Merge remote-tracking branch 'origin/Ghidra_9.2'

GPL/GnuDisassembler/src/gdis/c/disasm_1.c

@@ -21,7 +21,7 @@ void listSupportedArchMachTargets(void)
 	const char** targetList;
 	const char** archList;
 	int i, j;
-	
+
 	targetList = bfd_target_list();
 	if(targetList != NULL){
 		for(i=0, j=0; targetList[i] !=0; i++){
@@ -29,7 +29,7 @@ void listSupportedArchMachTargets(void)
 		}
 	}
 	printf("\ndone with targetList.\n");
-	
+
 	archList = bfd_arch_list();
 	if(archList != NULL){
 		for(i=0, j=0; archList[i] !=0; i++){
@@ -44,29 +44,29 @@ void listSupportedArchMachTargets(void)
 /* sprintf to a "stream".  */
 int objdump_sprintf (SFILE *f, const char *format, ...)
 {
-	
+
 	int i;
 	size_t n;
 	va_list args;
- 
+
 	va_start (args, format);
 	n = vsnprintf (f->buffer + f->pos, BUFF_SIZE, format, args);
 	strncat(disassembled_buffer, f->buffer, n);
 	va_end (args);
-  
+
 	return n;
 }
 
 
 void configureDisassembleInfo(bfd* abfd,
-							  disassemble_info* info, 
-							  enum bfd_architecture arch, 
-							  unsigned long mach, 
-							  enum bfd_endian end)
+		disassemble_info* info,
+		enum bfd_architecture arch,
+		unsigned long mach,
+		enum bfd_endian end)
 {
 
 	memset(sfile.buffer, 0x00, BUFF_SIZE);
-	
+
 	INIT_DISASSEMBLE_INFO(*info, stdout, objdump_sprintf);
 	info->arch = (enum bfd_architecture) arch;
 	info->mach = mach;
@@ -79,24 +79,24 @@ void configureDisassembleInfo(bfd* abfd,
 }
 
 disassembler_ftype configureBfd(bfd* abfd, 
-								enum bfd_architecture arch, 
-								unsigned long mach, 
-								enum bfd_endian endian, 
-								disassemble_info* DI,
-								disassembler_ftype* disassemble_fn)
+		enum bfd_architecture arch,
+		unsigned long mach,
+		enum bfd_endian endian,
+		disassemble_info* DI,
+		disassembler_ftype* disassemble_fn)
 {	
 	struct bfd_target *xvec;
-	
+
 	abfd->flags |= EXEC_P;
-	
-	
+
+
 	// set up xvec byteorder. 
 	xvec = (struct bfd_target *) malloc (sizeof (struct bfd_target));
 	memset(xvec, 0x00, sizeof (struct bfd_target));	
 	memcpy (xvec, abfd->xvec, sizeof (struct bfd_target));
 	xvec->byteorder = endian;
 	abfd->xvec = xvec;
-	
+
 	configureDisassembleInfo(abfd, DI, arch, mach, endian);
 	if(endian == BFD_ENDIAN_BIG){
 		bfd_big_endian(abfd);
@@ -106,29 +106,29 @@ disassembler_ftype configureBfd(bfd* abfd,
 		bfd_little_endian(abfd);
 		DI->display_endian = DI->endian = BFD_ENDIAN_LITTLE;
 	}
-	
+
 	/*
 	bfd_error_type err = bfd_get_error();
 	printf("bfd_error_msg: %s.\n", bfd_errmsg(err));
-	*/
-	
+	 */
+
 	/* Use libopcodes to locate a suitable disassembler.  */
 	*disassemble_fn = NULL;
 	*disassemble_fn = disassembler (arch, endian == BFD_ENDIAN_BIG, mach, abfd);
 	if (!*disassemble_fn){
 		printf("can't disassemble for arch 0x%08X, mach 0x%08lX\n", arch, mach);
 		exit(1);
-    }
-    
-    return *disassemble_fn;
+	}
+
+	return *disassemble_fn;
 }
 
 
 
 int disassemble_buffer( disassembler_ftype disassemble_fn,
-						disassemble_info *info,
-						int* offset,						
-						PDIS_INFO pDisInfo)
+		disassemble_info *info,
+		int* offset,
+		PDIS_INFO pDisInfo)
 {
 	int i, j, size = 0;
 	int len = 0;
@@ -136,7 +136,7 @@ int disassemble_buffer( disassembler_ftype disassemble_fn,
 	while ( *offset < info->buffer_length ) {
 		/* call the libopcodes disassembler */
 		memset(pDisInfo->disassemblyString, 0x00, MAX_DIS_STRING);
-		
+
 		/* set the insn_info_valid bit to 0, as explained in BFD's
 		 * include/dis-asm.h. The bit will then be set to tell us
 		 * whether the decoder supports "extra" information about the
@@ -147,7 +147,7 @@ int disassemble_buffer( disassembler_ftype disassemble_fn,
 		size = (*disassemble_fn)(info->buffer_vma + *offset, info);
 		/* -- analyze disassembled instruction here -- */
 		/* -- print any symbol names as labels here -- */
-		
+
 		/* save off corresponding hex bytes */
 		for ( j= 0,i = 0; i < 8; i++, j+=3) {
 			if ( i < size ){				
@@ -155,7 +155,7 @@ int disassemble_buffer( disassembler_ftype disassemble_fn,
 				pDisInfo->bytesBufferBin[i] = info->buffer[*offset + i];
 			}
 		}
-		
+
 		/* add the augmented information to our disassembly info struct */
 		pDisInfo->count = size;
 		pDisInfo->insn_info_valid = info->insn_info_valid;
@@ -167,44 +167,44 @@ int disassemble_buffer( disassembler_ftype disassemble_fn,
 
 		strcat(&(pDisInfo->disassemblyString[0]), disassembled_buffer);
 		memset(disassembled_buffer, 0x00, BUFF_SIZE);
-		
+
 		if(size != 0){
 			*offset += size; /* advance position in buffer */
 			goto END;
 		}
 	}
 
-END:	
+	END:
 	return size;
 }
 
 void processBuffer(unsigned char* buff, 
-		   int buff_len,
-		   bfd_vma buff_vma,
-		   disassembler_ftype disassemble_fn, 
-		   struct disassemble_info* DI)
+		int buff_len,
+		bfd_vma buff_vma,
+		disassembler_ftype disassemble_fn,
+		struct disassemble_info* DI)
 {
 	int bytesConsumed = -1;
 	int offset = 0;
 	int numDisassemblies = 0;
 	int i;
-		
+
 	DI->buffer = buff; /* buffer of bytes to disassemble */
 	DI->buffer_length = buff_len; /* size of buffer */
 	DI->buffer_vma = buff_vma; /* base RVA of buffer */
-								 
+
 	memset(disassemblyInfoBuffer, 0x00, sizeof(DIS_INFO)*MAX_NUM_ENTRIES);
-			
+
 	while((buff_len - offset) > 0 && bytesConsumed != 0 && numDisassemblies < MAX_NUM_ENTRIES){
 		bytesConsumed = disassemble_buffer( disassemble_fn, DI, &offset, &(disassemblyInfoBuffer[numDisassemblies++]));	
 	}
 	for (i = 0; i < numDisassemblies; i++) {
-	    printf("%s\nInfo: %d,%d,%d,%d,%d\n", disassemblyInfoBuffer[i].disassemblyString,
-		   disassemblyInfoBuffer[i].count, 
-		   disassemblyInfoBuffer[i].insn_info_valid, 
-		   disassemblyInfoBuffer[i].branch_delay_insns,
-		   disassemblyInfoBuffer[i].data_size,
-		   disassemblyInfoBuffer[i].insn_type);
+		printf("%s\nInfo: %d,%d,%d,%d,%d\n", disassemblyInfoBuffer[i].disassemblyString,
+				disassemblyInfoBuffer[i].count,
+				disassemblyInfoBuffer[i].insn_info_valid,
+				disassemblyInfoBuffer[i].branch_delay_insns,
+				disassemblyInfoBuffer[i].data_size,
+				disassemblyInfoBuffer[i].insn_type);
 	}
 }
 
@@ -224,7 +224,7 @@ int main(int argc, char* argv[]){
 	char elf_file_location[MAX_ELF_FILE_PATH_LEN];
 	char arch_str[256];
 	char mach_str[256];
-		
+
 	if ( argc < 8) {
 		fprintf(stderr, "Usage: %s target-str, arch, mach, disassembly base-addr (for rel offsets instrs), full-path to Little and Big Elfs, big/little ascii-byte-string up to %d chars\n", argv[0], MAX_ASCII_CHAR_BYTE_STRING);
 		listSupportedArchMachTargets();
@@ -247,16 +247,16 @@ int main(int argc, char* argv[]){
 	mach = 0x00000000;
 	arch = (enum bfd_architecture) 0x00;
 	offset = 0x00000000;
-	
+
 	sscanf(argv[2], "%128s", arch_str);
 	sscanf(argv[3], "%18lX", &mach);
 	sscanf(argv[4], "%10X", &end);
 	sscanf(argv[5], "%18lX", &offset);
-	
+
 	// if arch starts with 0x, then parse a number
 	//  else lookup the string in the table to get the arch, ignore the mach
 	if (arch_str[0] == '0' && arch_str[1] == 'x') {
-	   sscanf(arch_str, "%10X", &arch);
+		sscanf(arch_str, "%10X", &arch);
 	} else {
 		const char** archList = bfd_arch_list();
 		const bfd_arch_info_type* ait;
@@ -271,17 +271,17 @@ int main(int argc, char* argv[]){
 			archList++;
 		}
 		if (ait == NULL) {
-		    printf("Couldn't find arch %s\n", arch_str);
-		    return(-1);
+			printf("Couldn't find arch %s\n", arch_str);
+			return(-1);
 		}
 	}
-	    
-	
+
+
 	endian = (enum bfd_endian) end;
 	/* open a correct type of file to fill in most of the required data. */
-	
+
 	//	printf("Arch is: 0x%08X, Machine is: 0x%08lX Endian is: 0x%02X.\n", arch, mach, endian);
-	
+
 	memset(elf_file_location, 0x00, MAX_ELF_FILE_PATH_LEN);
 	strncpy(elf_file_location, argv[6], MAX_ELF_FILE_PATH_LEN-sizeof(LITTLE_ELF_FILE)-2); // actual file name and nulls
 
@@ -294,59 +294,66 @@ int main(int argc, char* argv[]){
 		stdin_mode = 1; // use STDIN
 	}
 
-	unsigned char byteBuffer[BYTE_BUFFER_SIZE];
-	char byteStringBuffer[(BYTE_BUFFER_SIZE*2)];
-
-	char addressStringBuffer[128];
-
 	if (endian == BFD_ENDIAN_BIG){
 		strcat(elf_file_location, BIG_ELF_FILE);
 	}
 	else {
 		strcat(elf_file_location, LITTLE_ELF_FILE);
 	}
-	
+
+	bfd_init();
+
 	while (stdin_mode) {
-	
+
+		//bfd_init();
 		// convert user input AsciiHex to Binary data for processing
 		char tmp[3];
 		unsigned int byteValue;
 		tmp[0] = tmp[1]  = tmp[2] = 0x00;
+		char disassemblerOptions[128] = {0};
+		unsigned char byteBuffer[BYTE_BUFFER_SIZE] = {0};
+		char byteStringBuffer[(BYTE_BUFFER_SIZE*2)] = {0};
+		char addressStringBuffer[128] = {0};
+		char bytesAndOptionsBuffer[BYTE_BUFFER_SIZE*2 + sizeof(disassemblerOptions)] = {0};
 
 		if (stdin_mode == 1) { // use stdin
 			// read in the address
 			if (fgets(addressStringBuffer, sizeof(addressStringBuffer), stdin)) {
-
-			    //fprintf(stderr, "read: %s\n", addressStringBuffer);
-				//char *p = strchr(addressStringBuffer, '\n');
-				//if (p) {
-				//	*p = '\0';
-				//}
-
 				sscanf(addressStringBuffer, "%18lX", &offset);
 			}
-			//getchar();
-			// read in the ASCII hex string from stdin
-			if (fgets(byteStringBuffer, sizeof(byteStringBuffer), stdin)) {
-
-			    //fprintf(stderr, "read: %s\n", byteStringBuffer);
-				// remove trailing newline 
-				char *p = strchr(byteStringBuffer, '\n');
+			//Read in the rest of the input. There are two possible styles:
+			//"old": input is just the bytes to disassemble
+		    //"new": input = bytes"*"<disassmbler_options>
+			//for compatibility reasons, handle both styles
+			if (fgets(bytesAndOptionsBuffer, sizeof(bytesAndOptionsBuffer), stdin)) {
+				char *p = strchr(bytesAndOptionsBuffer, '*');
 				if (p) {
-					*p = '\0';
+					strncpy(byteStringBuffer,bytesAndOptionsBuffer,(int) (p - bytesAndOptionsBuffer));
+					strncpy(disassemblerOptions,p+1,sizeof(disassemblerOptions));
+					p = strchr(disassemblerOptions,'\n');
+					if (p){
+						*p = '\0';
+					}
+				}
+				else {
+					//no "*" in the string, so no disassembly options
+					//replace newline with null terminator
+					strncpy(byteStringBuffer, bytesAndOptionsBuffer, sizeof(byteStringBuffer));
+					p = strchr(byteStringBuffer,'\n');
+					if (p){
+						*p = '\0';
+					}
 				}
-				//if (strcmp(byteStringBuffer, "EOF") == 0) {
-				//return 0; // terminate on EOF string
-				//}
-			} else {
-			    fprintf(stderr, "exiting, no ASCII hex found\n");
-			    return 0; // finished! #TODO
 			}
-
-		} else {
+			else {
+				fprintf(stderr, "exiting, no ASCII hex found\n");
+				return 0; // finished! #TODO
+			}
+		}
+		else {
 			if(strlen(byteString) > BYTE_BUFFER_SIZE*2) {
-				fprintf(stderr, "Max ascii string size is %d you provided: %lu chars. Exiting.\n", BYTE_BUFFER_SIZE*2, 
-				       strlen(byteString));
+				fprintf(stderr, "Max ascii string size is %d you provided: %lu chars. Exiting.\n", BYTE_BUFFER_SIZE*2,
+						strlen(byteString));
 				exit(-1);
 			}
 			strncpy(byteStringBuffer, byteString, BYTE_BUFFER_SIZE*2);
@@ -378,9 +385,9 @@ int main(int argc, char* argv[]){
 		  for(j=0; j < BYTE_BUFFER_SIZE; j++){
 		  printf("0x%02X ", byteBuffer[j]);
 		  }
-		*/
-	
-		bfd_init( );
+		 */
+
+		//bfd_init( );
 		target = argv[1];
 		bfd_set_default_target(target);
 
