diff --git a/CMakeLists.txt b/CMakeLists.txt
index ba3f718..a59d256 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -55,9 +55,8 @@ else ()
 endif ()
 
 ## Include directories
+include_directories(.)
 include_directories(include)
-include_directories(.) # TODO remove
-include_directories(src) # TODO remove
 
 ## Subdirectories
 add_subdirectory(src/core)
diff --git a/src/standalone/autotest.cc b/src/standalone/autotest.cc
index c7aec10..c408633 100644
--- a/src/standalone/autotest.cc
+++ b/src/standalone/autotest.cc
@@ -29,7 +29,7 @@
 #include <stdio.h>
 
 #include "config_loader.h"
-#include "core/math_utils.h"
+#include "src/core/math_utils.h"
 #include "model/host_forcing.h"
 #include "model/host_memory.h"
 #include "model/host_timestep.h"
@@ -37,7 +37,7 @@
 #include "model/model_reduce.h"
 #include "model/model_rk3.h"
 
-#include "core/errchk.h"
+#include "src/core/errchk.h"
 
 #define ARRAY_SIZE(x) (sizeof(x) / sizeof((x)[0]))
 
diff --git a/src/standalone/benchmark.cc b/src/standalone/benchmark.cc
index 6e01346..24f7f15 100644
--- a/src/standalone/benchmark.cc
+++ b/src/standalone/benchmark.cc
@@ -211,7 +211,7 @@ run_benchmark(void)
 #if AUTO_OPTIMIZE
 const char* benchmark_path = "benchmark.out";
 
-#include "core/kernels/rk3_threadblock.conf"
+#include "src/core/kernels/rk3_threadblock.conf"
 static int
 write_result_to_file(const float& ms_per_step)
 {
diff --git a/src/standalone/config_loader.cc b/src/standalone/config_loader.cc
index 7a0a509..eeb223e 100644
--- a/src/standalone/config_loader.cc
+++ b/src/standalone/config_loader.cc
@@ -31,8 +31,8 @@
 #include <stdio.h>  // print
 #include <string.h> // memset
 
-#include "core/errchk.h"
-#include "core/math_utils.h"
+#include "src/core/errchk.h"
+#include "src/core/math_utils.h"
 
 static inline void
 print(const AcMeshInfo& config)
diff --git a/src/standalone/main.cc b/src/standalone/main.cc
index c393ace..0e14842 100644
--- a/src/standalone/main.cc
+++ b/src/standalone/main.cc
@@ -1,5 +1,5 @@
 /*
-    Copyright (C) 2014-2019, Johannes Pekkilae, Miikka Vaeisalae.
+    Copyright (C) 2014-2018, Johannes Pekkilae, Miikka Vaeisalae.
 
     This file is part of Astaroth.
 
@@ -28,7 +28,7 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "core/errchk.h"
+#include "src/core/errchk.h"
 #include "run.h"
 
 // Write all errors from stderr to an <errorlog_name> in the current working
diff --git a/src/standalone/model/host_forcing.cc b/src/standalone/model/host_forcing.cc
index 423bf19..c0ee7f0 100644
--- a/src/standalone/model/host_forcing.cc
+++ b/src/standalone/model/host_forcing.cc
@@ -26,7 +26,7 @@
  */
 #include "host_forcing.h"
 
-#include "core/math_utils.h"
+#include "src/core/math_utils.h"
 
 // The is a wrapper for genering random numbers with a chosen system.
 AcReal
diff --git a/src/standalone/model/host_memory.cc b/src/standalone/model/host_memory.cc
index 5cda923..5a68d9b 100644
--- a/src/standalone/model/host_memory.cc
+++ b/src/standalone/model/host_memory.cc
@@ -28,7 +28,7 @@
 
 #include <math.h>
 
-#include "core/errchk.h"
+#include "src/core/errchk.h"
 
 #define AC_GEN_STR(X) #X
 const char* init_type_names[] = {AC_FOR_INIT_TYPES(AC_GEN_STR)};
diff --git a/src/standalone/model/host_timestep.cc b/src/standalone/model/host_timestep.cc
index 48f4134..9245cef 100644
--- a/src/standalone/model/host_timestep.cc
+++ b/src/standalone/model/host_timestep.cc
@@ -1,5 +1,5 @@
 /*
-    Copyright (C) 2014-2019, Johannes Pekkilae, Miikka Vaeisalae.
+    Copyright (C) 2014-2018, Johannes Pekkilae, Miikka Vaeisalae.
 
     This file is part of Astaroth.
 
@@ -26,7 +26,7 @@
  */
 #include "host_timestep.h"
 
-#include "core/math_utils.h"
+#include "src/core/math_utils.h"
 
 static AcReal timescale = AcReal(1.0);
 
diff --git a/src/standalone/model/model_boundconds.cc b/src/standalone/model/model_boundconds.cc
index f7a6aca..9490be1 100644
--- a/src/standalone/model/model_boundconds.cc
+++ b/src/standalone/model/model_boundconds.cc
@@ -26,7 +26,7 @@
  */
 #include "model_boundconds.h"
 
-#include "core/errchk.h"
+#include "src/core/errchk.h"
 
 void
 boundconds(const AcMeshInfo& mesh_info, ModelMesh* mesh)
diff --git a/src/standalone/model/model_diff.h b/src/standalone/model/model_diff.h
index 20678bf..303181d 100644
--- a/src/standalone/model/model_diff.h
+++ b/src/standalone/model/model_diff.h
@@ -25,7 +25,7 @@
  *
  */
 #pragma once
-#include "core/errchk.h"
+#include "src/core/errchk.h"
 
 typedef long double MODEL_REAL;
 
diff --git a/src/standalone/model/model_reduce.cc b/src/standalone/model/model_reduce.cc
index 6d48c4b..1de3b32 100644
--- a/src/standalone/model/model_reduce.cc
+++ b/src/standalone/model/model_reduce.cc
@@ -28,7 +28,7 @@
 
 #include <math.h>
 
-#include "core/errchk.h"
+#include "src/core/errchk.h"
 
 // Function pointer definitions
 typedef ModelScalar (*ReduceFunc)(const ModelScalar&, const ModelScalar&);
diff --git a/src/standalone/renderer.cc b/src/standalone/renderer.cc
index 1522cc5..6fd1913 100644
--- a/src/standalone/renderer.cc
+++ b/src/standalone/renderer.cc
@@ -32,8 +32,8 @@
 #include <string.h> // memcpy
 
 #include "config_loader.h"
-#include "core/errchk.h"
-#include "core/math_utils.h"
+#include "src/core/errchk.h"
+#include "src/core/math_utils.h"
 #include "model/host_memory.h"
 #include "model/host_timestep.h"
 #include "model/model_reduce.h"
@@ -423,7 +423,7 @@ run_renderer(void)
     return 0;
 }
 #else // BUILD_RT_VISUALIZATION == 0
-#include "core/errchk.h"
+#include "src/core/errchk.h"
 int
 run_renderer(void)
 {
diff --git a/src/standalone/simulation.cc b/src/standalone/simulation.cc
index f6b7e46..ebd527e 100644
--- a/src/standalone/simulation.cc
+++ b/src/standalone/simulation.cc
@@ -27,8 +27,8 @@
 #include "run.h"
 
 #include "config_loader.h"
-#include "core/errchk.h"
-#include "core/math_utils.h"
+#include "src/core/errchk.h"
+#include "src/core/math_utils.h"
 #include "model/host_forcing.h"
 #include "model/host_memory.h"
 #include "model/host_timestep.h"