diff --git a/host/scripts/inlretro2.lua b/host/scripts/inlretro2.lua
new file mode 100644
index 0000000..3402d9f
--- /dev/null
+++ b/host/scripts/inlretro2.lua
@@ -0,0 +1,75 @@
+-- Main application flow for interacting with cartridges via USB device.
+-- Refactored version that doesn't require commenting/uncommenting to change functionality.
+
+
+-- Helper function that checks if a string is empty or nil.
+local function isempty(s)
+    return s == nil or s == ''
+end
+
+
+-- Wrapper for managing NES/Famicom operations.
+function nes_exec(mapper, dump_filename, flash_filename, verify_filename)
+    local dict = require "scripts.app.dict"
+    local nes = require "scripts.app.nes"
+    
+    -- Always test!
+    local do_test = true
+    
+    -- If a dump filename was provided, dump data from cartridge to a file.
+    local do_read = not isempty(dump_filename)
+    
+    -- If a flash filename was provided, write its contents to the cartridge.
+    local do_erase = not isempty(flash_filename)
+    -- If writing, always erase.
+    local do_program = do_erase
+    
+    -- If a verify_filename was provided, dump data from cartridge after flash to a file.
+    local do_verify = not isempty(verify_filename)
+
+    -- TODO: Add other mappers.
+    local mappers = {
+        mmc1 = require "scripts.nes.mmc1",
+        mmc3 = require "scripts.nes.mmc3",
+        nrom = require "scripts.nes.nrom"
+    }
+
+    dict.io("IO_RESET")	
+	dict.io("NES_INIT")	
+    nes.detect_mapper_mirroring(true)
+    
+    m = mappers[mapper]
+    if m == nil then
+        print("UNSUPPORTED MAPPER")
+    else
+        -- Attempt requested operations with hardware!
+
+        -- TODO: Do plumbing for interacting with RAM.
+        m.process(do_test, do_read, do_erase, do_program, do_verify, dump_filename, flash_filename, verify_filename)
+    end
+end
+
+-- Point of entry from C language half of program.
+function main()
+
+    -- Globals passed in from C: 
+    --  console_name:    string, name of console.
+    --  mapper_name:     string, name of mapper.
+    --  dump_filename:   string, filename used for writing dumped data.
+    --  flash_filename:  string, filename containing data to write cartridge.
+    --  verify_filename: string, filename used for writing back data written to cartridge for verification.
+
+    -- TODO: Add SNES support, as it appears to be currently usable?
+    local consoles = {
+        NES = nes_exec,
+    }
+    f = consoles[console_name]
+    if f == nil then 
+        print("UNSUPPORTED CONSOLE")
+    else
+        f(mapper_name, dump_filename, flash_filename, verify_filename)
+    end
+end
+
+-- Don't do this. Next iteration will call a function, not the whole script.
+main()
\ No newline at end of file
diff --git a/host/source/inlprog.c b/host/source/inlprog.c
index 03456dd..a87088c 100644
--- a/host/source/inlprog.c
+++ b/host/source/inlprog.c
@@ -29,6 +29,144 @@
 #include "lua/lauxlib.h"
 #include "lua/lualib.h"
 
