API and implementation - Alex McCaskey
+#
+#**********************************************************************************/
 add_subdirectory(gate)
diff --git a/quantum/gate/CMakeLists.txt b/quantum/gate/CMakeLists.txt
index a8cf4d595f62a546ff3051efef7711b86142cb76..e84f9deb517b41868f229ef96fb8a5dc5594236c 100644
--- a/quantum/gate/CMakeLists.txt
+++ b/quantum/gate/CMakeLists.txt
@@ -1,2 +1,32 @@
+#***********************************************************************************
+# Copyright (c) 2016, UT-Battelle
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#   * Redistributions of source code must retain the above copyright
+#     notice, this list of conditions and the following disclaimer.
+#   * Redistributions in binary form must reproduce the above copyright
+#     notice, this list of conditions and the following disclaimer in the
+#     documentation and/or other materials provided with the distribution.
+#   * Neither the name of the xacc nor the
+#     names of its contributors may be used to endorse or promote products
+#     derived from this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+# DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY
+# DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+#
+# Contributors:
+#   Initial API and implementation - Alex McCaskey
+#
+#**********************************************************************************/
 add_subdirectory(scaffold)
 add_subdirectory(utils)
diff --git a/quantum/gate/scaffold/CMakeLists.txt b/quantum/gate/scaffold/CMakeLists.txt
index 180838dbcbada39046c193499ee99ba792ddf818..5a953bd5c76d2c16bfaec145c2422f47c358d6ac 100644
--- a/quantum/gate/scaffold/CMakeLists.txt
+++ b/quantum/gate/scaffold/CMakeLists.txt
@@ -1,34 +1,33 @@
-/***********************************************************************************
- * Copyright (c) 2016, UT-Battelle
- * All rights reserved.
- *
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions are met:
- *   * Redistributions of source code must retain the above copyright
- *     notice, this list of conditions and the following disclaimer.
- *   * Redistributions in binary form must reproduce the above copyright
- *     notice, this list of conditions and the following disclaimer in the
- *     documentation and/or other materials provided with the distribution.
- *   * Neither the name of the xacc nor the
- *     names of its contributors may be used to endorse or promote products
- *     derived from this software without specific prior written permission.
- *
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
- * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
- * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
- * DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY
- * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
- * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
- * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
- * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
- * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
- *
- * Contributors:
- *   Initial API and implementation - Alex McCaskey
- *
- **********************************************************************************/
-
+#***********************************************************************************
+# Copyright (c) 2016, UT-Battelle
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#   * Redistributions of source code must retain the above copyright
+#     notice, this list of conditions and the following disclaimer.
+#   * Redistributions in binary form must reproduce the above copyright
+#     notice, this list of conditions and the following disclaimer in the
+#     documentation and/or other materials provided with the distribution.
+#   * Neither the name of the xacc nor the
+#     names of its contributors may be used to endorse or promote products
+#     derived from this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+# DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY
+# DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+#
+# Contributors:
+#   Initial API and implementation - Alex McCaskey
+#
+#**********************************************************************************/
 set (PACKAGE_NAME "Scaffold XACC Runtime")
 set (PACKAGE_DESCIPTION "Scaffold XACC Programming Framework")
 set (LIBRARY_NAME xacc-scaffold)
diff --git a/quantum/gate/utils/CMakeLists.txt b/quantum/gate/utils/CMakeLists.txt
index be5f863b7b88c3e50a20e3e9147f2fa75a576f31..38812e294e901af6d93f0c3596112b6398fb5ddd 100644
--- a/quantum/gate/utils/CMakeLists.txt
+++ b/quantum/gate/utils/CMakeLists.txt
@@ -1,3 +1,33 @@
+#***********************************************************************************
+# Copyright (c) 2016, UT-Battelle
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#   * Redistributions of source code must retain the above copyright
+#     notice, this list of conditions and the following disclaimer.
+#   * Redistributions in binary form must reproduce the above copyright
+#     notice, this list of conditions and the following disclaimer in the
+#     documentation and/or other materials provided with the distribution.
+#   * Neither the name of the xacc nor the
+#     names of its contributors may be used to endorse or promote products
+#     derived from this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+# DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY
+# DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+#
+# Contributors:
+#   Initial API and implementation - Alex McCaskey
+#
+#**********************************************************************************/
 set (PACKAGE_NAME "Quantum XACC Utils Runtime")
 set (PACKAGE_DESCIPTION "Quantum XACC Common Utilities")
 