@@ -392,7 +399,7 @@ int main(int argc, char* argv[]){
 			bfdfile = bfd_openr(elf_file_location, target );
 			if ( ! bfdfile ) {
 				printf("Error opening BIG ELF file: %s\n", elf_file_location);
-				bfd_perror( "Error on bfdfile" );	
+				bfd_perror( "Error on bfdfile" );
 				return(3);
 			}
 		}
@@ -401,34 +408,37 @@ int main(int argc, char* argv[]){
 			if ( ! bfdfile ) {
 				printf("Error opening LITTLE ELF file: %s\n", elf_file_location);
 				// bfdfile = bfd_openr(elf_file_location, target );
-				bfd_perror( "Error on bfdfile" );	
+				bfd_perror( "Error on bfdfile" );
 				return(3);
 			}
 		}
-	
+
 		memset((void*) &DI, 0x00, sizeof(struct disassemble_info));
 
 		disassemble_fn = NULL;
-	
+
 		// important set up!
 		//---------------------------------------
 		ai.arch = arch;
 		ai.mach = mach;
 		bfd_set_arch_info(bfdfile, &ai);
 		//---------------------------------------
-	
+
 		/*
 		  bfd_error_type err = bfd_get_error();
 		  printf("bfd_error_msg: %s.\n", bfd_errmsg(err));
-		*/
-	
+		 */
+
+		/*if (disassemblerOptions[0] != '\0'){
+		    DI.disassembler_options = disassemblerOptions;
+		}*/
 		configureBfd(bfdfile, arch, mach, endian, &DI, &disassemble_fn);
 
 		/*
 		  err = bfd_get_error();
 		  printf("bfd_error_msg: %s.\n", bfd_errmsg(err));
-		*/
-	
+		 */
+
 		if (disassemble_fn == NULL){
 			fprintf(stderr, "Error: disassemble_fn is NULL. Nothing I can do.\n");
 			exit(1);
@@ -437,21 +447,25 @@ int main(int argc, char* argv[]){
 			/*
 			  printf("the disassemble_fn func pointer is: 0x%08X.\n", disassemble_fn);
 			  printf("We can try to disassemble for this arch/mach. calling disassemble_init_for_target().\n");
-			*/
+			 */
+
 			disassemble_init_for_target(&DI);
+			if (disassemblerOptions[0] != '\0'){
+				DI.disassembler_options = disassemblerOptions;
+			}
 
 			// go diassemble the buffer and build up the result in a accumulator string buffer.
-			processBuffer(byteBuffer, size >> 1, offset, disassemble_fn, &DI); // 
+			processBuffer(byteBuffer, size >> 1, offset, disassemble_fn, &DI); //
 
 		}
 
 		free((void*)bfdfile->xvec);
 		bfd_close(bfdfile);
-		
+
 		printf("EOF\n");
 		fflush(stdout);
 
 	} // while loop on lines of stdin
-	
+
 	return 0;
 }

Ghidra/Extensions/SleighDevTools/src/main/java/ghidra/app/util/disassemble/ExternalDisassembler.java

@@ -23,6 +23,8 @@ public interface ExternalDisassembler extends ExtensionPoint {
 
 	public String getDisassembly(CodeUnit cu) throws Exception;
 
+	public String getDisassemblyDisplayPrefix(CodeUnit cu) throws Exception;
+
 	public String getDisassemblyOfBytes(Language language, boolean isBigEndian, long address,
 			byte[] byteString) throws Exception;
 

Ghidra/Extensions/SleighDevTools/src/main/java/ghidra/app/util/disassemble/ExternalDisassemblyFieldFactory.java

@@ -150,7 +150,10 @@ public class ExternalDisassemblyFieldFactory extends FieldFactory {
 		if (disassembly == null) {
 			return null;
 		}
-
+		String prefix = disassembler.getDisassemblyDisplayPrefix(cu);
+		if (prefix != null) {
+			disassembly = prefix + " " + disassembly;
+		}
 		return disassembly;
 	}
 

Ghidra/Extensions/SleighDevTools/src/main/java/ghidra/app/util/disassemble/GNUExternalDisassembler.java

@@ -18,19 +18,23 @@ package ghidra.app.util.disassemble;
 import java.io.*;
 import java.util.*;
 
+import org.apache.commons.lang3.StringUtils;
+import org.jdom.*;
+import org.jdom.input.SAXBuilder;
+
 import generic.jar.ResourceFile;
 import ghidra.app.util.bin.ByteProvider;
 import ghidra.app.util.bin.MemoryByteProvider;
 import ghidra.framework.*;
 import ghidra.program.model.address.Address;
 import ghidra.program.model.address.AddressOutOfBoundsException;
-import ghidra.program.model.lang.Language;
-import ghidra.program.model.lang.LanguageID;
-import ghidra.program.model.listing.CodeUnit;
-import ghidra.program.model.listing.Program;
+import ghidra.program.model.lang.*;
+import ghidra.program.model.listing.*;
 import ghidra.program.model.mem.MemBuffer;
 import ghidra.program.model.mem.MemoryAccessException;
 import ghidra.util.Msg;
+import ghidra.util.xml.XmlUtilities;
+import util.CollectionUtils;
 
 public class GNUExternalDisassembler implements ExternalDisassembler {
 
@@ -39,6 +43,7 @@ public class GNUExternalDisassembler implements ExternalDisassembler {
 	// magic values for gdis that direct it to read bytes from stdin
 	private static final String READ_FROM_STDIN_PARAMETER = "stdin";
 	private static final String SEPARATOR_CHARACTER = "\n";
+	private static final String OPTIONS_SEPARATOR = "*";
 	private static final String ADDRESS_OUT_OF_BOUNDS = "is out of bounds.";
 	private static final String ENDING_STRING = "EOF";
 	private static final int NUM_BYTES = 32;
@@ -48,6 +53,8 @@ public class GNUExternalDisassembler implements ExternalDisassembler {
 	private static final String GDIS_EXE =
 		Platform.CURRENT_PLATFORM.getOperatingSystem() == OperatingSystem.WINDOWS ? "gdis.exe"
 				: "gdis";
+	private static final String EMPTY_DISASSEMBLER_OPTIONS = "";
+	private static final String GDIS_OPTIONS_FILENAME_PROPERTY = "gdis.disassembler.options.file";
 
 	private static HashMap<String, File> languageGdisMap;
 	private static File defaultGdisExecFile;
@@ -82,6 +89,21 @@ public class GNUExternalDisassembler implements ExternalDisassembler {
 		return gdisConfig != null && gdisConfig.architecture != UNSUPPORTED;
 	}
 
+	@Override
+	public String getDisassemblyDisplayPrefix(CodeUnit cu) throws Exception {
+		GdisConfig gdisConfig = checkLanguage(cu.getProgram().getLanguage());
+		if (gdisConfig == null || gdisConfig.architecture == UNSUPPORTED) {
+			return null;
+		}
+		Register contextRegister = gdisConfig.getContextRegister();
+		if (contextRegister == null) {
+			return null;
+		}
+		long value = getContextRegisterValue(cu, contextRegister);
+		String option = gdisConfig.getDisplayPrefixMap().get(value);
+		return option;
+	}
+
 	private static void reportMultipleMappings(Language language) {
 		List<String> externalNames = language.getLanguageDescription().getExternalNames("gnu");
 		if (externalNames != null && externalNames.size() > 1) {
@@ -89,8 +111,9 @@ public class GNUExternalDisassembler implements ExternalDisassembler {
 			StringBuilder sb = new StringBuilder();
 			boolean prependSeparator = false;
 			for (String name : externalNames) {
-				if (prependSeparator)
+				if (prependSeparator) {
 					sb.append(", ");
+				}
 				sb.append(name);
 				prependSeparator = true;
 			}
@@ -110,11 +133,17 @@ public class GNUExternalDisassembler implements ExternalDisassembler {
 		String machineId;
 		File gdisExecFile;
 		boolean usingDefault;
+		Register contextRegister;
+		Map<Long, String> valueToOptionString;
+		Map<Long, String> valueToDisplayPrefix;
+		Language lang;
+		String globalDisassemblerOptions;
 
 		GdisConfig(Language language, boolean isBigEndian) {
 
 			this.languageId = language.getLanguageID().toString();
 			this.isBigEndian = isBigEndian;
+			this.lang = language;
 
 			List<String> architectures = language.getLanguageDescription().getExternalNames("gnu");
 			//get first non-null
@@ -143,12 +172,123 @@ public class GNUExternalDisassembler implements ExternalDisassembler {
 				gdisExecFile = defaultGdisExecFile;
 				usingDefault = true;
 			}
+
+			List<String> gDisOptionsFile =
+				language.getLanguageDescription().getExternalNames(GDIS_OPTIONS_FILENAME_PROPERTY);
+			if (!CollectionUtils.isBlank(gDisOptionsFile)) {
+				try {
+					parseGdisOptionsFile(gDisOptionsFile.get(0));
+				}
+				catch (IOException e) {
+					Msg.error(this, "Error reading gdis options file " + e.getMessage());
+					contextRegister = null;
+					valueToOptionString = null;
+					valueToDisplayPrefix = null;
+				}
+			}
 		}
 
 		GdisConfig(Language lang) {
 			this(lang, lang.isBigEndian());
 		}
 
+		private void parseGdisOptionsFile(String fileName) throws IOException {
+			LanguageDescription desc = lang.getLanguageDescription();
+			if (!(desc instanceof SleighLanguageDescription)) {
+				throw new IOException("Not a Sleigh Language: " + lang.getLanguageID());
+			}
+
+			SleighLanguageDescription sld = (SleighLanguageDescription) desc;
+			ResourceFile defsFile = sld.getDefsFile();
+			ResourceFile parentFile = defsFile.getParentFile();
+			ResourceFile gdisOpts = new ResourceFile(parentFile, fileName);
+			SAXBuilder sax = XmlUtilities.createSecureSAXBuilder(false, false);
+			try (InputStream fis = gdisOpts.getInputStream()) {
+				Document doc = sax.build(fis);
+				Element rootElem = doc.getRootElement();
+				Element globalElement = rootElem.getChild("global");
+				if (globalElement != null) {
+					globalDisassemblerOptions = globalElement.getAttributeValue("optstring");
+				}
+				Element contextRegisterElement = rootElem.getChild("context_register");
+				if (contextRegisterElement == null) {
+					//no context_register element found in the xml file 
+					//this is not necessarily an error - might only be a global optstring
+					//global optstring has already been parsed, so we're done
+					if (globalElement != null) {
+						Msg.info(this,
+							"no context register element in " + gdisOpts.getAbsolutePath());
+						return;
+					}
+					//no context register element or global element, error
+					throw new JDOMException(
+						"No context_register element or global element in gdis options file");
+				}
+				if (contextRegisterElement.getContentSize() == 0) {
+					throw new JDOMException("No context register name provided.");
+				}
+				String contextRegisterName = contextRegisterElement.getContent(0).getValue();
+				contextRegister = lang.getRegister(contextRegisterName);
+				if (contextRegister == null) {
+					//the context register named in the xml file does not exist in the sleigh language
+					//this is an error
+					throw new JDOMException("Unknown context register " + contextRegisterName +
+						" for language " + lang.getLanguageID().getIdAsString());
+				}
+				valueToOptionString = new HashMap<>();
+				valueToDisplayPrefix = new HashMap<>();
+				Element options = rootElem.getChild("options");
+				List<Element> optList = options.getChildren("option");
+				for (Element opt : optList) {
+					Long value = Long.decode(opt.getAttributeValue("value"));
+					String optString = opt.getAttributeValue("optstring");
+					valueToOptionString.put(value, optString);
+					String displayPrefix = opt.getAttributeValue("display_prefix");
+					valueToDisplayPrefix.put(value, displayPrefix);
+				}
+
+			}
+			catch (JDOMException e) {
+				Msg.error(this, "Error reading " + fileName + ": " + e.getMessage());
+				contextRegister = null;
+				valueToOptionString = null;
+				valueToDisplayPrefix = null;
+			}
+		}
+
+		/**
+		 * Returns the global disassembler options
+		 * @return global option string, or {@code null} if the
+		 * global is unspecified.
+		 */
+		public String getGlobalDisassemblerOptions() {
+			return globalDisassemblerOptions;
+		}
+
+		/**
+		 * Return the context register determine by the gdis options file
+		 * @return the context register
+		 */
+		public Register getContextRegister() {
+			return contextRegister;
+		}
+
+		/**
+		 * Returns the map from context register values to gdis disassembler options
+		 * @return map values->options
+		 */
+		public Map<Long, String> getOptionsMap() {
+			return valueToOptionString;
+		}
+
+		/**
+		 * Returns the map from context register values to disassembly display prefixes
+		 * @return map values->prefixes
+		 */
+		public Map<Long, String> getDisplayPrefixMap() {
+			return valueToDisplayPrefix;
+		}
+
 		@Override
 		public boolean equals(Object obj) {
 			if (!(obj instanceof GdisConfig)) {
@@ -260,7 +400,7 @@ public class GNUExternalDisassembler implements ExternalDisassembler {
 