+// Struct used to control functionality.
+typedef struct {
+	char *console_name;
+	char *mapper_name;
+	int display_help;
+
+	char *dump_filename;
+	char *program_filename;
+	char *lua_filename;
+} INLOptions;
+
+// Parse options and flags, create struct to drive program.
+INLOptions* parseOptions(int argc, char *argv[]) {
+	// lower case flags suggested for average user
+
+	const char *FLAG_FORMAT = "hc:d:m:p:s:";
+	int index = 0;
+	int rv = 0;
+	// opterr = 0;
+	/* FLAGS NOT YET SUPPORTED
+	int e_flag = 0; //FORCE ERASE
+	int f_flag = 0; //FORCE ALL CHECKS PASSING
+	int i_flag = 0; //input file is interlaced
+	int n_flag = 0;	//LED OFF
+	int o_flag = 0;	//LED ON
+	int t_flag = 0; //test all SRAMs found
+	int x_flag = 0; //disable all auto detecting
+	int y_flag = 0; //diable all auto doubling
+
+	char *b_value = NULL; //SUBMAPPER #
+	char *p_value = NULL; //PROGRAM FILE
+	char *v_value = NULL; //MAPPER VARIANT
+
+	//upper case flags suggested for ADVANCED users
+	int T_flag = 0; //TEST
+
+	char *C_value = NULL; //program chr file
+	char *L_value = NULL; //LIBUSB debugging value
+	char *K_value = NULL; //connect to kazzo firmware version #
+	char *O_value = NULL; //start read/writing at offset base value
+	char *P_value = NULL; //program prg file
+	char *S_value = NULL; //program SNES binary file
+	char *W_value = NULL; //program WRAM/SRAM file
+	*/
+	INLOptions *opts = calloc(1, sizeof(INLOptions));
+	
+	//getopt returns args till done then returns -1
+	//string of possible args : denotes 1 required additional arg
+	//:: denotes optional additional arg follows	
+	while((rv = getopt(argc, argv, FLAG_FORMAT)) != -1) {
+		
+		switch(rv) {
+			// case 'o': o_flag = 1; break;
+			// case 'n': n_flag = 1; break;
+			// case 'e': e_flag = 1; break;
+			// case 'f': f_flag = 1; break;
+			case 'h': opts->display_help = 1; break;
+			// case 'i': i_flag = 1; break;
+			// case 't': t_flag = 1; break;
+			// case 'x': x_flag = 1; break;
+			// case 'y': y_flag = 1; break;
+			// case 'T': T_flag = 1; break;
+
+			// case 'b': b_value = optarg; break;
+			case 'c': opts->console_name = optarg; break;
+			case 'd': opts->dump_filename = optarg; break;
+			case 'm': opts->mapper_name = optarg; break;
+			case 'p': opts->program_filename = optarg; break;
+			case 's': opts->lua_filename = optarg; break;
+			// case 'v': v_value = optarg; break;
+			// case 'C': C_value = optarg; break;
+			// case 'L': L_value = optarg; break;
+			// case 'K': K_value = optarg; break;
+			// case 'O': O_value = optarg; break;
+			// case 'P': P_value = optarg; break;
+			// case 'S': S_value = optarg; break;
+			// case 'W': W_value = optarg; break;
+
+			case '?':
+				if(
+				// ( optopt == 'b' ) ||
+				   ( optopt == 'c' )
+				|| ( optopt == 'd' )
+				|| ( optopt == 'm' )
+				|| ( optopt == 'p' )
+				|| ( optopt == 's' )
+				// || ( optopt == 'v' )
+				// || ( optopt == 'C' )
+				// || ( optopt == 'L' )
+				// || ( optopt == 'K' )
+				// || ( optopt == 'O' )
+				// || ( optopt == 'P' )
+				// || ( optopt == 'S' )
+				// || ( optopt == 'W' )
+				){
+					log_err("Option -%c requires an argument.", optopt);
+					//goto error;
+					return NULL;
+
+				} else if ( isprint(optopt)) {
+					log_err("Unknown option -%c .", optopt);
+					return NULL;
+					// goto error;
+				} else {
+					log_err("Unknown option character '\\x%x'", optopt);
+					// goto error;
+					return NULL;
+				}
+				log_err("Improper arguements passed");
+					// goto error;
+					return NULL;
+				break;
+			default:
+				//sentinel("getopt failed to catch all arg cases");
+				printf("getopt failed to catch all arg cases");
+				return 0;
+		}
+	
+	}
+
+	// debug("flags= o:%d n:%d e:%d f:%d h:%d i:%d t:%d x:%d y:%d T:%d", 
+	// 	o_flag, n_flag, e_flag, f_flag, h_flag, i_flag, t_flag, x_flag, y_flag, T_flag ); 
+	// debug("args= b:%s c:%s d:%s m:%s p:%s", b_value, c_value, d_value, m_value, p_value); 
+	// debug("args= s:%s v:%s C:%s L:%s K:%s", s_value, v_value, C_value, L_value, K_value); 
+	// debug("args= O:%s P:%s S:%s W:%s", O_value, P_value, S_value, W_value); 
+
+	for( index = optind; index < argc; index++) {
+		log_err("Non-option arguement: %s \n", argv[index]);
+	}
+
+	//TODO display better help message 
+	if (opts->display_help) {
+		printf("You've asked for help but the help message still needs created...\n");
+		return NULL;
+	}
+	return opts;
+}
+
 void error_lua (lua_State *L, const char *fmt, ...) {
 	va_list argp;
 	va_start(argp, fmt);
@@ -55,148 +193,80 @@ void load (lua_State *L, const char *fname, int *w, int *h) {
 	*h = getglobint(L, "height");
 }
 
