diff --git a/org.lflang/src/lib/c/reactor-c b/org.lflang/src/lib/c/reactor-c
index ebc4187838..5f472b3eb9 160000
--- a/org.lflang/src/lib/c/reactor-c
+++ b/org.lflang/src/lib/c/reactor-c
@@ -1 +1 @@
-Subproject commit ebc41878384d9158127ac1c8d4a31780f0546f63
+Subproject commit 5f472b3eb958e986a63ad88b9ca0d32e0cc50d18
diff --git a/org.lflang/src/lib/py/reactor-c-py b/org.lflang/src/lib/py/reactor-c-py
index a5b82a1eaa..e0f8615431 160000
--- a/org.lflang/src/lib/py/reactor-c-py
+++ b/org.lflang/src/lib/py/reactor-c-py
@@ -1 +1 @@
-Subproject commit a5b82a1eaad03050adaab7671e98f02816dd9306
+Subproject commit e0f861543122a660694643aad329aa7c93450d61
diff --git a/org.lflang/src/org/lflang/generator/c/CCoreFilesUtils.java b/org.lflang/src/org/lflang/generator/c/CCoreFilesUtils.java
index cc1b6ef02e..64ed1169d8 100644
--- a/org.lflang/src/org/lflang/generator/c/CCoreFilesUtils.java
+++ b/org.lflang/src/org/lflang/generator/c/CCoreFilesUtils.java
@@ -13,8 +13,8 @@
  */
 public class CCoreFilesUtils {
     public static List<String> getCoreFiles(
-        boolean isFederated, 
-        boolean threading, 
+        boolean isFederated,
+        boolean threading,
         SchedulerOption scheduler
     ) {
         List<String> coreFiles = new ArrayList<>();
@@ -26,13 +26,30 @@ public static List<String> getCoreFiles(
         coreFiles.addAll(getThreadSupportFiles(threading, scheduler));
         return coreFiles;
     }
+
     public static List<String> getCTargetSrc() {
         return List.of(
-            "ctarget/schedule.c",
-            "ctarget/util.c"
+            "lib/schedule.c",
+            "lib/util.c",
+            "lib/tag.c",
+            "lib/time.c"
+        );
+    }
+
+    public static List<String> getCTargetHeader() {
+        return List.of(
+            "include/ctarget/ctarget.h"
         );
     }
 
+    public static String getCTargetSetHeader() {
+        return "include/ctarget/set.h";
+    }
+
+    public static String getCTargetSetUndefHeader() {
+        return "include/ctarget/set_undef.h";
+    }
+
     private static List<String> getBaseCoreFiles() {
         return List.of(
             "reactor_common.c",
@@ -48,7 +65,7 @@ private static List<String> getBaseCoreFiles() {
             "utils/vector.h",
             "utils/semaphore.h",
             "utils/semaphore.c",
-            "utils/util.h", 
+            "utils/util.h",
             "utils/util.c",
             "platform.h",
             "platform/Platform.cmake",
@@ -82,19 +99,19 @@ private static List<String> getFederatedFiles() {
         return List.of(
             "federated/net_util.c",
             "federated/net_util.h",
-            "federated/net_common.h", 
-            "federated/federate.c", 
-            "federated/federate.h", 
-            "federated/clock-sync.h", 
+            "federated/net_common.h",
+            "federated/federate.c",
+            "federated/federate.h",
+            "federated/clock-sync.h",
             "federated/clock-sync.c"
         );
     }
 
