Update copyright and clang-format scripts for new structure

clang-format-all

@@ -36,8 +36,8 @@ args = parser.parse_args()
 clang_format = args.executable
 paths = ['cpp', 'testing']
 extensions = ['.h', '.cpp']
-exclusion_list = ['cpp/lib/src/gui/gl_core_3_3.h',
-                  'cpp/lib/src/gui/gl_core_3_3.cpp']
+exclusion_list = ['cpp/gui/opengl/gl_core_3_3.h',
+                  'cpp/gui/opengl/gl_core_3_3.cpp']
 
 # if clang-format path contains spaces, wrap it in quotes
 if ' ' in clang_format and not clang_format.startswith('"'):

update_copyright

@@ -43,19 +43,18 @@ SearchPath = namedtuple('SearchPath', 'dirname recursive need_shebang comment ex
 ProcessFile = namedtuple('ProcessFile', 'path keep_shebang comment')
 
 MRTRIX_ROOT = os.path.abspath(os.path.dirname(__file__))
-APP_CPP_PATH = os.path.join(MRTRIX_ROOT, 'cpp', 'lib', 'core', 'app.cpp')
+APP_CPP_PATH = os.path.join(MRTRIX_ROOT, 'cpp', 'core', 'app.cpp')
 APP_CPP_STRING = 'std::string COPYRIGHT ='
 APP_PY_PATH = os.path.join(MRTRIX_ROOT, 'python', 'mrtrix3', 'app.py')
 APP_PY_STRING = '_DEFAULT_COPYRIGHT ='
 
 SEARCH_PATHS = [
     SearchPath('.', False, True, '#', [], ['mrtrix-mrview.desktop']),
-    SearchPath(os.path.join('cpp', 'cmd'), False, False, '*', ['.cpp'], []),
+    SearchPath(os.path.join('cpp'), True, False, '*', ['.cpp', '.h'], []),
     SearchPath('docs', False, True, '#', [], []),
     SearchPath('matlab', True, False, '%', ['.m'], []),
     SearchPath('python', True, False, '#', ['.py'], [os.path.join('mrtrix3', 'version.py.in'), os.path.join('mrtrix3', 'commands', '__init__.py.in')]),
     SearchPath(os.path.join('share', 'mrtrix3'), True, False, '#', ['.txt'], []),
-    SearchPath(os.path.join('cpp', 'lib'), True, False, '*', ['.cpp', '.h'], []),
     SearchPath(os.path.join('testing', 'tools'), False, False, '*', ['.cpp'], []),
     SearchPath(os.path.join('testing', 'unit_tests'), False, False, '*', ['.cpp'], []),
     SearchPath(os.path.join('testing', 'lib'), False, False, '*', ['.h'], []),