-int main(int argc, char *argv[]) 
-{	
-
-
-	//lower case flags suggested for average user
-	int e_flag = 0; //FORCE ERASE
-	int f_flag = 0; //FORCE ALL CHECKS PASSING
-	int h_flag = 0; //HELP MESSAGE
-	int i_flag = 0; //input file is interlaced
-	int n_flag = 0;	//LED OFF
-	int o_flag = 0;	//LED ON
-	int t_flag = 0; //test all SRAMs found
-	int x_flag = 0; //disable all auto detecting
-	int y_flag = 0; //diable all auto doubling
-
-	char *b_value = NULL; //SUBMAPPER #
-	char *c_value = NULL; //CONSOLE NAME
-	char *d_value = NULL; //DUMP TO FILE
-	char *m_value = NULL; //MAPPER #
-	char *p_value = NULL; //PROGRAM FILE
-	char *s_value = NULL; //SCRIPT FILE
-	char *v_value = NULL; //MAPPER VARIANT
-
-
-	//upper case flags suggested for ADVANCED users
-	int T_flag = 0; //TEST
-
-	char *C_value = NULL; //program chr file
-	char *L_value = NULL; //LIBUSB debugging value
-	char *K_value = NULL; //connect to kazzo firmware version #
-	char *O_value = NULL; //start read/writing at offset base value
-	char *P_value = NULL; //program prg file
-	char *S_value = NULL; //program SNES binary file
-	char *W_value = NULL; //program WRAM/SRAM file
-
-//	int operation = 0;	//used to denote the overall operation being requested flash/dump/verify etc
-	int index = 0;
-	int rv = 0;
-	opterr = 0;
-
-	//usb variables
-	USBtransfer *transfer = NULL;
-
-	//lua variables
-	lua_State *L = NULL;
-
-
-	//getopt returns args till done then returns -1
-	//string of possible args : denotes 1 required additional arg
-	//:: denotes optional additional arg follows	
-	while( (rv = getopt( argc, argv, "onefhitxyTb:c:d:m:p:s:v:C:L:K:O:P:S:W:")) != -1) {
-		
-		switch(rv) {
-			case 'o': o_flag = 1; break;
-			case 'n': n_flag = 1; break;
-			case 'e': e_flag = 1; break;
-			case 'f': f_flag = 1; break;
-			case 'h': h_flag = 1; break;
-			case 'i': i_flag = 1; break;
-			case 't': t_flag = 1; break;
-			case 'x': x_flag = 1; break;
-			case 'y': y_flag = 1; break;
-			case 'T': T_flag = 1; break;
-
-			case 'b': b_value = optarg; break;
-			case 'c': c_value = optarg; break;
-			case 'd': d_value = optarg; break;
-			case 'm': m_value = optarg; break;
-			case 'p': p_value = optarg; break;
-			case 's': s_value = optarg; break;
-			case 'v': v_value = optarg; break;
-			case 'C': C_value = optarg; break;
-			case 'L': L_value = optarg; break;
-			case 'K': K_value = optarg; break;
-			case 'O': O_value = optarg; break;
-			case 'P': P_value = optarg; break;
-			case 'S': S_value = optarg; break;
-			case 'W': W_value = optarg; break;
-
-			case '?':
-				if(( optopt == 'b' )
-				|| ( optopt == 'c' )
-				|| ( optopt == 'd' )
-				|| ( optopt == 'm' )
-				|| ( optopt == 'p' )
-				|| ( optopt == 's' )
-				|| ( optopt == 'v' )
-				|| ( optopt == 'C' )
-				|| ( optopt == 'L' )
-				|| ( optopt == 'K' )
-				|| ( optopt == 'O' )
-				|| ( optopt == 'P' )
-				|| ( optopt == 'S' )
-				|| ( optopt == 'W' )){
-					log_err("Option -%c requires an argument.", optopt);
-					goto error;
-
-				} else if ( isprint(optopt)) {
-					log_err("Unknown option -%c .", optopt);
-					goto error;
-				} else {
-					log_err("Unknown option character '\\x%x'", optopt);
-					goto error;
-				}
-				log_err("Improper arguements passed");
-					goto error;
-				break;
-			default:
-				sentinel("getopt failed to catch all arg cases");
-		}
-	
-	}
-
-	debug("flags= o:%d n:%d e:%d f:%d h:%d i:%d t:%d x:%d y:%d T:%d", 
-		o_flag, n_flag, e_flag, f_flag, h_flag, i_flag, t_flag, x_flag, y_flag, T_flag ); 
-	debug("args= b:%s c:%s d:%s m:%s p:%s", b_value, c_value, d_value, m_value, p_value); 
-	debug("args= s:%s v:%s C:%s L:%s K:%s", s_value, v_value, C_value, L_value, K_value); 
-	debug("args= O:%s P:%s S:%s W:%s", O_value, P_value, S_value, W_value); 
-
-	for( index = optind; index < argc; index++) {
-		log_err("Non-option arguement: %s \n", argv[index]);
-	}
-
-	//TODO display better help message 
-	if (h_flag) {
-		printf("You've asked for help but the help message still needs created...\n");
-		return 0;
-	}
-/*
-	if ( O_value || v_value || b_value || y_flag || t_flag || f_flag ) {
-		printf("option not currently supported sorry...\n");
-	}
-*/
-
-	//Start up Lua
-	L = luaL_newstate(); //opens Lua
+// Setup Lua environment.
+lua_State *lua_init() {
+	lua_State *L = luaL_newstate(); //opens Lua
 	luaL_openlibs(L); //opens the standard libraries
 