@@ -5,7 +35,3 @@ file (GLOB HEADERS *.hpp)
 
 install(FILES ${HEADERS} DESTINATION include)
 
-# Gather tests
-#file (GLOB test_files tests/*.cpp)
-#add_tests("${test_files}" "${CMAKE_CURRENT_SOURCE_DIR}" "${LIBRARY_NAME}")
-
diff --git a/tools/CMakeLists.txt b/tools/CMakeLists.txt
index daa9a6f799b5d361b6814eae058d6ef8c3a6a040..b68a57ed8190d99cfd1116ad3721c8977041ee6e 100644
--- a/tools/CMakeLists.txt
+++ b/tools/CMakeLists.txt
@@ -1 +1,31 @@
+#***********************************************************************************
+# Copyright (c) 2016, UT-Battelle
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#   * Redistributions of source code must retain the above copyright
+#     notice, this list of conditions and the following disclaimer.
+#   * Redistributions in binary form must reproduce the above copyright
+#     notice, this list of conditions and the following disclaimer in the
+#     documentation and/or other materials provided with the distribution.
+#   * Neither the name of the xacc nor the
+#     names of its contributors may be used to endorse or promote products
+#     derived from this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+# DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY
+# DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+#
+# Contributors:
+#   Initial API and implementation - Alex McCaskey
+#
+#**********************************************************************************/
 add_subdirectory(quantum)
diff --git a/tools/quantum/CMakeLists.txt b/tools/quantum/CMakeLists.txt
index 52ce35dde5b1b62e56b5910c8cf3826369ad2184..700cfdd5409e4377ef3b02789167b64c7b07a42f 100644
--- a/tools/quantum/CMakeLists.txt
+++ b/tools/quantum/CMakeLists.txt
@@ -1,33 +1,33 @@
-/***********************************************************************************
- * Copyright (c) 2016, UT-Battelle
- * All rights reserved.
- *
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions are met:
- *   * Redistributions of source code must retain the above copyright
- *     notice, this list of conditions and the following disclaimer.
- *   * Redistributions in binary form must reproduce the above copyright
- *     notice, this list of conditions and the following disclaimer in the
- *     documentation and/or other materials provided with the distribution.
- *   * Neither the name of the xacc nor the
- *     names of its contributors may be used to endorse or promote products
- *     derived from this software without specific prior written permission.
- *
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
- * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
- * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
- * DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY
- * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
- * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
- * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
- * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
- * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
- *
- * Contributors:
- *   Initial API and implementation - Alex McCaskey
- *
- **********************************************************************************/
-
+#***********************************************************************************
+# Copyright (c) 2016, UT-Battelle
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#   * Redistributions of source code must retain the above copyright
+#     notice, this list of conditions and the following disclaimer.
+#   * Redistributions in binary form must reproduce the above copyright
+#     notice, this list of conditions and the following disclaimer in the
+#     documentation and/or other materials provided with the distribution.
+#   * Neither the name of the xacc nor the
+#     names of its contributors may be used to endorse or promote products
+#     derived from this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+# DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY
+# DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+#
+# Contributors:
+#   Initial API and implementation - Alex McCaskey
+#
+#**********************************************************************************/
+include_directories(${CMAKE_SOURCE_DIR}/quantum/gate/utils)
 add_executable(qasm2graphir qasm2graphir.cpp)
 target_link_libraries(qasm2graphir ${Boost_LIBRARIES})
diff --git a/tools/quantum/qasm2graphir.cpp b/tools/quantum/qasm2graphir.cpp
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0c1bcc5316903b7333209afeeaa76feecfc6aaac 100644
--- a/tools/quantum/qasm2graphir.cpp
+++ b/tools/quantum/qasm2graphir.cpp
@@ -0,0 +1,74 @@
+/***********************************************************************************
+ * Copyright (c) 2016, UT-Battelle
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *   * Redistributions of source code must retain the above copyright
+ *     notice, this list of conditions and the following disclaimer.
+ *   * Redistributions in binary form must reproduce the above copyright
+ *     notice, this list of conditions and the following disclaimer in the
+ *     documentation and/or other materials provided with the distribution.
+ *   * Neither the name of the xacc nor the
+ *     names of its contributors may be used to endorse or promote products
+ *     derived from this software without specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+ * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ * DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY
+ * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ * Contributors:
+ *   Initial API and implementation - Alex McCaskey
+ *
+ **********************************************************************************/
+#include "QasmToGraph.hpp"
+#include <boost/program_options.hpp>
+#include <iostream>
+#include "GraphIR.hpp"
+
+using namespace boost::program_options;
+
+int main(int argc, char** argv) {
+	// Declare the supported options.
+	options_description desc("QASM to XACC Graph IR Utility");
+	desc.add_options()("help",
+			"The following arguments are valid for this utility.")("input",
+			value<std::string>()->required(), "Provide the name of the input qasm file.")(
+			"output", value<std::string>()->default_value("graphIR.xir"),
+			"Provide the name of the output file *.xir file name - "
+			"default is graphIR.xir");
+	// Get the user-specified compiler parameters as a map
+	variables_map compileParameters;
+	store(command_line_parser(argc, argv).options(desc).run(),
+			compileParameters);
+
+	auto inputFileName = compileParameters["input"].as<std::string>();
+	auto outputFileName = (
+			compileParameters.count("output") ?
+					compileParameters["output"].as<std::string>() :
+					"graphIR.xir");
+
+	std::ifstream inputStream(inputFileName);
+	std::ofstream outputStream(outputFileName);
+	std::stringstream ss;
+	if (!inputStream) {
+		QCIError("Invalid input qasm file");
+	}
+
+	ss << inputStream.rdbuf();
+	inputStream.close();
+
+	auto graph = xacc::quantum::QasmToGraph::getCircuitGraph(ss.str());
+
+	xacc::GraphIR<decltype(graph)> xir(graph);
+	xir.persist(outputStream);
+
+	return 0;
+}
diff --git a/xacc/CMakeLists.txt b/xacc/CMakeLists.txt
index e51e642188cfe737a4bc636d3bc59a44b4fdddd1..3dc7d859d69ed119e6353e318e1ba4d146f51190 100644
--- a/xacc/CMakeLists.txt
+++ b/xacc/CMakeLists.txt
@@ -1,3 +1,33 @@
+#***********************************************************************************
+# Copyright (c) 2016, UT-Battelle
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#   * Redistributions of source code must retain the above copyright
+#     notice, this list of conditions and the following disclaimer.
+#   * Redistributions in binary form must reproduce the above copyright
+#     notice, this list of conditions and the following disclaimer in the
+#     documentation and/or other materials provided with the distribution.
+#   * Neither the name of the xacc nor the
+#     names of its contributors may be used to endorse or promote products
+#     derived from this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+# DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY
+# DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+#
+# Contributors:
+#   Initial API and implementation - Alex McCaskey
+#
+#**********************************************************************************/
 set (PACKAGE_NAME "XACC Runtime")
 set (PACKAGE_DESCIPTION "The XACC Programming Framework")
 set (LIBRARY_NAME xacc)
diff --git a/xacc/compiler/GraphIR.hpp b/xacc/compiler/GraphIR.hpp
index 1c9bea42bacb45c81cbe1e90a05e56960ff7db16..7c082769aeafd8f3ea88d36e19af8088f0bbd19d 100644
--- a/xacc/compiler/GraphIR.hpp
+++ b/xacc/compiler/GraphIR.hpp
@@ -65,6 +65,11 @@ public:
 		graph.write(outStream);
 	}
 