 		String bytes = getBytes(byteProvider, blockSize);
 
-		return runDisassembler(gdisConfig, address, bytes);
+		return runDisassembler(gdisConfig, address, bytes, EMPTY_DISASSEMBLER_OPTIONS);
 	}
 
 	public List<GnuDisassembledInstruction> getBlockDisassembly(Program program, Address addr,
@@ -272,8 +412,8 @@ public class GNUExternalDisassembler implements ExternalDisassembler {
 		int blockSize = pow2(blockSizeFactor);
 
 		Address blockAddr = addr.getNewAddress(addr.getOffset() & -blockSize); // block
-																				// aligned
-																				// address
+		// aligned
+		// address
 
 		return getBlockDisassembly(program.getLanguage(), blockAddr, blockSizeFactor,
 			new MemoryByteProvider(program.getMemory(), blockAddr));
@@ -301,7 +441,37 @@ public class GNUExternalDisassembler implements ExternalDisassembler {
 			return "";
 		}
 
-		List<GnuDisassembledInstruction> disassembly = runDisassembler(gdisConfig, address, bytes);
+		String disOptions = EMPTY_DISASSEMBLER_OPTIONS;
+		String globalOptions = gdisConfig.getGlobalDisassemblerOptions();
+		boolean hasGlobal = false;
+		if (globalOptions != null) {
+			hasGlobal = true;
+			//set the disOptions to the global options here in case there are global
+			//options but no options for context register values
+			disOptions = globalOptions;
+		}
+		Register contextRegister = gdisConfig.getContextRegister();
+		if (contextRegister != null) {
+			long value = getContextRegisterValue(cu, contextRegister);
+			String contextRegisterValueOption = gdisConfig.getOptionsMap().get(value);
+			if (contextRegisterValueOption == null) {
+				Msg.warn(this, "No option for value " + value + " of context register " +
+					contextRegister.getName());
+			}
+			else {
+				//need to put a comma between the global options and the options
+				//for this context register value
+				if (hasGlobal) {
+					disOptions = globalOptions + "," + contextRegisterValueOption;
+				}
+				//no global options, just send the options for this context register
+				else {
+					disOptions = contextRegisterValueOption;
+				}
+			}
+		}
+		List<GnuDisassembledInstruction> disassembly =
+			runDisassembler(gdisConfig, address, bytes, disOptions);
 
 		if (disassembly == null || disassembly.size() == 0 || disassembly.get(0) == null) {
 			return "(bad)";
@@ -324,7 +494,7 @@ public class GNUExternalDisassembler implements ExternalDisassembler {
 		String address = "0x" + Long.toHexString(addressOffset);
 
 		List<GnuDisassembledInstruction> disassembly =
-			runDisassembler(gdisConfig, address, bytesString);
+			runDisassembler(gdisConfig, address, bytesString, EMPTY_DISASSEMBLER_OPTIONS);
 
 		if (disassembly == null || disassembly.isEmpty() || disassembly.get(0) == null) {
 			return "(bad)";
@@ -332,14 +502,26 @@ public class GNUExternalDisassembler implements ExternalDisassembler {
 		return disassembly.get(0).toString();
 	}
 
+	private long getContextRegisterValue(CodeUnit cu, Register contextRegister) {
+		ProgramContext context = cu.getProgram().getProgramContext();
+		RegisterValue value = context.getRegisterValue(contextRegister, cu.getAddress());
+		if (value != null) {
+			return value.getUnsignedValue().longValue();
+		}
+		//we tried, return 0 to match SLEIGH default
+		return 0;
+	}
+
 	private String converBytesToString(byte[] bytes) {
 		String byteString = null;
 		for (byte thisByte : bytes) {
 			String thisByteString = Integer.toHexString(thisByte);
-			if (thisByteString.length() == 1)
+			if (thisByteString.length() == 1) {
 				thisByteString = "0" + thisByteString; // pad single digits
-			if (thisByteString.length() > 2)
+			}
+			if (thisByteString.length() > 2) {
 				thisByteString = thisByteString.substring(thisByteString.length() - 2);
+			}
 			// append this byte's hex string to the larger word length string
 			byteString = byteString + thisByteString;
 		}
@@ -402,7 +584,7 @@ public class GNUExternalDisassembler implements ExternalDisassembler {
 	}
 
 	private List<GnuDisassembledInstruction> runDisassembler(GdisConfig gdisConfig,
-			String addrString, String bytes) throws IOException {
+			String addrString, String bytes, String disassemblerOptions) throws IOException {
 
 		// if this is the first time running the disassembler process, or a
 		// parameter has changed (notably, not the address--we pass that in
@@ -414,8 +596,9 @@ public class GNUExternalDisassembler implements ExternalDisassembler {
 
 		if (disassemblerProcess == null || !sameConfig) {
 
-			if (!setupDisassembler(gdisConfig))
+			if (!setupDisassembler(gdisConfig)) {
 				return null;
+			}
 
 			outputWriter = new OutputStreamWriter(disassemblerProcess.getOutputStream());
 
@@ -432,7 +615,14 @@ public class GNUExternalDisassembler implements ExternalDisassembler {
 			return null; // if process previously died return nothing - quickly
 		}
 
-		String disassemblyRequest = addrString + SEPARATOR_CHARACTER + bytes + SEPARATOR_CHARACTER;
+		String disassemblyRequest = addrString + SEPARATOR_CHARACTER + bytes;
+		if (StringUtils.isEmpty(disassemblerOptions)) {
+			disassemblyRequest += '\n';
+		}
+		else {
+			disassemblyRequest += OPTIONS_SEPARATOR + disassemblerOptions + SEPARATOR_CHARACTER;
+		}
+
 		try {
 			outputWriter.write(disassemblyRequest);
 			outputWriter.flush();

Ghidra/Features/Base/src/main/java/ghidra/app/plugin/core/calltree/CallNode.java

@@ -141,4 +141,28 @@ public abstract class CallNode extends GTreeSlowLoadingNode {
 		}
 		return false;
 	}
+
+	// overridden since we may have multiple children with the same function name, but in 
+	// different namespaces
+	@Override
+	public boolean equals(Object obj) {
+		if (this == obj) {
+			return true;
+		}
+		if (obj == null) {
+			return false;
+		}
+		if (getClass() != obj.getClass()) {
+			return false;
+		}
+
+		CallNode other = (CallNode) obj;
+		return getSourceAddress().equals(other.getSourceAddress());
+	}
+
+	@Override
+	public int hashCode() {
+		return getSourceAddress().hashCode();
+	}
+
 }

Ghidra/Features/Base/src/main/java/ghidra/app/plugin/core/compositeeditor/EditComponentAction.java

@@ -16,6 +16,7 @@
 package ghidra.app.plugin.core.compositeeditor;
 
 import docking.ActionContext;
+import ghidra.app.plugin.core.datamgr.util.DataTypeUtils;
 import ghidra.app.services.DataTypeManagerService;
 import ghidra.program.model.data.*;
 import ghidra.program.model.data.Enum;
@@ -43,29 +44,43 @@ public class EditComponentAction extends CompositeEditorTableAction {
 	@Override
 	public void actionPerformed(ActionContext context) {
 		int row = model.getRow();
-		if (row < model.getNumComponents()) {
-			DataTypeComponent comp = model.getComponent(row);
-			DataType dt = DataTypeHelper.getBaseType(comp.getDataType());
-			if ((dt instanceof Structure) || (dt instanceof Union) || (dt instanceof Enum)) {
-				DataTypeManager dtm = model.getOriginalDataTypeManager();
-				if (dtm != null) {
-					dt = dtm.getDataType(dt.getDataTypePath());
-					if (dt != null) {
-						this.dtmService.edit(dt);
-						return;
-					}
-				}
-				String name =
-					(dt != null) ? dt.getDisplayName() : comp.getDataType().getDisplayName();
-				model.setStatus("Can't edit \"" + name + "\".");
-			}
-			else {
-				model.setStatus("Can only edit a structure, union or enum.");
-			}
+		if (row >= model.getNumComponents()) {
+			requestTableFocus();
+			return;
+		}
+
+		DataTypeComponent comp = model.getComponent(row);
+		DataType clickedType = comp.getDataType();
+		DataType dt = DataTypeUtils.getBaseDataType(clickedType);
+		boolean isEditableType =
+			(dt instanceof Structure) || (dt instanceof Union) || (dt instanceof Enum);
+		if (isEditableType) {
+			edit(dt, clickedType.getName());
+		}
+		else {
+			model.setStatus("Can only edit a structure, union or enum.");
 		}
 		requestTableFocus();
 	}
 
+	private void edit(DataType dt, String clickedName) {
+
+		DataTypeManager dtm = model.getOriginalDataTypeManager();
+		if (dtm == null) {
+			// shouldn't happen
+			model.setStatus("No Data Type Manager found for '" + clickedName + "'");
+			return;
+		}
+
+		DataType actualType = dtm.getDataType(dt.getDataTypePath());
+		if (actualType == null) {
+			model.setStatus("Can't edit '" + dt.getDisplayName() + "' - type not found.");
+			return;
+		}
+
+		dtmService.edit(actualType);
+	}
+
 	@Override
 	public void adjustEnablement() {
 		setEnabled(model.isEditComponentAllowed());

Ghidra/Features/Base/src/main/java/ghidra/app/util/bin/BinaryReader.java

@@ -314,7 +314,7 @@ public class BinaryReader {
 	 * @exception IOException if an I/O error occurs
 	 */
 	public String readNextNullTerminatedAsciiString() throws IOException {
-		StringBuffer buffer = new StringBuffer();
+		StringBuilder buffer = new StringBuilder();
 		while (currentIndex < provider.length()) {
 			byte b = provider.readByte(currentIndex++);
 			if (b == 0) {
@@ -430,7 +430,7 @@ public class BinaryReader {
 	 * @exception IOException if an I/O error occurs
 	 */
 	public String readAsciiString(long index) throws IOException {
-		StringBuffer buffer = new StringBuffer();
+		StringBuilder buffer = new StringBuilder();
 		long len = provider.length();
 		while (true) {
 			if (index == len) {
@@ -459,7 +459,7 @@ public class BinaryReader {
 	 * @exception IOException if an I/O error occurs
 	 */
 	public String readAsciiString(long index, int length) throws IOException {
-		StringBuffer buffer = new StringBuffer();
+		StringBuilder buffer = new StringBuilder();
 		for (int i = 0; i < length; ++i) {
 			byte b = provider.readByte(index++);
 			buffer.append((char) (b & 0x00FF));
@@ -479,7 +479,7 @@ public class BinaryReader {
 	 * @exception IOException if an I/O error occurs
 	 */
 	public String readTerminatedString(long index, char termChar) throws IOException {
-		StringBuffer buffer = new StringBuffer();
+		StringBuilder buffer = new StringBuilder();
 		long len = provider.length();
 		while (index < len) {
 			char c = (char) provider.readByte(index++);
@@ -503,7 +503,7 @@ public class BinaryReader {
 	 * @exception IOException if an I/O error occurs
 	 */
 	public String readTerminatedString(long index, String termChars) throws IOException {
-		StringBuffer buffer = new StringBuffer();
+		StringBuilder buffer = new StringBuilder();
 		long len = provider.length();
 		while (index < len) {
 			char c = (char) provider.readByte(index++);
@@ -544,7 +544,7 @@ public class BinaryReader {
 	 * @exception IOException if an I/O error occurs
 	 */
 	public String readUnicodeString(long index) throws IOException {
-		StringBuffer buffer = new StringBuffer();
+		StringBuilder buffer = new StringBuilder();
 		while (index < length()) {
 			int ch = readUnsignedShort(index);
 			if (ch == 0) {
@@ -571,7 +571,7 @@ public class BinaryReader {
 	 * @exception IOException if an I/O error occurs
 	 */
 	public String readUnicodeString(long index, int length) throws IOException {
-		StringBuffer buffer = new StringBuffer(length);
+		StringBuilder buffer = new StringBuilder(length);
 		long endOffset = index + (length * 2);
 		while (index < endOffset) {
 			int ch = readUnsignedShort(index);

Ghidra/Features/Base/src/main/java/ghidra/app/util/bin/GhidraRandomAccessFile.java

@@ -27,7 +27,7 @@ import ghidra.util.Msg;
  * This implementation relies on java.net.RandomAccessFile,
  * but adds buffering to limit the amount.
  */
-public class GhidraRandomAccessFile {
+public class GhidraRandomAccessFile implements AutoCloseable {
 	private static final byte[] EMPTY = new byte[0];
 	private static final int BUFFER_SIZE = 0x100000;
 
@@ -112,6 +112,7 @@ public class GhidraRandomAccessFile {
 	 * If this file has an associated channel then the channel is closed as well.
 	 * @exception  IOException  if an I/O error occurs.
 	 */
+	@Override
 	public void close() throws IOException {
 		checkOpen();
 		open = false;
@@ -291,8 +292,11 @@ public class GhidraRandomAccessFile {
 
 				buffer = new byte[BUFFER_SIZE];
 				randomAccessFile.seek(bufferFileStartIndex);
-				randomAccessFile.read(buffer);
+				int bytesRead = randomAccessFile.read(buffer);
 				bufferOffset = 0;
+				if (bytesRead <= 0) {
+					throw new EOFException();
+				}
 			}
 			else {
 				bufferOffset = newBufferOffset;