-	//register C functions that can be called from Lua
-//	lua_pushcfunction(L, lua_dictionary_call);
+	// Register C functions that can be called from Lua.
+	// lua_pushcfunction(L, lua_dictionary_call);
 	lua_pushcfunction(L, lua_usb_vend_xfr);
 	lua_setglobal(L, "usb_vend_xfr");
+	return L;
+}
+
+// Setup INL USB Device.
+USBtransfer *usb_init_inldevice(libusb_context *context, int libusb_log) {
+	// Create USBtransfer struct to hold all transfer info
+	USBtransfer *transfer = calloc(1, sizeof(USBtransfer));	
+
+	// Create USB device handle pointer to interact with retro-prog.
+	transfer->handle = open_usb_device( context, libusb_log );
+
+	return transfer;
+}
+
+// Close and cleanup INL USB Device.
+void usb_close_inldevice(libusb_context* context, USBtransfer* transfer) {
+	if (context && transfer) {
+		close_usb(context, transfer->handle);
+	}
+	if (transfer) {
+		free(transfer);
+	}
+}
+
+// Safely cleanup for exiting program and release resources.
+void cleanup(libusb_context *context, USBtransfer *transfer, lua_State *L) {
+	usb_close_inldevice(context, transfer);
+
+	if (L) {
+		lua_close(L);
+	}
+
+	/* 
+	if(rom->fileptr != NULL) {
+		fclose(rom->fileptr);
+	}
+	*/
+}
+
+int main(int argc, char *argv[]) 
+{	
+	// int operation = 0;	//used to denote the overall operation being requested flash/dump/verify etc
+	// opterr = 0;
+
+	// USB variables
+	USBtransfer *transfer = NULL;
+	// Context set to NULL since only acting as single user of libusb.
+	libusb_context *context = NULL;
+	
+	// Default to no libusb logging.
+	int libusb_log = LIBUSB_LOG_LEVEL_NONE;
+
+	// Lua variables.
+	lua_State *L = NULL;
+	const char *LUA_SCRIPT_USB = "scripts/app/usb_device.lua";
+
+	// Parse command-line options and flags.
+	INLOptions *opts = parseOptions(argc, argv);
+	if(!opts) {
+		// If unparseable, exit.
+		return 1;
+	}
+
+	//Start up Lua
+	L = lua_init();
 	