+	virtual void read(std::istream& inStream) {
+
+	}
+
+
 };
 }
 
diff --git a/xacc/tests/CompilerTester.cpp b/xacc/tests/CompilerTester.cpp
index f038320a0185cf093ab22984273c7833b5f8c921..e3ee6a9fc9d2d7eb2a4c129871e8d18d5e3b88a8 100644
--- a/xacc/tests/CompilerTester.cpp
+++ b/xacc/tests/CompilerTester.cpp
@@ -42,6 +42,7 @@ public:
 	}
 	virtual std::string toString() { return std::string();}
 	virtual void persist(std::ostream& stream) {}
+	virtual void read(std::istream& inStream) {}
 };
 class FakeCompiler: public Compiler<FakeCompiler> {
 	friend Compiler<FakeCompiler>;
diff --git a/xacc/tests/ProgramTester.cpp b/xacc/tests/ProgramTester.cpp
index 55c28ee6218ca52ca905e747aa48d957962046ca..dd1293297f969292fd37ee2fedd28ecf0bbf9109 100644
--- a/xacc/tests/ProgramTester.cpp
+++ b/xacc/tests/ProgramTester.cpp
@@ -54,6 +54,8 @@ public:
 	}
 	virtual std::string toString() { return std::string();}
 	virtual void persist(std::ostream& stream) {}
+	virtual void read(std::istream& inStream) {}
+
 };
 
 class DummyCompiler : public Compiler<DummyCompiler> {