Ghidra/Features/Base/src/main/java/ghidra/app/util/bin/RandomAccessByteProvider.java

@@ -18,6 +18,7 @@ package ghidra.app.util.bin;
 import java.io.*;
 
 import ghidra.formats.gfilesystem.FSRL;
+import ghidra.util.Msg;
 
 /**
  * An implementation of ByteProvider where the underlying
@@ -33,15 +34,15 @@ public class RandomAccessByteProvider implements ByteProvider {
 	protected File file;
 	protected GhidraRandomAccessFile randomAccessFile;
 	private FSRL fsrl;
-	private Long cachedLength;
+	private long fileLength;
 
 	/**
 	 * Constructs a {@link ByteProvider} using the specified {@link File}.
 	 * 
 	 * @param file the {@link File} to open for random access
-	 * @throws FileNotFoundException if the {@link File} does not exist
+	 * @throws IOException if the {@link File} does not exist or other error
 	 */
-	public RandomAccessByteProvider(File file) throws FileNotFoundException {
+	public RandomAccessByteProvider(File file) throws IOException {
 		this(file, "r");
 	}
 
@@ -50,11 +51,10 @@ public class RandomAccessByteProvider implements ByteProvider {
 	 *
 	 * @param file the {@link File} to open for random access
 	 * @param fsrl the {@link FSRL} to use for the {@link File}'s path
-	 * @throws FileNotFoundException if the {@link File} does not exist
+	 * @throws IOException if the {@link File} does not exist or other error
 	 */
-	public RandomAccessByteProvider(File file, FSRL fsrl) throws FileNotFoundException {
-		this(file, "r");
-		this.fsrl = fsrl;
+	public RandomAccessByteProvider(File file, FSRL fsrl) throws IOException {
+		this(file, fsrl, "r");
 	}
 
 	/**
@@ -62,11 +62,17 @@ public class RandomAccessByteProvider implements ByteProvider {
 	 * 
 	 * @param file the {@link File} to open for random access
 	 * @param permissions indicating permissions used for open
-	 * @throws FileNotFoundException if the {@link File} does not exist
+	 * @throws IOException if the {@link File} does not exist or other error
 	 */
-	public RandomAccessByteProvider(File file, String permissions) throws FileNotFoundException {
+	public RandomAccessByteProvider(File file, String permissions) throws IOException {
+		this(file, null, permissions);
+	}
+
+	private RandomAccessByteProvider(File file, FSRL fsrl, String permissions) throws IOException {
 		this.file = file;
+		this.fsrl = fsrl;
 		this.randomAccessFile = new GhidraRandomAccessFile(file, permissions);
+		this.fileLength = randomAccessFile.length();
 	}
 
 	@Override
@@ -111,21 +117,13 @@ public class RandomAccessByteProvider implements ByteProvider {
 	}
 
 	@Override
-	public long length() throws IOException {
-		if (cachedLength == null) {
-			cachedLength = randomAccessFile.length();
-		}
-		return cachedLength;
+	public long length() {
+		return fileLength;
 	}
 
 	@Override
 	public boolean isValidIndex(long index) {
-		try {
-			return index >= 0 && index < length();
-		}
-		catch (IOException e) {
-			return false;
-		}
+		return 0 <= index && index < fileLength;
 	}
 
 	@Override
@@ -136,12 +134,27 @@ public class RandomAccessByteProvider implements ByteProvider {
 
 	@Override
 	public byte[] readBytes(long index, long length) throws IOException {
-		randomAccessFile.seek(index);
 		byte[] b = new byte[(int) length];
+		if (index > fileLength) {
+			throw new EOFException(
+				"Invalid file offset " + index + " while reading " + file.getName());
+		}
+		if (index + length > fileLength) {
+			Msg.trace(this, "Read at EOF, can't return partial buffer, throwing IOException: " +
+				file.getName());
+			throw new EOFException("EOF: unable to read " + length + " bytes at " + index);
+		}
+		randomAccessFile.seek(index);
 		int nRead = randomAccessFile.read(b);
 		if (nRead != length) {
 			throw new IOException("Unable to read " + length + " bytes");
 		}
 		return b;
 	}
+	
+	@Override
+	public String toString() {
+		return "RandomAccessByteProvider [\n  file=" + file + ",\n  fsrl=" + fsrl +
+			",\n  fileLength=" + fileLength + "\n]";
+	}	
 }

Ghidra/Features/Base/src/main/java/ghidra/app/util/bin/format/coff/archive/CoffArchiveHeader.java

@@ -15,16 +15,17 @@
  */
 package ghidra.app.util.bin.format.coff.archive;
 
-import ghidra.app.util.bin.*;
-import ghidra.app.util.bin.format.coff.CoffException;
-import ghidra.program.model.data.*;
-import ghidra.util.exception.DuplicateNameException;
-import ghidra.util.task.TaskMonitor;
-
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
 
+import ghidra.app.util.bin.*;
+import ghidra.app.util.bin.format.coff.CoffException;
+import ghidra.program.model.data.*;
+import ghidra.util.Msg;
+import ghidra.util.exception.DuplicateNameException;
+import ghidra.util.task.TaskMonitor;
+
 /**
  * A class that represents a COFF archive file (ie. MS .lib files, Unix .ar files)
  * <p>
@@ -74,39 +75,54 @@ public final class CoffArchiveHeader implements StructConverter {
 
 		CoffArchiveHeader cah = new CoffArchiveHeader();
 
-		while (reader.getPointerIndex() < reader.length() - 1) {
+		long eofPos = reader.length() - CoffArchiveMemberHeader.CAMH_MIN_SIZE;
+
+		while (reader.getPointerIndex() < eofPos) {
 			if (monitor.isCancelled()) {
 				break;
 			}
 
-			CoffArchiveMemberHeader camh =
-				CoffArchiveMemberHeader.read(reader, cah._longNameMember);
+			try {
+				CoffArchiveMemberHeader camh =
+					CoffArchiveMemberHeader.read(reader, cah._longNameMember);
 
-			if (camh.getName().equals(CoffArchiveMemberHeader.SLASH)) {
-				switch (memberNum) {
-					case 0:
-						cah._firstLinkerMember = new FirstLinkerMember(reader, camh, true);
-						break;
-					case 1:
-						cah._secondLinkerMember = new SecondLinkerMember(reader, camh, true);
-						break;
-					default:
+				if (camh.getName().equals(CoffArchiveMemberHeader.SLASH)) {
+					switch (memberNum) {
+						case 0:
+							cah._firstLinkerMember = new FirstLinkerMember(reader, camh, true);
+							break;
+						case 1:
+							cah._secondLinkerMember = new SecondLinkerMember(reader, camh, true);
+							break;
+						default:
+							throw new CoffException(
+								"Invalid COFF: multiple 1st and 2nd linker members detected.");
+					}
+				}
+				else if (camh.getName().equals(CoffArchiveMemberHeader.SLASH_SLASH)) {
+					if (cah._longNameMember == null) {
+						cah._longNameMember = new LongNamesMember(reader, camh);
+					}
+					else {
 						throw new CoffException(
-							"Invalid COFF: multiple 1st and 2nd linker members detected.");
+							"Invalid COFF: multiple long name members detected.");
+					}
 				}
-			}
-			else if (camh.getName().equals(CoffArchiveMemberHeader.SLASH_SLASH)) {
-				if (cah._longNameMember == null) {
-					cah._longNameMember = new LongNamesMember(reader, camh);
-				}
-				else {
-					throw new CoffException("Invalid COFF: multiple long name members detected.");
-				}
-			}
-			cah._memberHeaders.add(camh);
-			memberNum++;
+				cah._memberHeaders.add(camh);
+				memberNum++;
 
-			reader.setPointerIndex(camh.getPayloadOffset() + camh.getSize());
+				reader.setPointerIndex(camh.getPayloadOffset() + camh.getSize());
+			}
+			catch (IOException e) {
+				// if we run into bad data, return partial success if there has been at least some
+				// good ones, otherwise propagate the exception upwards
+				if (memberNum <= 3) {
+					throw e;
+				}
+				Msg.warn(CoffArchiveMemberHeader.class, "Problem reading COFF archive headers in " +
+					provider.getFSRL() + ", only " + memberNum + " members found.", e);
+				break;
+			}
 		}
 
 		// TODO: check for null terminators in the longname string table vs. \n terminators
@@ -125,6 +141,7 @@ public final class CoffArchiveHeader implements StructConverter {
 	protected CoffArchiveHeader() {
 	}
 
+	@Override
 	public DataType toDataType() throws DuplicateNameException, IOException {
 		Structure struct = new StructureDataType(StructConverterUtil.parseName(CoffArchiveHeader.class), 0);
 		struct.add(STRING, CoffArchiveConstants.MAGIC_LEN, "magic", null);

Ghidra/Features/Base/src/main/java/ghidra/app/util/bin/format/coff/archive/CoffArchiveMemberHeader.java

@@ -50,6 +50,7 @@ public class CoffArchiveMemberHeader implements StructConverter {
 	private static final String CAMH_EOH_MAGIC = "`\n";
 
 	private static final int CAMH_PAYLOAD_OFF = 60;
+	public static final int CAMH_MIN_SIZE = CAMH_PAYLOAD_OFF;
 
 	/**
 	 * Reads a COFF archive member header from the specified {@link BinaryReader reader},
@@ -162,8 +163,9 @@ public class CoffArchiveMemberHeader implements StructConverter {
 			try {
 				long offset = Long.parseLong(name.substring(1));
 				name = longNames.getStringAtOffset(reader.getByteProvider(), offset);
-				if (name.endsWith("/"))
+				if (name.endsWith("/")) {
 					name = name.substring(0, name.length() - 1);
+				}
 			}
 			catch (NumberFormatException nfe) {
 				throw new IOException("Bad long name offset: " + name);

Ghidra/Features/Base/src/main/java/ghidra/app/util/bin/format/macho/MachConstants.java

@@ -1,6 +1,5 @@
 /* ###
  * IP: GHIDRA
- * REVIEWED: YES
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

Ghidra/Features/Base/src/main/java/ghidra/app/util/bin/format/macho/MachHeader.java

@@ -16,13 +16,11 @@
 package ghidra.app.util.bin.format.macho;
 
 import java.io.IOException;
-import java.io.InputStream;
 import java.util.ArrayList;
 import java.util.List;
 
 import generic.continues.GenericFactory;
-import ghidra.app.util.bin.ByteProvider;
-import ghidra.app.util.bin.StructConverter;
+import ghidra.app.util.bin.*;
 import ghidra.app.util.bin.format.FactoryBundledWithBinaryReader;
 import ghidra.app.util.bin.format.macho.commands.*;
 import ghidra.program.model.data.*;
@@ -44,12 +42,28 @@ public class MachHeader implements StructConverter {
 	private int reserved;//only used in 64-bit
 
 	private boolean _is32bit;
-	private List<LoadCommand> _commands = new ArrayList<LoadCommand>();
+	private List<LoadCommand> _commands = new ArrayList<>();
 	private long _commandIndex;
 	private FactoryBundledWithBinaryReader _reader;
 	private long _machHeaderStartIndexInProvider;
 	private boolean _parsed = false;
 
+	/**
+	 * Returns true if the specified ByteProvider starts with a Mach header magic signature.
+	 * 
+	 * @param provider {@link ByteProvider} to check
+	 * @return boolean true if byte provider starts with a MachHeader
+	 */
+	public static boolean isMachHeader(ByteProvider provider) {
+		try {
+			return provider.length() > Integer.BYTES &&
+				MachConstants.isMagic(readMagic(provider, 0));
+		}
+		catch (IOException e) {
+			// dont care
+		}
+		return false;
+	}
 	/**
 	 * Assumes the MachHeader starts at index 0 in the ByteProvider.
 	 * @param provider the ByteProvider
@@ -233,7 +247,7 @@ public class MachHeader implements StructConverter {
 	}
 
 	public List<Section> getAllSections() {
-		List<Section> tmp = new ArrayList<Section>();
+		List<Section> tmp = new ArrayList<>();
 		for (SegmentCommand segment : getAllSegments()) {
 			tmp.addAll(segment.getSections());
 		}
@@ -245,7 +259,7 @@ public class MachHeader implements StructConverter {
 	}
 
 	public <T> List<T> getLoadCommands(Class<T> classType) {
-		List<T> tmp = new ArrayList<T>();
+		List<T> tmp = new ArrayList<>();
 		for (LoadCommand command : _commands) {
 			if (classType.isAssignableFrom(command.getClass())) {
 				tmp.add(classType.cast(command));
@@ -282,22 +296,14 @@ public class MachHeader implements StructConverter {
 		return buffer.toString();
 	}
 
-	public InputStream getDataStream() throws IOException {
-		return _reader.getByteProvider().getInputStream(0);
-	}
-
 	@Override
 	public String toString() {
 		return getDescription();
 	}
 
-	private int readMagic(ByteProvider provider, long machHeaderStartIndexInProvider)
+	private static int readMagic(ByteProvider provider, long machHeaderStartIndexInProvider)
 			throws IOException {
-		int value = 0;
-		value |= (provider.readByte(machHeaderStartIndexInProvider + 0) << 0x18) & 0xff000000;
-		value |= (provider.readByte(machHeaderStartIndexInProvider + 1) << 0x10) & 0x00ff0000;
-		value |= (provider.readByte(machHeaderStartIndexInProvider + 2) << 0x08) & 0x0000ff00;
-		value |= (provider.readByte(machHeaderStartIndexInProvider + 3) << 0x00) & 0x000000ff;
-		return value;
+		BinaryReader br = new BinaryReader(provider, false);
+		return br.readInt(machHeaderStartIndexInProvider);
 	}
 }

