GT-3334: Changing how we resolve NationalSecurityAgency#1250 (fixes NationalSecurityAgency#1270).

Author: ryanmkurtz

Ghidra/Features/Base/src/main/java/ghidra/app/script/GhidraScript.java

@@ -371,7 +371,7 @@ private void executeNormal() throws Exception {
 	}
 
 	@Override
-	protected DomainFolder getProjectRootFolder() {
+	public DomainFolder getProjectRootFolder() {
 		if (isRunningHeadless()) {
 			Project project = state.getProject();
 			ProjectData projectData = project.getProjectData();

Ghidra/Features/Base/src/main/java/ghidra/program/flatapi/FlatProgramAPI.java

@@ -2473,7 +2473,7 @@ public void saveProgram(Program program, List<String> path) throws Exception {
 	 * the root domain folder.
 	 * @return the root domain folder of the current project
 	 */
-	protected DomainFolder getProjectRootFolder() {
+	public DomainFolder getProjectRootFolder() {
 		Project project = AppInfo.getActiveProject();
 		ProjectData projectData = project.getProjectData();
 		DomainFolder folder = projectData.getRootFolder();

Ghidra/Features/Python/src/main/java/ghidra/python/GhidraPythonInterpreter.java

@@ -69,11 +69,6 @@ public static GhidraPythonInterpreter get() {
 				// Setup python cache directory
 				PythonUtils.setupPythonCacheDir(TaskMonitor.DUMMY);
 
-				// Enable protected java methods to be accessed from python sub-classes.
-				// This is necessary to be able to call protected GhidraScript/FlatProgram API
-				// methods from a python script.
-				System.setProperty("python.security.respectJavaAccessibility", "false");
-
 				// Indicate that we've initialized the python environment, which should
 				// only happen once.
 				pythonInitialized = true;
@@ -348,12 +343,16 @@ private void injectScriptHierarchy(PythonScript script) {
 				}
 			}
 
-			// Add public and protected methods (only once). Ignore inner classes.
+			// Add public methods (only once). Ignore inner classes.
+			//
+			// NOTE: We currently do not have a way to safely add protected methods.  Disabling
+			// python.security.respectJavaAccessibility and adding in protected methods in the below
+			// loop caused an InaccessibleObjectException for some users (relating to core Java 
+			// modules, not the GhidraScript class hierarchy).
 			if (!scriptMethodsInjected) {
 				for (Method method : scriptClass.getDeclaredMethods()) {
 					if (!method.getName().contains("$") &&
-						(Modifier.isPublic(method.getModifiers()) ||
-							Modifier.isProtected(method.getModifiers()))) {
+						Modifier.isPublic(method.getModifiers())) {
 						method.setAccessible(true);
 						setMethod(script, method);
 					}