     private static List<String> getThreadSupportFiles(
-        boolean threading, 
+        boolean threading,
         SchedulerOption scheduler
     ) {
-        return threading ? 
+        return threading ?
                 List.of(
                     "threaded/scheduler.h",
                     "threaded/scheduler_instance.h",
diff --git a/org.lflang/src/org/lflang/generator/c/CGenerator.java b/org.lflang/src/org/lflang/generator/c/CGenerator.java
index 6bb25d69e6..897375a43f 100644
--- a/org.lflang/src/org/lflang/generator/c/CGenerator.java
+++ b/org.lflang/src/org/lflang/generator/c/CGenerator.java
@@ -1276,12 +1276,12 @@ protected void initializeClockSynchronization() {
     private void copyTargetFiles() throws IOException{
         FileUtil.copyDirectoryFromClassPath(
             "/lib/c/reactor-c/include", 
-            fileConfig.getSrcGenPath(),
+            fileConfig.getSrcGenPath().resolve("include"),
             false
         );
         FileUtil.copyDirectoryFromClassPath(
             "/lib/c/reactor-c/lib", 
-            fileConfig.getSrcGenPath(),
+            fileConfig.getSrcGenPath().resolve("lib"),
             false
         );
     }
diff --git a/org.lflang/src/org/lflang/generator/c/CPreambleGenerator.java b/org.lflang/src/org/lflang/generator/c/CPreambleGenerator.java
index 332420089b..c68eb57798 100644
--- a/org.lflang/src/org/lflang/generator/c/CPreambleGenerator.java
+++ b/org.lflang/src/org/lflang/generator/c/CPreambleGenerator.java
@@ -10,14 +10,15 @@
 import org.lflang.TargetProperty.CoordinationType;
 import org.lflang.generator.CodeBuilder;
 import org.lflang.generator.GeneratorBase;
+import org.lflang.util.StringUtil;
 
 import static org.lflang.util.StringUtil.addDoubleQuotes;
 
 /**
  * Generates code for preambles for the C and CCpp target.
  * This includes #include and #define directives at the top
- * of each generated ".c" file. 
- * 
+ * of each generated ".c" file.
+ *
  * @author{Edward A. Lee <eal@berkeley.edu>}
  * @author{Marten Lohstroh <marten@berkeley.edu>}
  * @author{Mehrdad Niknami <mniknami@berkeley.edu>}
@@ -30,12 +31,14 @@
 public class CPreambleGenerator {
     /** Add necessary source files specific to the target language.  */
     public static String generateIncludeStatements(
-        TargetConfig targetConfig, 
+        TargetConfig targetConfig,
         boolean isFederated
     ) {
         var tracing = targetConfig.tracing;
         CodeBuilder code = new CodeBuilder();
-        code.pr("#include \"ctarget/ctarget.h\"");
+        CCoreFilesUtils.getCTargetHeader().forEach(
+            it -> code.pr("#include " + StringUtil.addDoubleQuotes(it))
+        );
         if (targetConfig.threading) {
             code.pr("#include \"core/threaded/reactor_threaded.c\"");
             code.pr("#include \"core/threaded/scheduler.h\"");
@@ -71,7 +74,7 @@ public static String generateDefineDirectives(
             code.pr("#define NUMBER_OF_FEDERATES " + numFederates);
             code.pr(generateFederatedDefineDirective(coordinationType));
             if (advanceMessageInterval != null) {
-                code.pr("#define ADVANCE_MESSAGE_INTERVAL " + 
+                code.pr("#define ADVANCE_MESSAGE_INTERVAL " +
                     GeneratorBase.timeInTargetLanguage(advanceMessageInterval));
             }
         }
@@ -92,12 +95,12 @@ public static String generateDefineDirectives(
 
     /**
      * Returns the #define directive for the given coordination type.
-     * 
+     *
      * NOTE: Instead of checking #ifdef FEDERATED, we could
      *       use #if (NUMBER_OF_FEDERATES > 1).
      *       To Soroush Bateni, the former is more accurate.
      */
-    private static String generateFederatedDefineDirective(CoordinationType coordinationType) {        
+    private static String generateFederatedDefineDirective(CoordinationType coordinationType) {
         List<String> directives = new ArrayList<>();
         directives.add("#define FEDERATED");
         if (coordinationType == CoordinationType.CENTRALIZED) {
@@ -122,12 +125,12 @@ private static String generateTracingDefineDirective(
 