Ghidra/Features/Base/src/main/java/ghidra/app/util/bin/format/macho/Section.java

@@ -48,7 +48,7 @@ public class Section implements StructConverter {
 
 	private FactoryBundledWithBinaryReader reader;
 	private boolean is32bit;
-	private List<RelocationInfo> relocations = new ArrayList<RelocationInfo>();
+	private List<RelocationInfo> relocations = new ArrayList<>();
 
 	public static Section createSection(FactoryBundledWithBinaryReader reader, boolean is32bit)
 			throws IOException {
@@ -71,8 +71,8 @@ public class Section implements StructConverter {
 		sectname = reader.readNextAsciiString(MachConstants.NAME_LENGTH);
 		segname = reader.readNextAsciiString(MachConstants.NAME_LENGTH);
 		if (is32bit) {
-			addr = reader.readNextInt() & 0xffffffffL;
-			size = reader.readNextInt() & 0xffffffffL;
+			addr = reader.readNextUnsignedInt();
+			size = reader.readNextUnsignedInt();
 		}
 		else {
 			addr = reader.readNextLong();

Ghidra/Features/Base/src/main/java/ghidra/app/util/bin/format/pe/FileHeader.java

@@ -15,7 +15,8 @@
  */
 package ghidra.app.util.bin.format.pe;
 
-import java.io.*;
+import java.io.IOException;
+import java.io.RandomAccessFile;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -144,7 +145,7 @@ public class FileHeader implements StructConverter {
     private short characteristics;
 
     private SectionHeader [] sectionHeaders;
-    private List<DebugCOFFSymbol>symbols = new ArrayList<DebugCOFFSymbol>();
+    private List<DebugCOFFSymbol>symbols = new ArrayList<>();
 
     private FactoryBundledWithBinaryReader reader;
     private int startIndex;
@@ -560,8 +561,4 @@ public class FileHeader implements StructConverter {
 		}
 		return PortableExecutable.computeAlignment( lastPos, optionalHeader.getFileAlignment( ) );
 	}
-
-    public InputStream getDataStream() throws IOException {
-        return reader.getByteProvider().getInputStream(0);
-    }
 }

Ghidra/Features/Base/src/main/java/ghidra/app/util/opinion/MachoLoader.java

@@ -94,6 +94,9 @@ public class MachoLoader extends AbstractLibrarySupportLoader {
 				MachoProgramBuilder.buildProgram(program, provider, fileBytes, log, monitor);
 			}
 		}
+		catch (IOException e) {
+			throw e;
+		}
 		catch (Exception e) {
 			throw new IOException(e.getMessage());
 		}

Ghidra/Features/Base/src/main/java/ghidra/formats/gfilesystem/factory/FileSystemFactoryMgr.java

@@ -212,27 +212,35 @@ public class FileSystemFactoryMgr {
 		try (ByteProvider bp = new RandomAccessByteProvider(containerFile, containerFSRL)) {
 			byte[] startBytes = bp.readBytes(0, pboByteCount);
 			for (FileSystemInfoRec fsir : sortedFactories) {
-				if (fsir.getFactory() instanceof GFileSystemProbeBytesOnly) {
-					GFileSystemProbeBytesOnly factoryProbe =
-						(GFileSystemProbeBytesOnly) fsir.getFactory();
-					if (factoryProbe.getBytesRequired() <= startBytes.length) {
-						if (factoryProbe.probeStartBytes(containerFSRL, startBytes)) {
+				try {
+					if (fsir.getFactory() instanceof GFileSystemProbeBytesOnly) {
+						GFileSystemProbeBytesOnly factoryProbe =
+							(GFileSystemProbeBytesOnly) fsir.getFactory();
+						if (factoryProbe.getBytesRequired() <= startBytes.length) {
+							if (factoryProbe.probeStartBytes(containerFSRL, startBytes)) {
+								return true;
+							}
+						}
+					}
+					if (fsir.getFactory() instanceof GFileSystemProbeWithFile) {
+						GFileSystemProbeWithFile factoryProbe =
+							(GFileSystemProbeWithFile) fsir.getFactory();
+						if (factoryProbe.probe(containerFSRL, containerFile, fsService, monitor)) {
+							return true;
+						}
+					}
+					if (fsir.getFactory() instanceof GFileSystemProbeFull) {
+						GFileSystemProbeFull factoryProbe =
+							(GFileSystemProbeFull) fsir.getFactory();
+						if (factoryProbe.probe(containerFSRL, bp, containerFile, fsService,
+							monitor)) {
 							return true;
 						}
 					}
 				}
-				if (fsir.getFactory() instanceof GFileSystemProbeWithFile) {
-					GFileSystemProbeWithFile factoryProbe =
-						(GFileSystemProbeWithFile) fsir.getFactory();
-					if (factoryProbe.probe(containerFSRL, containerFile, fsService, monitor)) {
-						return true;
-					}
-				}
-				if (fsir.getFactory() instanceof GFileSystemProbeFull) {
-					GFileSystemProbeFull factoryProbe = (GFileSystemProbeFull) fsir.getFactory();
-					if (factoryProbe.probe(containerFSRL, bp, containerFile, fsService, monitor)) {
-						return true;
-					}
+				catch (IOException e) {
+					Msg.trace(this, "File system probe error for " + fsir.getDescription() +
+						" with " + containerFSRL, e);
 				}
 			}
 		}
@@ -303,34 +311,41 @@ public class FileSystemFactoryMgr {
 			byte[] startBytes = probeBP.readBytes(0, pboByteCount);
 			List<FileSystemInfoRec> probeMatches = new ArrayList<>();
 			for (FileSystemInfoRec fsir : sortedFactories) {
-				if (fsir.getPriority() < priorityFilter) {
-					break;
-				}
-				if (fsir.getFactory() instanceof GFileSystemProbeBytesOnly) {
-					GFileSystemProbeBytesOnly factoryProbe =
-						(GFileSystemProbeBytesOnly) fsir.getFactory();
-					if (factoryProbe.getBytesRequired() <= startBytes.length) {
-						if (factoryProbe.probeStartBytes(containerFSRL, startBytes)) {
+				try {
+					if (fsir.getPriority() < priorityFilter) {
+						break;
+					}
+					if (fsir.getFactory() instanceof GFileSystemProbeBytesOnly) {
+						GFileSystemProbeBytesOnly factoryProbe =
+							(GFileSystemProbeBytesOnly) fsir.getFactory();
+						if (factoryProbe.getBytesRequired() <= startBytes.length) {
+							if (factoryProbe.probeStartBytes(containerFSRL, startBytes)) {
+								probeMatches.add(fsir);
+								continue;
+							}
+						}
+					}
+					if (fsir.getFactory() instanceof GFileSystemProbeWithFile) {
+						GFileSystemProbeWithFile factoryProbe =
+							(GFileSystemProbeWithFile) fsir.getFactory();
+						if (factoryProbe.probe(containerFSRL, containerFile, fsService, monitor)) {
+							probeMatches.add(fsir);
+							continue;
+						}
+					}
+					if (fsir.getFactory() instanceof GFileSystemProbeFull) {
+						GFileSystemProbeFull factoryProbe =
+							(GFileSystemProbeFull) fsir.getFactory();
+						if (factoryProbe.probe(containerFSRL, probeBP, containerFile, fsService,
+							monitor)) {
 							probeMatches.add(fsir);
 							continue;
 						}
 					}
 				}
-				if (fsir.getFactory() instanceof GFileSystemProbeWithFile) {
-					GFileSystemProbeWithFile factoryProbe =
-						(GFileSystemProbeWithFile) fsir.getFactory();
-					if (factoryProbe.probe(containerFSRL, containerFile, fsService, monitor)) {
-						probeMatches.add(fsir);
-						continue;
-					}
-				}
-				if (fsir.getFactory() instanceof GFileSystemProbeFull) {
-					GFileSystemProbeFull factoryProbe = (GFileSystemProbeFull) fsir.getFactory();
-					if (factoryProbe.probe(containerFSRL, probeBP, containerFile, fsService,
-						monitor)) {
-						probeMatches.add(fsir);
-						continue;
-					}
+				catch (IOException e) {
+					Msg.trace(this, "File system probe error for " + fsir.getDescription() +
+						" with " + containerFSRL, e);
 				}
 			}
 

Ghidra/Features/Base/src/main/java/ghidra/program/examiner/ProgramExaminer.java

@@ -1,231 +0,0 @@
-/* ###
- * IP: GHIDRA
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- *      http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-package ghidra.program.examiner;
-
-import java.io.File;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.List;
-
-import ghidra.GhidraException;
-import ghidra.GhidraTestApplicationLayout;
-import ghidra.app.plugin.core.analysis.EmbeddedMediaAnalyzer;
-import ghidra.app.util.bin.*;
-import ghidra.app.util.importer.AutoImporter;
-import ghidra.app.util.importer.MessageLog;
-import ghidra.framework.Application;
-import ghidra.framework.HeadlessGhidraApplicationConfiguration;
-import ghidra.program.model.data.*;
-import ghidra.program.model.lang.*;
-import ghidra.program.model.listing.*;
-import ghidra.program.model.mem.MemoryAccessException;
-import ghidra.program.util.DefaultLanguageService;
-import ghidra.util.exception.CancelledException;
-import ghidra.util.task.TaskMonitorAdapter;
-import utility.application.ApplicationLayout;
-
-/**
- * Wrapper for Ghidra code to find images (and maybe other artifacts later) in a program
- *
- */
-public class ProgramExaminer {
-
-	private MessageLog messageLog;
-	private Program program;
-
-	private static Language defaultLanguage;
-
-	/**
-	 * Constructs a new ProgramExaminer.
-	 * @param bytes the bytes of the potential program to be examined.
-	 * @throws GhidraException if any exception occurs while processing the bytes.
-	 */
-	public ProgramExaminer(byte[] bytes) throws GhidraException {
-		this(createByteProvider(bytes));
-	}
-
-	/**
-	 * Constructs a new ProgramExaminer.
-	 * @param file file object containing the bytes to be examined.
-	 * @throws GhidraException if any exception occurs while processing the bytes.
-	 */
-	public ProgramExaminer(File file) throws GhidraException {
-		this(createByteProvider(file));
-	}
-
-	/**
-	 * Returns a string indication the program format. i.e. PE, elf, raw
-	 */
-	public String getType() {
-		return program.getExecutableFormat();
-	}
-
-	private ProgramExaminer(ByteProvider provider) throws GhidraException {
-		initializeGhidra();
-		messageLog = new MessageLog();
-		try {
-			program =
-				AutoImporter.importByUsingBestGuess(provider, null, this, messageLog,
-					TaskMonitorAdapter.DUMMY_MONITOR);
-
-			if (program == null) {
-				program =
-					AutoImporter.importAsBinary(provider, null, defaultLanguage, null, this,
-						messageLog, TaskMonitorAdapter.DUMMY_MONITOR);
-			}
-			if (program == null) {
-				throw new GhidraException("Can't create program from input: " +
-					messageLog.toString());
-			}
-		}
-		catch (Exception e) {
-			messageLog.appendException(e);
-			throw new GhidraException(e);
-		}
-		finally {
-			try {
-				provider.close();
-			}
-			catch (IOException e) {
-				// tried to close
-			}
-		}
-	}
-
-	public synchronized static void initializeGhidra() throws GhidraException {
-		if (!Application.isInitialized()) {
-			ApplicationLayout layout;
-			try {
-				layout =
-					new GhidraTestApplicationLayout(new File(System.getProperty("java.io.tmpdir")));
-			}
-			catch (IOException e) {
-				throw new GhidraException(e);
-			}
-			HeadlessGhidraApplicationConfiguration config =
-				new HeadlessGhidraApplicationConfiguration();
-			config.setInitializeLogging(false);
-			Application.initializeApplication(layout, config);
-		}
-		if (defaultLanguage == null) {
-			LanguageService languageService = DefaultLanguageService.getLanguageService();
-			try {
-				defaultLanguage = languageService.getDefaultLanguage(
-					Processor.findOrPossiblyCreateProcessor("DATA"));
-			}
-			catch (LanguageNotFoundException e) {
-				throw new GhidraException("Can't load default language: DATA");
-			}
-		}
-	}
-
-	/**
-	 * Releases file/database resources.
-	 */
-	public void dispose() {
-		program.release(this);
-	}
-
-	/**
-	 * Returns a list of byte[] containing image data.  The bytes will be either a png, a gif, or
-	 * a bitmap
-	 */
-	public List<byte[]> getImages() {
-		runImageAnalyzer();
-
-		List<byte[]> imageList = new ArrayList<byte[]>();
-		DataIterator it = program.getListing().getDefinedData(true);
-		while (it.hasNext()) {
-			accumulateImageData(imageList, it.next());
-		}
-		return imageList;
-	}
-
-	private void accumulateImageData(List<byte[]> imageList, Data data) {
-		if (!isImage(data)) {
-			return;
-		}
-
-		try {
-			imageList.add(data.getBytes());
-		}
-		catch (MemoryAccessException e) {
-			// suppress (this shouldn't happen
-		}
-	}
-
-	private void runImageAnalyzer() {
-		int txID = program.startTransaction("find images");
-		try {
-			EmbeddedMediaAnalyzer imageAnalyzer = new EmbeddedMediaAnalyzer();
-			imageAnalyzer.added(program, program.getMemory(), TaskMonitorAdapter.DUMMY_MONITOR,
-				messageLog);
-		}
-		catch (CancelledException e) {
-			// using Dummy, can't happen
-		}
-		finally {
-			program.endTransaction(txID, true);
-		}
-	}
-
-	private boolean isImage(Data data) {
-		DataType dataType = data.getDataType();
-		if (dataType instanceof PngDataType) {
-			return true;
-		}
-		if (dataType instanceof GifDataType) {
-			return true;
-		}
-		if (dataType instanceof BitmapResourceDataType) {
-			return true;
-		}
-		if (dataType instanceof IconResourceDataType) {
-			return true;
-		}
-		if (dataType instanceof JPEGDataType) {
-			return true;
-		}
-		return false;
-	}
-
-//==================================================================================================
-// static methods
-//==================================================================================================
-
-	private static ByteProvider createByteProvider(byte[] bytes) throws GhidraException {
-		if (bytes == null) {
-			throw new GhidraException("Attempted to process a null byte[].");
-		}
-		if (bytes.length == 0) {
-			throw new GhidraException("Attempted to process an empty byte[].");
-		}
-		return new ByteArrayProvider("Bytes", bytes);
-	}
-
-	private static ByteProvider createByteProvider(File file) throws GhidraException {
-		if (file == null) {
-			throw new GhidraException("Attempted to process a null file");
-		}
-		try {
-			return new RandomAccessByteProvider(file);
-		}
-		catch (IOException e) {
-			throw new GhidraException(e);
-		}
-	}
-
-}