 /*
 	//flags about input files only used for writes
@@ -214,17 +284,6 @@ int main(int argc, char *argv[])
 
 //TODO all commandline args must be collected and passed into lua
 
-	//context set to NULL since only acting as single user of libusb
-	libusb_context *context = NULL;
-
-	//create USBtransfer struct to hold all transfer info
-	transfer = malloc( sizeof(USBtransfer));	
-	check_mem(transfer);
-
-	//create usb device handle pointer to interact with retro-prog
-	transfer->handle = NULL;
-
-
 	//create file object/struct 
 //	rom_image *rom = malloc( sizeof(rom_image));	
 //
@@ -232,36 +291,57 @@ int main(int argc, char *argv[])
 //	init_rom_elements(rom);
 
 
-	//lua script arg to set different LIBUSB debugging options
-	check( !(luaL_loadfile(L, "scripts/app/usb_device.lua") || lua_pcall(L, 0, 0, 0)),
-		"cannot run config. file: %s", lua_tostring(L, -1));
+	
+    // Setup and check connection to USB Device.
+	// TODO get usb device settings from usb_device.lua
 
-	int libusb_log = LIBUSB_LOG_LEVEL_NONE;	// 0: default no msgs ever printed
-       	libusb_log = getglobint(L, "libusb_log");
+	// Lua script arg to set different libusb debugging options.
+	check(!(luaL_loadfile(L, LUA_SCRIPT_USB) || lua_pcall(L, 0, 0, 0)),
+	      "Cannot run config. file: %s", lua_tostring(L, -1));
 
-	//any value > 0 also prints debug statements in open_usb_device function
-	check( ((libusb_log >= LIBUSB_LOG_LEVEL_NONE) && (libusb_log <=LIBUSB_LOG_LEVEL_DEBUG)), 
-		"Invalid LIBUSB_LOG_LEVEL: %d, must be from 0 to 4", libusb_log );
+	// Any value > 0 for libusb_log also prints debug statements in open_usb_device function.
+	libusb_log = getglobint(L, "libusb_log");
+	check(((libusb_log >= LIBUSB_LOG_LEVEL_NONE) && (libusb_log <= LIBUSB_LOG_LEVEL_DEBUG)), 
+		  "Invalid LIBUSB_LOG_LEVEL: %d, must be from 0 to 4", libusb_log );
 
-	//TODO get usb device settings from usb_device.lua
+	transfer = usb_init_inldevice(context, libusb_log);
+	check_mem(transfer);
+	check(transfer->handle != NULL, "Unable to open INL retro-prog usb device handle.");
 
 	//open INL retro prog with firmware version 2.0 or greater
 	//if (K_value != NULL) {
 	//	//TODO take K_value option to connect to different version kazzo
 	//}
-	transfer->handle = open_usb_device( context, libusb_log );
-	check( transfer->handle != NULL, "Unable to open INL retro-prog usb device handle.");
+	
+
 
 	
 	//provide dictionary.c with pointer to transfer so it can update it's local pointer
 	//init_dictionary( transfer );
 
