diff --git a/GhidraBuild/EclipsePlugins/GhidraDev/GhidraDevPlugin/README.md b/GhidraBuild/EclipsePlugins/GhidraDev/GhidraDevPlugin/README.md
index 2862c17572..61d489188c 100644
--- a/GhidraBuild/EclipsePlugins/GhidraDev/GhidraDevPlugin/README.md
+++ b/GhidraBuild/EclipsePlugins/GhidraDev/GhidraDevPlugin/README.md
@@ -32,6 +32,8 @@ change with future releases.
 ## Change History
 __4.0.1:__
 * New Ghidra module projects now contain a default `README.md` file.
+* Fixed a bug that prevented an imported module source project from being discovered by Ghidra when
+  launched with the project's run/debug configuration.
 
 __4.0.0:__
 * GhidraDev has been upgraded to be compatible with Ghidra 11.2 and later. It is not backwards
diff --git a/GhidraBuild/EclipsePlugins/GhidraDev/GhidraDevPlugin/src/main/java/ghidradev/ghidraprojectcreator/utils/GhidraModuleUtils.java b/GhidraBuild/EclipsePlugins/GhidraDev/GhidraDevPlugin/src/main/java/ghidradev/ghidraprojectcreator/utils/GhidraModuleUtils.java
index fbf377ff1c..97993967d8 100644
--- a/GhidraBuild/EclipsePlugins/GhidraDev/GhidraDevPlugin/src/main/java/ghidradev/ghidraprojectcreator/utils/GhidraModuleUtils.java
+++ b/GhidraBuild/EclipsePlugins/GhidraDev/GhidraDevPlugin/src/main/java/ghidradev/ghidraprojectcreator/utils/GhidraModuleUtils.java
@@ -62,13 +62,14 @@ public class GhidraModuleUtils {
 		}
 	}
 
-	/**
-	 * Stores a source folder and its corresponding output folder
-	 * 
-	 * @param sourceFolder The source folder
-	 * @param outputFolder The output folder
-	 */
-	private record SourceFolderInfo(IFolder sourceFolder, IFolder outputFolder) {}
+	private static String defaultOutputPath = "bin/main";
+
+	private static Map<String, String> sourceToOutputMap =
+		Map.ofEntries(Map.entry("src/main/java", defaultOutputPath),
+			Map.entry("src/main/help", defaultOutputPath),
+			Map.entry("src/main/resources", defaultOutputPath),
+			Map.entry("src/test/java", "bin/test"),
+			Map.entry("ghidra_scripts", "bin/scripts"));
 
 	/**
 	 * Creates a new Ghidra module project with the given name.
@@ -97,28 +98,17 @@ public class GhidraModuleUtils {
 				runConfigMemory, ghidraLayout, jythonInterpreterName, monitor);
 		IProject project = javaProject.getProject();
 
-		// Create source directories
-		List<SourceFolderInfo> sourceFolderInfos = new ArrayList<>();
-		sourceFolderInfos.add(new SourceFolderInfo(project.getFolder("src/main/java"),
-			project.getFolder("bin/main")));
-		sourceFolderInfos.add(new SourceFolderInfo(project.getFolder("src/main/help"),
-			project.getFolder("bin/main")));
-		sourceFolderInfos.add(new SourceFolderInfo(project.getFolder("src/main/resources"),
-			project.getFolder("bin/main")));
-		sourceFolderInfos.add(new SourceFolderInfo(project.getFolder("src/test/java"),
-			project.getFolder("bin/test")));
-		sourceFolderInfos.add(new SourceFolderInfo(project.getFolder("ghidra_scripts"),
-			project.getFolder("bin/scripts")));
-		for (SourceFolderInfo sourceFolderInfo : sourceFolderInfos) {
-			GhidraProjectUtils.createFolder(sourceFolderInfo.sourceFolder(), monitor);
-		}
-
-		// Put the source directories in the project's classpath
+		// Set default output location
+		javaProject.setOutputLocation(project.getFolder(defaultOutputPath).getFullPath(), monitor);
+		
+		// Create source directories and add them to the project's classpath
 		List<IClasspathEntry> classpathEntries = new LinkedList<>();
-		for (SourceFolderInfo sourceFolderInfo : sourceFolderInfos) {
-			classpathEntries
-					.add(JavaCore.newSourceEntry(sourceFolderInfo.sourceFolder().getFullPath(),
-						new IPath[0], sourceFolderInfo.outputFolder().getFullPath()));
+		for (String sourcePath : sourceToOutputMap.keySet()) {
+			IFolder sourceFolder = project.getFolder(sourcePath);
+			IFolder outputFolder = project.getFolder(sourceToOutputMap.get(sourcePath));
+			GhidraProjectUtils.createFolder(sourceFolder, monitor);
+			classpathEntries.add(JavaCore.newSourceEntry(sourceFolder.getFullPath(), new IPath[0],
+				outputFolder.getFullPath()));
 		}
 		GhidraProjectUtils.addToClasspath(javaProject, classpathEntries, monitor);
 