Ghidra/Features/Base/src/test.slow/java/docking/ComponentProviderActionsTest.java

@@ -271,7 +271,7 @@ public class ComponentProviderActionsTest extends AbstractGhidraHeadedIntegratio
 
 		try {
 			setErrorsExpected(true);
-			runSwingWithExceptions(this::showProvider, true);
+			runSwingWithException(this::showProvider);
 			setErrorsExpected(false);
 			fail();
 		}
@@ -289,7 +289,7 @@ public class ComponentProviderActionsTest extends AbstractGhidraHeadedIntegratio
 
 		try {
 			setErrorsExpected(true);
-			runSwingWithExceptions(() -> provider.setIcon(null), true);
+			runSwingWithException(() -> provider.setIcon(null));
 			setErrorsExpected(false);
 			fail("Expected an exception passing a null icon when specifying a toolbar action");
 		}

Ghidra/Features/Base/src/test.slow/java/ghidra/app/plugin/core/calltree/CallTreePluginTest.java

@@ -42,6 +42,7 @@ import ghidra.app.plugin.core.codebrowser.CodeBrowserPlugin;
 import ghidra.app.plugin.core.gotoquery.GoToServicePlugin;
 import ghidra.app.services.GoToService;
 import ghidra.app.services.ProgramManager;
+import ghidra.app.util.NamespaceUtils;
 import ghidra.framework.plugintool.PluginTool;
 import ghidra.program.database.ProgramBuilder;
 import ghidra.program.database.ProgramDB;
@@ -158,6 +159,10 @@ public class CallTreePluginTest extends AbstractGhidraHeadedIntegrationTest {
 		}
 	}
 
+	private Function function(int addr) throws Exception {
+		return ensureFunction(addr);
+	}
+
 	private void function(int from, int to) throws Exception {
 		ensureFunction(from);
 		ensureFunction(to);
@@ -168,16 +173,39 @@ public class CallTreePluginTest extends AbstractGhidraHeadedIntegrationTest {
 		}
 	}
 
-	private void ensureFunction(long from) throws Exception {
+	private Function function(String namespace, String name, int addr) throws Exception {
+		Function f = ensureFunction(addr);
+		tx(program, () -> {
+
+			f.setName(name, SourceType.ANALYSIS);
+			Namespace ns = NamespaceUtils.createNamespaceHierarchy(namespace, null, program,
+				SourceType.ANALYSIS);
+			f.setParentNamespace(ns);
+		});
+
+		return f;
+	}
+
+	private void function(Function from, Function to) {
+
+		// a bit of space so the function call is not at the entry point
+		int offset = (int) from.getEntryPoint().getOffset() + 5;
+		int toOffset = (int) to.getEntryPoint().getOffset();
+		while (!createReference(offset, toOffset)) {
+			offset++;
+		}
+	}
+
+	private Function ensureFunction(long from) throws Exception {
 		ProgramDB p = builder.getProgram();
 		FunctionManager fm = p.getFunctionManager();
 		Function f = fm.getFunctionAt(addr(from));
 		if (f != null) {
-			return;
+			return f;
 		}
 
 		String a = Long.toHexString(from);
-		builder.createEmptyFunction("Function_" + a, "0x" + a, 50, DataType.DEFAULT);
+		return builder.createEmptyFunction("Function_" + a, "0x" + a, 50, DataType.DEFAULT);
 	}
 
 	private boolean createReference(long from, long to) {
@@ -580,12 +608,10 @@ public class CallTreePluginTest extends AbstractGhidraHeadedIntegrationTest {
 
 		setProviderFunction("0x5000");
 
-		final ToggleDockingAction filterDuplicatesAction =
+		ToggleDockingAction filterDuplicatesAction =
 			(ToggleDockingAction) getAction("Filter Duplicates");
 
-		if (!filterDuplicatesAction.isSelected()) {
-			performAction(filterDuplicatesAction, true);
-		}
+		setToggleActionSelected(filterDuplicatesAction, new ActionContext(), true);
 
 		waitForTree(outgoingTree);
 		GTreeNode rootNode = getRootNode(outgoingTree);
@@ -597,8 +623,7 @@ public class CallTreePluginTest extends AbstractGhidraHeadedIntegrationTest {
 		// copy the names of the children into a map so that we can verify that there are 
 		// no duplicates
 		boolean shouldHaveDuplicates = false;
-		Map<String, Integer> nameCountMap = createNameCountMap(rootNode);
-		System.out.println("nameCountMap: before: = " + nameCountMap);
+		Map<GTreeNode, Integer> nameCountMap = createNameCountMap(rootNode);
 		assertDuplicateChildStatus(nameCountMap, shouldHaveDuplicates);
 
 		performAction(filterDuplicatesAction, true);// deselect
@@ -608,7 +633,47 @@ public class CallTreePluginTest extends AbstractGhidraHeadedIntegrationTest {
 		rootNode = getRootNode(outgoingTree);
 		nameCountMap = createNameCountMap(rootNode);
 		shouldHaveDuplicates = true;
-		System.out.println("nameCountMap: after: = " + nameCountMap);
+		assertDuplicateChildStatus(nameCountMap, shouldHaveDuplicates);
+	}
+
+	@Test
+	public void testFilterIncomingDuplicates_SameFunctionNameInDifferentNamespaces()
+			throws Exception {
+
+		/*
+		Create a function call tree that looks like:
+		
+		
+			NS1::Foo
+					root
+			NS2::Foo
+					root
+					
+				 */
+
+		Function f1 = function("NS1", "Foo", 0x11000);
+		Function f2 = function("NS2", "Foo", 0x12000);
+		Function root = function(0x0000);
+		function(f1, root);
+		function(f2, root);
+
+		setProviderFunction("0x0000");
+
+		ToggleDockingAction filterDuplicatesAction =
+			(ToggleDockingAction) getAction("Filter Duplicates");
+		setToggleActionSelected(filterDuplicatesAction, new ActionContext(), true);
+		waitForTree(incomingTree);
+
+		GTreeNode rootNode = getRootNode(incomingTree);
+		List<GTreeNode> children = rootNode.getChildren();
+		assertTrue(
+			"Outgoing tree does not have callers as expected for function: " + getListingFunction(),
+			children.size() > 0);
+
+		// copy the names of the children into a map so that we can verify that there are 
+		// no duplicates
+		boolean shouldHaveDuplicates = false;
+		Map<GTreeNode, Integer> nameCountMap = createNameCountMap(rootNode);
 		assertDuplicateChildStatus(nameCountMap, shouldHaveDuplicates);
 	}
 
@@ -1071,27 +1136,26 @@ public class CallTreePluginTest extends AbstractGhidraHeadedIntegrationTest {
 		return codeBrowserPlugin.getCurrentAddress();
 	}
 
-	private Map<String, Integer> createNameCountMap(GTreeNode node) {
-		Map<String, Integer> map = new HashMap<>();
+	private Map<GTreeNode, Integer> createNameCountMap(GTreeNode node) {
+		Map<GTreeNode, Integer> map = new HashMap<>();
 		List<GTreeNode> children = node.getChildren();
 		for (GTreeNode child : children) {
-			String name = child.getName();
-			Integer integer = map.get(name);
+			Integer integer = map.get(child);
 			if (integer == null) {
 				integer = 0;
 			}
 			int asInt = integer;
 			asInt++;
-			map.put(name, asInt);
+			map.put(child, asInt);
 		}
 		return map;
 	}
 
-	private void assertDuplicateChildStatus(Map<String, Integer> childCountMap,
+	private void assertDuplicateChildStatus(Map<GTreeNode, Integer> childCountMap,
 			boolean shouldHaveDuplicates) {
 		boolean foundDuplicates = false;
-		Set<Entry<String, Integer>> entrySet = childCountMap.entrySet();
-		for (Entry<String, Integer> entry : entrySet) {
+		Set<Entry<GTreeNode, Integer>> entrySet = childCountMap.entrySet();
+		for (Entry<GTreeNode, Integer> entry : entrySet) {
 			int value = entry.getValue();
 			if (value != 1) {
 				foundDuplicates = true;

Ghidra/Features/Base/src/test.slow/java/ghidra/app/plugin/core/compositeeditor/StructureEditorUnlockedActions2Test.java

@@ -166,7 +166,7 @@ public class StructureEditorUnlockedActions2Test
 		assertEquals(getDataType(4), dt3);
 
 		invoke(action);
-		dialog = env.waitForDialogComponent(NumberInputDialog.class, 1000);
+		dialog = waitForDialogComponent(NumberInputDialog.class);
 		assertNotNull(dialog);
 		okInput(dialog, 2);
 		dialog = null;
@@ -180,7 +180,7 @@ public class StructureEditorUnlockedActions2Test
 
 		setSelection(new int[] { 2 });
 		invoke(action);
-		dialog = env.waitForDialogComponent(NumberInputDialog.class, 1000);
+		dialog = waitForDialogComponent(NumberInputDialog.class);
 		assertNotNull(dialog);
 		okInput(dialog, 2);
 		dialog = null;
@@ -223,7 +223,7 @@ public class StructureEditorUnlockedActions2Test
 		assertEquals(getDataType(1), dt1);
 		assertEquals(getDataType(2), dt2);
 		assertEquals(getDataType(3), dt3);
-		assertTrue(!"".equals(model.getStatus()));
+		assertNotEquals("", model.getStatus());
 	}
 
 	@Test

Ghidra/Features/Base/src/test.slow/java/ghidra/app/plugin/core/compositeeditor/StructureEditorUnlockedActions3Test.java

@@ -45,7 +45,7 @@ public class StructureEditorUnlockedActions3Test
 		DataType dt7 = getDataType(7);// SimpleUnion
 
 		invoke(duplicateMultipleAction);
-		dialog = env.waitForDialogComponent(NumberInputDialog.class, 1000);
+		dialog = waitForDialogComponent(NumberInputDialog.class);
 		assertNotNull(dialog);
 		okInput(dialog, 2);
 		dialog = null;
@@ -102,7 +102,7 @@ public class StructureEditorUnlockedActions3Test
 	public void testEditFieldOnBlankLine() throws Exception {
 		init(emptyStructure, pgmTestCat);
 
-		assertTrue(!model.isEditingField());
+		assertFalse(model.isEditingField());
 		triggerActionKey(getTable(), editFieldAction);
 		assertTrue(model.isEditingField());
 		assertEquals(0, model.getRow());
@@ -116,7 +116,7 @@ public class StructureEditorUnlockedActions3Test
 		init(complexStructure, pgmTestCat);
 
 		setSelection(new int[] { 3 });
-		assertTrue(!model.isEditingField());
+		assertFalse(model.isEditingField());
 		invoke(editFieldAction);
 		JTable table = getTable();
 		Container component = (Container) table.getEditorComponent();
@@ -140,10 +140,10 @@ public class StructureEditorUnlockedActions3Test
 
 		DataTypeComponent dtc = model.getComponent(3);
 		assertNotNull(dtc);
-		assertTrue(!dtc.isBitFieldComponent());
+		assertFalse(dtc.isBitFieldComponent());
 
 		setSelection(new int[] { 3 });
-		assertTrue(!model.isEditingField());
+		assertFalse(model.isEditingField());
 		invoke(editFieldAction);
 		JTable table = getTable();
 		Container component = (Container) table.getEditorComponent();
@@ -156,7 +156,7 @@ public class StructureEditorUnlockedActions3Test
 
 		waitForSwing();
 
-		assertTrue(!model.isEditingField());
+		assertFalse(model.isEditingField());
 		assertEquals(3, model.getRow());
 		assertNotEditingField();
 
@@ -192,7 +192,7 @@ public class StructureEditorUnlockedActions3Test
 
 		int num = model.getNumComponents();
 		setSelection(new int[] { 3 });
-		assertTrue(!getDataType(3).isEquivalent(dt));
+		assertFalse(getDataType(3).isEquivalent(dt));
 		invoke(fav);// replacing dword with byte followed by 3 undefineds
 		assertEquals(num + 3, model.getNumComponents());
 		assertTrue(getDataType(3).isEquivalent(dt));

Ghidra/Features/Base/src/test.slow/java/ghidra/app/plugin/core/compositeeditor/StructureEditorUnlockedActions4Test.java

@@ -25,8 +25,7 @@ import org.junit.Test;
 
 import docking.widgets.dialogs.NumberInputDialog;
 import ghidra.program.model.data.*;
-import ghidra.util.InvalidNameException;
-import ghidra.util.exception.*;
+import ghidra.util.exception.UsrException;
 import ghidra.util.task.TaskMonitor;
 
 public class StructureEditorUnlockedActions4Test
@@ -76,7 +75,7 @@ public class StructureEditorUnlockedActions4Test
 