-	//usb device is open, pass args and control over to lua
-	if (s_value) {
-	check( !(luaL_loadfile(L, s_value) || lua_pcall(L, 0, 0, 0)),
-		"cannot run config. file: %s", lua_tostring(L, -1));
-	}
+	// Pass args to Lua
+	lua_pushstring(L, opts->console_name);
+	lua_setglobal(L, "console_name");
 
+	lua_pushstring(L, opts->mapper_name);
+	lua_setglobal(L, "mapper_name");
+
+	lua_pushstring(L, opts->dump_filename);
+	lua_setglobal(L, "dump_filename");
+
+	lua_pushstring(L, opts->program_filename);
+	lua_setglobal(L, "flash_filename");
+
+	// USB device is open, pass args and control over to Lua.
+	// If lua_filename isn't set from args, use default script.
+	const char *DEFAULT_SCRIPT = "scripts/inlretro.lua";
+	char *script = DEFAULT_SCRIPT;
+	if (opts->lua_filename) {
+		script = opts->lua_filename;
+	}
+	check(!(luaL_loadfile(L, script) || lua_pcall(L, 0, 0, 0)),
+		   "cannot run config. file: %s", lua_tostring(L, -1));
+	
 	//program flow doesn't come back to this point until script call ends/returns
 	
 /*
@@ -407,36 +487,13 @@ int main(int argc, char *argv[])
 	}
 */
 
-
-//close:
-	lua_close(L);
-
-	close_usb( context, transfer->handle);	
-
-	free(transfer);
-
-//	if(rom->fileptr != NULL){
-//	//close file
-//		fclose(rom->fileptr);
-//	}
-	
+	cleanup(context, transfer, L);
 	return 0;
 
-error: 	//checks goto error when failed
-	printf("main program went to error\n");
-
-	if ( transfer != NULL )
-		free(transfer);
-
-	if ( L != NULL )
-		lua_close(L);
-//
-//	close_usb( context, transfer->handle);	
-//	if(rom->fileptr != NULL){
-//		fclose(rom->fileptr);
-//	}
-
-
+// 'check' macros goto this label if they fail.
+error:
+	printf("Fatal error encountered, exiting.\n");
+	cleanup(context, transfer, L);
 	return 1;
 
 }
diff --git a/host/source/usb_operations.c b/host/source/usb_operations.c
index 7f0d673..2ffa57e 100644
--- a/host/source/usb_operations.c
+++ b/host/source/usb_operations.c
@@ -22,7 +22,7 @@ static libusb_device_handle *lua_usb_handle = NULL;
 //LIBUSB_ENDPOINT_IN		In: device-to-host.
 //LIBUSB_ENDPOINT_OUT		Out: host-to-device. 
 
-libusb_device_handle * open_usb_device( libusb_context *context, int log_level )
+libusb_device_handle *open_usb_device( libusb_context *context, int log_level )
 {	
 	int rv = 0;
 
@@ -90,12 +90,12 @@ libusb_device_handle * open_usb_device( libusb_context *context, int log_level )
 	const char *rprog_prod = "INL Retro-Prog";
 	uint16_t min_fw_ver = 0x200;
 
-	if (log_level>0) printf("Searching %d total devices\n", dev_count-1);
+	if (log_level>0) printf("Searching %ld total devices\n", dev_count-1);
 	for( i=0; i<dev_count; i++) {
 		device = device_list[i];
-		if (log_level>0) printf("getting dev desc #%d ", i);
+		if (log_level>0) printf("getting dev desc #%zd ", i);
 		rv = libusb_get_device_descriptor( device, &desc);
-		check( rv == LIBUSB_SUCCESS, "Unable to get device #%d descriptor: %s", i, libusb_strerror(rv));
+		check( rv == LIBUSB_SUCCESS, "Unable to get device #%zd descriptor: %s", i, libusb_strerror(rv));
 				
 		if (log_level>0) printf("checking %x vendor ", desc.idVendor);
 		if (log_level>0) printf("checking %x product\n", desc.idProduct);