     /**
      * Initialize clock synchronization (if enabled) and its related options for a given federate.
-     * 
+     *
      * Clock synchronization can be enabled using the clock-sync target property.
      * @see https://github.com/icyphy/lingua-franca/wiki/Distributed-Execution#clock-synchronization
      */
     private static String generateClockSyncDefineDirective(
-        ClockSyncMode mode, 
+        ClockSyncMode mode,
         ClockSyncOptions options
     ) {
         List<String> code = new ArrayList<>();
diff --git a/org.lflang/src/org/lflang/generator/c/CReactionGenerator.java b/org.lflang/src/org/lflang/generator/c/CReactionGenerator.java
index f778e22336..3e0961e035 100644
--- a/org.lflang/src/org/lflang/generator/c/CReactionGenerator.java
+++ b/org.lflang/src/org/lflang/generator/c/CReactionGenerator.java
@@ -33,6 +33,8 @@
 import org.lflang.lf.TriggerRef;
 import org.lflang.lf.VarRef;
 import org.lflang.lf.Variable;
+import org.lflang.util.StringUtil;
+
 import static org.lflang.util.StringUtil.addDoubleQuotes;
 
 public class CReactionGenerator {
@@ -1187,7 +1189,9 @@ public static String generateReaction(
                         types, errorReporter, mainDef, 
                         isFederatedAndDecentralized, 
                         requiresType);
-        code.pr("#include \"ctarget/set.h\"");
+        code.pr(
+            "#include " + StringUtil.addDoubleQuotes(
+                CCoreFilesUtils.getCTargetSetHeader()));
         code.pr(generateFunction(
             generateReactionFunctionHeader(decl, reactionIndex),
             init, reaction.getCode()
@@ -1208,7 +1212,9 @@ public static String generateReaction(
                 generateDeadlineFunctionHeader(decl, reactionIndex), 
                 init, reaction.getDeadline().getCode()));
         }
-        code.pr("#include \"ctarget/set_undef.h\"");
+        code.pr(
+            "#include " + StringUtil.addDoubleQuotes(
+                CCoreFilesUtils.getCTargetSetUndefHeader()));
         return code.toString();
     }
 
diff --git a/org.lflang/src/org/lflang/generator/python/PythonReactionGenerator.java b/org.lflang/src/org/lflang/generator/python/PythonReactionGenerator.java
index 16d7758cb3..82ff226a21 100644
--- a/org.lflang/src/org/lflang/generator/python/PythonReactionGenerator.java
+++ b/org.lflang/src/org/lflang/generator/python/PythonReactionGenerator.java
@@ -14,10 +14,12 @@
 import org.lflang.lf.Code;
 import org.lflang.lf.TriggerRef;
 import org.lflang.lf.VarRef;
+import org.lflang.util.StringUtil;
 import org.lflang.lf.Instantiation;
 import org.lflang.lf.Port;
 import org.lflang.lf.Input;
 import org.lflang.lf.Output;
+import org.lflang.generator.c.CCoreFilesUtils;
 import org.lflang.generator.c.CReactionGenerator;
 import org.lflang.generator.c.CTypes;
 import org.lflang.generator.c.CUtil;
@@ -129,7 +131,9 @@ public static String generateCReaction(
                                                 types, errorReporter, mainDef, 
                                                 isFederatedAndDecentralized, 
                                                 Target.Python.requiresTypes);
-        code.pr("#include \"ctarget/set.h\"");
+        code.pr(
+            "#include " + StringUtil.addDoubleQuotes(
+                CCoreFilesUtils.getCTargetSetHeader()));
         code.pr(generateFunction(
                     CReactionGenerator.generateReactionFunctionHeader(decl, reactionIndex), 
                     cInit, reaction.getCode(), 
@@ -144,7 +148,9 @@ public static String generateCReaction(
                 generateCPythonDeadlineCaller(decl, reactionIndex, pyObjects)
             ));
         }
-        code.pr("#include \"ctarget/set_undef.h\"");
+        code.pr(
+            "#include " + StringUtil.addDoubleQuotes(
+                CCoreFilesUtils.getCTargetSetUndefHeader()));
         return code.toString();
     }