 		// Make array of 3 pointers
 		invoke(arrayAction);
-		dialog = env.waitForDialogComponent(NumberInputDialog.class, 1000);
+		dialog = waitForDialogComponent(NumberInputDialog.class);
 		assertNotNull(dialog);
 		okInput(dialog, 3);
 		dialog = null;
@@ -103,25 +102,12 @@ public class StructureEditorUnlockedActions4Test
 	}
 
 	@Test
-	public void testDuplicateAction() throws Exception {
+	public void testDuplicateAction() throws Throwable {
 		init(complexStructure, pgmTestCat);
-		runSwing(() -> {
-			try {
-				model.setComponentName(1, "comp1");
-				model.setComponentComment(1, "comment 1");
-				model.clearComponent(2);
-			}
-			catch (InvalidInputException e) {
-				failWithException("Unexpected error", e);
-			}
-			catch (InvalidNameException e) {
-				// TODO Auto-generated catch block
-				e.printStackTrace();
-			}
-			catch (DuplicateNameException e) {
-				// TODO Auto-generated catch block
-				e.printStackTrace();
-			}
+		runSwingWithException(() -> {
+			model.setComponentName(1, "comp1");
+			model.setComponentComment(1, "comment 1");
+			model.clearComponent(2);
 		});
 		int len = model.getLength();
 		int num = model.getNumComponents();
@@ -150,7 +136,7 @@ public class StructureEditorUnlockedActions4Test
 
 	@Test
 	public void testEditComponentAction() throws Exception {
-		//		init(complexStructure, pgmTestCat);
+
 		runSwing(() -> {
 			installProvider(new StructureEditorProvider(plugin, complexStructure, false));
 			model = provider.getModel();
@@ -159,12 +145,46 @@ public class StructureEditorUnlockedActions4Test
 		getActions();
 
 		assertEquals("", model.getStatus());
-		setSelection(new int[] { 21 });
+		setSelection(new int[] { 21 }); // 'simpleStructure'
 		String complexSubTitle = getProviderSubTitle(complexStructure);
 		String simpleSubTitle = getProviderSubTitle(simpleStructure);
 		assertTrue("Couldn't find editor = " + complexSubTitle,
 			isProviderShown(tool.getToolFrame(), "Structure Editor", complexSubTitle));
-		assertTrue(!isProviderShown(tool.getToolFrame(), "Structure Editor", simpleSubTitle));
+		assertFalse(isProviderShown(tool.getToolFrame(), "Structure Editor", simpleSubTitle));
+
+		invoke(editComponentAction);
+		assertEquals("", model.getStatus());
+		assertTrue("Couldn't find editor = " + complexSubTitle,
+			isProviderShown(tool.getToolFrame(), "Structure Editor", complexSubTitle));
+		assertTrue("Couldn't find editor = " + simpleSubTitle,
+			isProviderShown(tool.getToolFrame(), "Structure Editor", simpleSubTitle));
+
+		runSwing(() -> provider.closeComponent());
+	}
+
+	@Test
+	public void testEditComponentAction_ComplexStructure() throws Exception {
+
+		//
+		// Test that the Edit Component action will work when the type is multi-layered, like
+		// a pointer to a pointer to a structure
+		//
+
+		runSwing(() -> {
+			installProvider(new StructureEditorProvider(plugin, complexStructure, false));
+			model = provider.getModel();
+		});
+		waitForSwing();
+		getActions();
+
+		assertEquals("", model.getStatus());
+		setSelection(new int[] { 20 }); // 'simpleStructureTypedef * *[2][3]'		
+		String complexSubTitle = getProviderSubTitle(complexStructure);
+		String simpleSubTitle = getProviderSubTitle(simpleStructure);
+		assertTrue("Couldn't find editor = " + complexSubTitle,
+			isProviderShown(tool.getToolFrame(), "Structure Editor", complexSubTitle));
+		assertFalse(isProviderShown(tool.getToolFrame(), "Structure Editor", simpleSubTitle));
+
 		invoke(editComponentAction);
 		assertEquals("", model.getStatus());
 		assertTrue("Couldn't find editor = " + complexSubTitle,
@@ -194,58 +214,6 @@ public class StructureEditorUnlockedActions4Test
 		assertEquals(num + 13, model.getNumComponents());
 	}
 
-	//	public void testCancelPointerOnFixedDt() throws Exception {
-	//      // FUTURE
-	//		init(complexStructure,  pgmTestCat);
-	//		NumberInputDialog dialog;
-	//		int num = model.getNumComponents();
-	//
-	//		setSelection(new int[] {2});
-	//		DataType dt2 = getDataType(2);
-	//		assertTrue(getDataType(2).isEquivalent(new WordDataType()));
-	//		invoke(pointerAction);
-	//		dialog = (NumberInputDialog)env.waitForDialog(NumberInputDialog.class, 1000);
-	//		assertNotNull(dialog);
-	//		cancelInput(dialog);
-	//		dialog.dispose();
-	//		dialog = null;
-	//		assertEquals(num, model.getNumComponents());
-	//		assertEquals("word", getDataType(2).getDisplayName());
-	//		assertTrue(getDataType(2).isEquivalent(dt2));
-	//		assertEquals(4, model.getComponent(2).getLength());
-	//	}
-
-	//	@Test
-	//	public void testCreatePointerOnArray() throws Exception {
-	//		init(complexStructure, pgmTestCat);
-	//		int num = model.getNumComponents();
-	//
-	//		setSelection(new int[] { 14 });
-	//		DataType dt14 = getDataType(14);
-	//		assertEquals("byte[7]", dt14.getDisplayName());
-	//		invoke(pointerAction);
-	//		assertEquals(num + 3, model.getNumComponents());
-	//		assertEquals("byte[7] *", getDataType(14).getDisplayName());
-	//		assertTrue(((Pointer) getDataType(14)).getDataType().isEquivalent(dt14));
-	//		assertEquals(4, getDataType(14).getLength());
-	//		assertEquals(4, model.getComponent(14).getLength());
-	//	}
-	//
-	//	@Test
-	//	public void testCreatePointerOnTypedef() throws Exception {
-	//		init(complexStructure, pgmTestCat);
-	//		int num = model.getNumComponents();
-	//
-	//		setSelection(new int[] { 19 });
-	//		DataType dt19 = getDataType(19);
-	//		assertEquals("simpleStructureTypedef", dt19.getDisplayName());
-	//		invoke(pointerAction);
-	//		assertEquals(num + 25, model.getNumComponents());
-	//		assertEquals("simpleStructureTypedef *", getDataType(19).getDisplayName());
-	//		assertTrue(((Pointer) getDataType(19)).getDataType().isEquivalent(dt19));
-	//		assertEquals(4, model.getComponent(19).getLength());
-	//	}
-
 	@Test
 	public void testApplyComponentChange() throws Exception {
 		init(complexStructure, pgmTestCat);
@@ -262,7 +230,7 @@ public class StructureEditorUnlockedActions4Test
 		});
 		DataType viewCopy = model.viewComposite.clone(null);
 
-		assertTrue(!complexStructure.isEquivalent(model.viewComposite));
+		assertFalse(complexStructure.isEquivalent(model.viewComposite));
 		assertTrue(viewCopy.isEquivalent(model.viewComposite));
 		invoke(applyAction);
 		assertTrue(viewCopy.isEquivalent(complexStructure));

Ghidra/Features/FileFormats/src/main/java/ghidra/file/formats/ios/prelink/PrelinkFileSystem.java

@@ -76,7 +76,8 @@ public class PrelinkFileSystem extends GFileSystemBase implements GFileSystemPro
 	@Override
 	public boolean isValid(TaskMonitor monitor) throws IOException {
 		try {
-			return !MachoPrelinkUtils.parsePrelinkXml(provider, monitor).isEmpty();
+			return MachHeader.isMachHeader(provider) &&
+				!MachoPrelinkUtils.parsePrelinkXml(provider, monitor).isEmpty();
 		}
 		catch (JDOMException e) {
 			Msg.warn(this, e.getMessage());

Ghidra/Features/GnuDemangler/src/main/java/ghidra/app/util/demangler/gnu/GnuDemanglerParser.java

@@ -1109,8 +1109,11 @@ public class GnuDemanglerParser {
 		@Override
 		public String toString() {
 			ToStringBuilder builder = new ToStringBuilder(this, ToStringStyle.JSON_STYLE);
-			return builder.append("name", name).append("prefix", prefix).append("type",
-				type).append("demangled", demangled).toString();
+			return builder.append("name", name)
+					.append("prefix", prefix)
+					.append("type", type)
+					.append("demangled", demangled)
+					.toString();
 		}
 	}
 
@@ -1246,31 +1249,36 @@ public class GnuDemanglerParser {
 			//
 			String operatorChars = matcher.group(2);
 			String templates = matcher.group(3);
-			templates = templates == null ? "" : templates;
+			int start = matcher.start(2); // operator chars start
+			int end = matcher.end(3); // templates end
+
+			if (templates == null) {
+				templates = "";
+				end = matcher.end(2); // no templates; end of the operator chars
+			}
 
 			//
 			// The 'operator' functions have symbols that confuse our default function parsing.  
 			// Specifically, operators that use shift symbols (<, <<, >, >>) will cause our 
-			// template parsing to fail.  To default the failure, we will install a temporary 
+			// template parsing to fail.  To defeat the failure, we will install a temporary 
 			// function name here and then restore it after parsing is finished.
 			//
-			String originalPrefix = OPERATOR + operatorChars + templates;
+			String rawPrefix = OPERATOR + demangled.substring(start, end);
 			String placeholder = "TEMPNAMEPLACEHOLDERVALUE";
-			String tempName = demangled.replace(originalPrefix, placeholder);
+			String tempName = demangled.replace(rawPrefix, placeholder);
 
 			DemangledFunction function = (DemangledFunction) parseFunctionOrVariable(tempName);
 			function.setOverloadedOperator(true);
-			function.setName(originalPrefix);
 
-			if (!StringUtils.isBlank(templates)) {
-				String escapedPrefix = removeBadSpaces(originalPrefix);
+			String simpleName = OPERATOR + operatorChars;
+			if (StringUtils.isBlank(templates)) {
+				function.setName(simpleName);
+			}
+			else {
 				String escapedTemplates = removeBadSpaces(templates);
-				int templateIndex = escapedPrefix.indexOf(escapedTemplates);
-				String operatorName = escapedPrefix.substring(0, templateIndex);
 				DemangledTemplate demangledTemplate = parseTemplate(escapedTemplates);
-
 				function.setTemplate(demangledTemplate);
-				function.setName(operatorName);
+				function.setName(simpleName);
 			}
 
 			return function;
@@ -1431,8 +1439,10 @@ public class GnuDemanglerParser {
 		@Override
 		public String toString() {
 			ToStringBuilder builder = new ToStringBuilder(this, ToStringStyle.JSON_STYLE);
-			return builder.append("text", text).append("paramStart", paramStart).append("paramEnd",
-				paramEnd).toString();
+			return builder.append("text", text)
+					.append("paramStart", paramStart)
+					.append("paramEnd", paramEnd)
+					.toString();
 		}
 
 		private boolean isContainedWithinNamespace() {
@@ -1490,8 +1500,10 @@ public class GnuDemanglerParser {
 		@Override
 		public String toString() {
 			ToStringBuilder builder = new ToStringBuilder(this, ToStringStyle.JSON_STYLE);
-			return builder.append("fullText", fullText).append("params", params).append("trailing",
-				trailing).toString();
+			return builder.append("fullText", fullText)
+					.append("params", params)
+					.append("trailing", trailing)
+					.toString();
 		}
 	}
 

Ghidra/Features/GnuDemangler/src/test/java/ghidra/app/util/demangler/GnuDemanglerParserTest.java

@@ -843,7 +843,7 @@ public class GnuDemanglerParserTest extends AbstractGenericTest {
 	}
 
 	@Test
-	public void testOverloadedShiftOperatorParsingBug() {
+	public void testOverloadedShiftOperatorTemplated_RightShift() {
 		parser = new GnuDemanglerParser();
 		DemangledObject object = parser.parse("fakemangled",
 			"std::basic_istream<char, std::char_traits<char> >& " +
@@ -858,6 +858,24 @@ public class GnuDemanglerParserTest extends AbstractGenericTest {
 			object.getSignature());
 	}
 
+	@Test
+	public void testOverloadedShiftOperatorTemplated_LeftShift() {
+
+		String raw =
+			"std::basic_ostream<char, std::char_traits<char> >& " +
+				"std::operator<< <std::char_traits<char> >" +
+				"(std::basic_ostream<char, std::char_traits<char> >&, char const*)";
+		String formatted = "std::basic_ostream<char,std::char_traits<char>> & " +
+			"std::operator<<<std::char_traits<char>>" +
+			"(std::basic_ostream<char,std::char_traits<char>> &,char const *)";
+		DemangledObject object = parser.parse(
+			"_ZStlsISt11char_traitsIcEERSt13basic_ostreamIcT_ES5_PKc",
+			raw);
+		String name = object.getName();
+		assertEquals("operator<<", name);
+		assertEquals(formatted, object.getSignature());
+	}
+
 	@Test
 	public void testOverloadedLeftShiftOperatorWithFunctionPointer() {
 

Ghidra/Framework/Generic/src/main/java/generic/test/AbstractGenericTest.java

@@ -55,6 +55,7 @@ import sun.awt.AppContext;
 import utilities.util.FileUtilities;
 import utilities.util.reflection.ReflectionUtilities;
 import utility.application.ApplicationLayout;
+import utility.function.ExceptionalCallback;
 
 public abstract class AbstractGenericTest extends AbstractGTest {
 
@@ -1115,23 +1116,32 @@ public abstract class AbstractGenericTest extends AbstractGTest {
 	}
 