@@ -256,42 +246,30 @@ public class GhidraModuleUtils {
 				createRunConfig, runConfigMemory, ghidraLayout, jythonInterpreterName, monitor);
 		IProject project = javaProject.getProject();
 
-		// Find source directory paths
-		List<IPath> sourcePaths = new ArrayList<>();
-		IFolder srcFolder = project.getFolder("src");
-		List<IFolder> srcSubFolders = getSubFolders(srcFolder);
-		if (!srcSubFolders.isEmpty()) {
-			for (IFolder srcSubFolder : srcSubFolders) {
-				List<IFolder> subSubFolders = getSubFolders(srcSubFolder);
-				if (!subSubFolders.isEmpty()) {
-					sourcePaths.addAll(subSubFolders.stream().map(e -> e.getFullPath()).toList());
-				}
-				else {
-					sourcePaths.add(srcSubFolder.getFullPath());
-				}
-			}
-		}
-		else {
-			sourcePaths.add(srcFolder.getFullPath());
-		}
+		// Set default output location
+		IFolder defaultOutputFolder = project.getFolder(defaultOutputPath);
+		javaProject.setOutputLocation(defaultOutputFolder.getFullPath(), monitor);
 
-		// Find jar file paths
-		List<IPath> jarPaths = new ArrayList<>();
+		// Put the source and jar paths in the project's classpath
+		List<IClasspathEntry> classpathEntries = new LinkedList<>();
+		for (String sourcePath : sourceToOutputMap.keySet()) {
+			IFolder sourceFolder = project.getFolder(sourcePath);
+			IFolder outputFolder = project.getFolder(sourceToOutputMap.get(sourcePath));
+			GhidraProjectUtils.createFolder(sourceFolder, monitor);
+			classpathEntries.add(JavaCore.newSourceEntry(sourceFolder.getFullPath(), new IPath[0],
+				outputFolder.getFullPath()));
+		}
 		IFolder libFolder = project.getFolder("lib");
 		if (libFolder.exists()) {
 			for (IResource resource : libFolder.members()) {
 				if (resource.getType() == IResource.FILE &&
 					resource.getFileExtension().equals("jar")) {
-					jarPaths.add(resource.getFullPath());
+					classpathEntries
+							.add(JavaCore.newLibraryEntry(resource.getFullPath(), null, null));
 				}
 			}
 		}
-
-		// Put the source and jar paths in the project's classpath
-		List<IClasspathEntry> cp = new ArrayList<>();
-		cp.addAll(sourcePaths.stream().map(e -> JavaCore.newSourceEntry(e)).toList());
-		cp.addAll(jarPaths.stream().map(e -> JavaCore.newLibraryEntry(e, null, null)).toList());
-		GhidraProjectUtils.addToClasspath(javaProject, cp, monitor);
+		GhidraProjectUtils.addToClasspath(javaProject, classpathEntries, monitor);
 
 		// Update language ant properties file
 		GhidraModuleUtils.writeAntProperties(project, ghidraLayout);