 	/**
-	 * Call this version of {@link #runSwing(Runnable)} when you expect your runnable to throw
-	 * an exception 
-	 * @param runnable the runnable
-	 * @param wait true signals to wait for the Swing operation to finish
-	 * @throws Throwable any exception that is thrown on the Swing thread
+	 * Call this version of {@link #runSwing(Runnable)} when you expect your runnable <b>may</b> 
+	 * throw exceptions
+	 * 
+	 * @param callback the runnable code snippet to call
+	 * @throws Exception any exception that is thrown on the Swing thread
 	 */
-	public static void runSwingWithExceptions(Runnable runnable, boolean wait) throws Throwable {
+	public static <E extends Exception> void runSwingWithException(ExceptionalCallback<E> callback)
+			throws Exception {
 
 		if (Swing.isSwingThread()) {
 			throw new AssertException("Unexpectedly called from the Swing thread");
 		}
 
-		ExceptionHandlingRunner exceptionHandlingRunner = new ExceptionHandlingRunner(runnable);
+		ExceptionHandlingRunner exceptionHandlingRunner = new ExceptionHandlingRunner(callback);
 		Throwable throwable = exceptionHandlingRunner.getException();
-		if (throwable != null) {
-			throw throwable;
+		if (throwable == null) {
+			return;
 		}
+
+		if (throwable instanceof Exception) {
+			// this is what the client expected
+			throw (Exception) throwable;
+		}
+
+		// a runtime exception; re-throw
+		throw new AssertException(throwable);
 	}
 
 	public static void runSwing(Runnable runnable, boolean wait) {
@@ -1170,11 +1180,18 @@ public abstract class AbstractGenericTest extends AbstractGTest {
 	}
 
 	protected static class ExceptionHandlingRunner {
-		private final Runnable delegateRunnable;
+		private final ExceptionalCallback<? extends Exception> delegateCallback;
 		private Throwable exception;
 
 		ExceptionHandlingRunner(Runnable delegateRunnable) {
-			this.delegateRunnable = delegateRunnable;
+			this.delegateCallback = () -> {
+				delegateRunnable.run();
+			};
+			run();
+		}
+
+		ExceptionHandlingRunner(ExceptionalCallback<? extends Exception> delegateCallback) {
+			this.delegateCallback = delegateCallback;
 			run();
 		}
 
@@ -1213,7 +1230,7 @@ public abstract class AbstractGenericTest extends AbstractGTest {
 
 			Runnable swingExceptionCatcher = () -> {
 				try {
-					delegateRunnable.run();
+					delegateCallback.call();
 				}
 				catch (Throwable t) {
 					exception = t;

Ghidra/Framework/Utility/src/main/java/ghidra/GhidraApplicationLayout.java

@@ -96,14 +96,21 @@ public class GhidraApplicationLayout extends ApplicationLayout {
 		// Application properties
 		applicationProperties = new ApplicationProperties(applicationRootDirs);
 
-		// Modules
-		modules = findGhidraModules();
-
 		// User directories
 		userTempDir = ApplicationUtilities.getDefaultUserTempDir(getApplicationProperties());
 		userCacheDir = ApplicationUtilities.getDefaultUserCacheDir(getApplicationProperties());
 		userSettingsDir = ApplicationUtilities.getDefaultUserSettingsDir(getApplicationProperties(),
 			getApplicationInstallationDir());
+		
+		// Extensions
+		extensionInstallationDirs = findExtensionInstallationDirectories();
+		extensionArchiveDir = findExtensionArchiveDirectory();
+
+		// Patch directory
+		patchDir = findPatchDirectory();
+		
+		// Modules
+		modules = findGhidraModules();
 	}
 
 	/**
@@ -145,7 +152,7 @@ public class GhidraApplicationLayout extends ApplicationLayout {
 
 		// Find standard module root directories from within the application root directories
 		Collection<ResourceFile> moduleRootDirectories =
-			ModuleUtilities.findModuleRootDirectories(applicationRootDirs, new ArrayList<>());
+			ModuleUtilities.findModuleRootDirectories(applicationRootDirs, new LinkedHashSet<>());
 
 		// Find installed extension modules
 		for (ResourceFile extensionInstallDir : extensionInstallationDirs) {

Ghidra/Processors/ARM/certification.manifest

@@ -3,6 +3,7 @@ Module.manifest||GHIDRA||||END|
 build.gradle||GHIDRA||||END|
 data/languages/ARM.cspec||GHIDRA||||END|
 data/languages/ARM.dwarf||GHIDRA||||END|
+data/languages/ARM.gdis||GHIDRA||||END|
 data/languages/ARM.ldefs||GHIDRA||||END|
 data/languages/ARM.opinion||GHIDRA||||END|
 data/languages/ARM.sinc||GHIDRA||||END|

Ghidra/Processors/ARM/data/languages/ARM.gdis

@@ -0,0 +1,41 @@
+<!-- 
+     This file determines the disassembler options sent to the GNU external disassembler.
+     You can see which options are available for all architectures in the objdump man page.
+     Given a version of objdump compiled for a specific architecture, you can see what options
+     are available with "objdump -i -m" 
+     
+      The options for ARM are:
+       "reg-names-std" (the default)
+       "reg-names-apcs"
+       "reg-names-raw"
+       "reg-names-apcs"
+       "reg-names-special-apcs"
+       "force-thumb"      (force thumb disassembly)
+       "no-force-thumb"   (force arm disassembly)
+       (see the objdump manpage for the precise details about the different register 
+       naming options)
+     
+     "optstring" is the string of options, and "display_prefix" is an optional prefix prepended to the 
+     external disassembly field.  In this file, "A: " is prepended to ARM disassembly, and
+     "T: " is prepended to Thumb disassembly. 
+     
+     To send multiple options, concatenate them into a CSV list.  For example, "no-force-thumb,reg-names-raw"
+     is a valid optstring. You can also have a "global" element whose "optstring" attribute is 
+     always sent to the GNU disassembler.
+    
+     If there is not a context register defined, the global optstring is sent by itself (see x86-16.gdis for
+     an example).  If there is a context register defined, the global optstring is prepended to the 
+     optstring determined by a context register value.  
+     
+     This file must be listed in the .ldefs file for the processor, e.g.
+     <external_name tool="gdis.disassembler.options.file" name="ARM.gdis"/>
+-->
+
+<gdis> 
+    <context_register>TMode</context_register>
+    <options>
+        <option value="0x0" optstring="no-force-thumb" display_prefix = "A: "/>
+        <option value="0x1" optstring="force-thumb" display_prefix = "T: "/>
+    </options>
+</gdis>
+

Ghidra/Processors/ARM/data/languages/ARM.ldefs

@@ -14,6 +14,7 @@
     <compiler name="default" spec="ARM.cspec" id="default"/>
     <compiler name="Visual Studio" spec="ARM_win.cspec" id="windows"/>
     <external_name tool="gnu" name="iwmmxt"/>
+    <external_name tool="gdis.disassembler.options.file" name="ARM.gdis"/>
     <external_name tool="IDA-PRO" name="arm"/>
     <external_name tool="DWARF.register.mapping.file" name="ARMneon.dwarf"/>
   </language>
@@ -31,6 +32,7 @@
     <compiler name="default" spec="ARM.cspec" id="default"/>
     <compiler name="Visual Studio" spec="ARM_win.cspec" id="windows"/>
     <external_name tool="gnu" name="iwmmxt"/>
+    <external_name tool="gdis.disassembler.options.file" name="ARM.gdis"/>
     <external_name tool="IDA-PRO" name="arm"/>
     <external_name tool="DWARF.register.mapping.file" name="ARMneon.dwarf"/>
   </language>
@@ -63,6 +65,7 @@
     <description>Generic ARM/Thumb v8 big endian</description>
     <compiler name="default" spec="ARM.cspec" id="default"/>
     <external_name tool="gnu" name="iwmmxt"/>
+    <external_name tool="gdis.disassembler.options.file" name="ARM.gdis"/>
     <external_name tool="IDA-PRO" name="armb"/>
     <external_name tool="DWARF.register.mapping.file" name="ARMneon.dwarf"/>
   </language>
@@ -96,6 +99,7 @@
     <compiler name="default" spec="ARM.cspec" id="default"/>
     <compiler name="Visual Studio" spec="ARM_win.cspec" id="windows"/>
     <external_name tool="gnu" name="iwmmxt"/>
+    <external_name tool="gdis.disassembler.options.file" name="ARM.gdis"/>
     <external_name tool="IDA-PRO" name="arm"/>
     <external_name tool="DWARF.register.mapping.file" name="ARMneon.dwarf"/>
   </language>
@@ -128,6 +132,7 @@
     <description>Generic ARM/Thumb v7 big endian</description>
     <compiler name="default" spec="ARM.cspec" id="default"/>
     <external_name tool="gnu" name="iwmmxt"/>
+    <external_name tool="gdis.disassembler.options.file" name="ARM.gdis"/>
     <external_name tool="IDA-PRO" name="armb"/>
     <external_name tool="DWARF.register.mapping.file" name="ARMneon.dwarf"/>
   </language>
@@ -174,6 +179,7 @@
     <description>Generic ARM/Thumb v6 little endian</description>
     <compiler name="default" spec="ARM_v45.cspec" id="default"/>
     <external_name tool="gnu" name="xscale"/>
+    <external_name tool="gdis.disassembler.options.file" name="ARM.gdis"/>
     <external_name tool="IDA-PRO" name="arm"/>
     <external_name tool="DWARF.register.mapping.file" name="ARM.dwarf"/>
     <!-- change DWARF register mapping to ARMneon.dwarf if VFPv2 is enabled --> 
@@ -192,6 +198,7 @@
     <description>Generic ARM/Thumb v6 big endian</description>
     <compiler name="default" spec="ARM_v45.cspec" id="default"/>
     <external_name tool="gnu" name="xscale"/>
+    <external_name tool="gdis.disassembler.options.file" name="ARM.gdis"/>
     <external_name tool="IDA-PRO" name="armb"/>
     <external_name tool="DWARF.register.mapping.file" name="ARM.dwarf"/>
     <!-- change DWARF register mapping to ARMneon.dwarf if VFPv2 is enabled --> 
@@ -210,6 +217,7 @@
     <description>Generic ARM/Thumb v5 little endian (T-variant)</description>
     <compiler name="default" spec="ARM_v45.cspec" id="default"/>
     <external_name tool="gnu" name="armv5t"/>
+    <external_name tool="gdis.disassembler.options.file" name="ARM.gdis"/>
     <external_name tool="IDA-PRO" name="arm"/>
     <external_name tool="DWARF.register.mapping.file" name="ARM.dwarf"/>
   </language>
@@ -226,6 +234,7 @@
     <description>Generic ARM/Thumb v5 big endian (T-variant)</description>
     <compiler name="default" spec="ARM_v45.cspec" id="default"/>
     <external_name tool="gnu" name="armv5t"/>
+    <external_name tool="gdis.disassembler.options.file" name="ARM.gdis"/>
     <external_name tool="IDA-PRO" name="armb"/>
     <external_name tool="DWARF.register.mapping.file" name="ARM.dwarf"/>
   </language>
@@ -274,6 +283,7 @@
     <description>Generic ARM/Thumb v4 little endian (T-variant)</description>
     <compiler name="default" spec="ARM_v45.cspec" id="default"/>
     <external_name tool="gnu" name="armv4t"/>
+    <external_name tool="gdis.disassembler.options.file" name="ARM.gdis"/>
     <external_name tool="IDA-PRO" name="arm"/>
     <external_name tool="DWARF.register.mapping.file" name="ARM.dwarf"/>
   </language>
@@ -290,6 +300,7 @@
     <description>Generic ARM/Thumb v4 big endian (T-variant)</description>
     <compiler name="default" spec="ARM_v45.cspec" id="default"/>
     <external_name tool="gnu" name="armv4t"/>
+    <external_name tool="gdis.disassembler.options.file" name="ARM.gdis"/>
     <external_name tool="IDA-PRO" name="armb"/>
     <external_name tool="DWARF.register.mapping.file" name="ARM.dwarf"/>
   </language>

Ghidra/Processors/x86/certification.manifest

@@ -30,6 +30,7 @@ data/languages/sha.sinc||GHIDRA||||END|
 data/languages/smx.sinc||GHIDRA||||END|
 data/languages/x86-16-real.pspec||GHIDRA||||END|
 data/languages/x86-16.cspec||GHIDRA||||END|
+data/languages/x86-16.gdis||GHIDRA||||END|
 data/languages/x86-16.pspec||GHIDRA||||END|
 data/languages/x86-64-gcc.cspec||GHIDRA||||END|
 data/languages/x86-64-win.cspec||GHIDRA||||END|

Ghidra/Processors/x86/data/languages/x86-16.gdis

@@ -0,0 +1,3 @@
+<gdis>
+    <global optstring="intel"/>
+</gdis>

Ghidra/Processors/x86/data/languages/x86.ldefs

@@ -59,6 +59,8 @@
 	<external_name tool="IDA-PRO" name="80486r"/>
 	<external_name tool="IDA-PRO" name="80586r"/>
 	<external_name tool="IDA-PRO" name="metapc"/>
+    <external_name tool="gnu" name="i8086"/>
+    <external_name tool="gdis.disassembler.options.file" name="x86-16.gdis"/>
     </language>
   <language processor="x86"
             endian="little"
@@ -72,6 +74,8 @@
     <description>Intel/AMD 16-bit x86 Protected Mode</description>
     <compiler name="default" spec="x86-16.cspec" id="default"/>
 	<external_name tool="IDA-PRO" name="8086p"/>
+    <external_name tool="gnu" name="i8086"/>
+    <external_name tool="gdis.disassembler.options.file" name="x86-16.gdis"/>
     </language>
     <language processor="x86"
             endian="little"