Fixed plugin and scan bugs when -A and -B were used together.

src/bin/binwalk

@@ -92,6 +92,7 @@ def main():
 	show_grids = False
 	show_legend = True
 	entropy_scan = False
+	sig_scan_done = False
 	enable_plugins = True
 	exec_commands = True
 	show_invalid = False
@@ -212,8 +213,6 @@ def main():
 			magic_flags |= binwalk.magic.MAGIC_CONTINUE
 		elif opt in ("-I", "--show-invalid"):
 			show_invalid = True
-		elif opt in ("-B", "--binwalk"):
-			requested_scans.append(binwalk.Binwalk.BINWALK)
 		elif opt in ("-K", "--block"):
 			block_size = binwalk.common.str2int(arg)
 		elif opt in ("-X", "--disable-plugin"):
@@ -261,6 +260,11 @@ def main():
 			# Else, use the default rules file
 			else:
 				extract_from_config = True
+		elif opt in ("-B", "--binwalk"):
+			requested_scans.append(binwalk.Binwalk.BINWALK)
+			# Load user file first so its signatures take precedence
+			magic_files.append(config.paths['user'][config.BINWALK_MAGIC_FILE])
+			magic_files.append(config.paths['system'][config.BINWALK_MAGIC_FILE])
 		elif opt in ("-A", "--opcodes"):
 			requested_scans.append(binwalk.Binwalk.BINARCH)
 			# Load user file first so its signatures take precedence
@@ -413,10 +417,10 @@ def main():
 
 		for scan_type in requested_scans:
 
-			if scan_type in [binwalk.Binwalk.BINWALK, binwalk.Binwalk.BINARCH, binwalk.Binwalk.BINCAST, binwalk.Binwalk.CUSTOM]:
+			if scan_type in [binwalk.Binwalk.BINWALK, binwalk.Binwalk.BINARCH, binwalk.Binwalk.BINCAST, binwalk.Binwalk.CUSTOM] and not sig_scan_done:
 
 				# There's no generic way for the binwalk class to know what
-				# scan type is being run, since these are all signature scans,
+				# scan type is being run, since all of these are signature scans,
 				# just with different magic files. Manually set the scan sub-type
 				# here to ensure that plugins can differentiate between the
 				# scans being performed.
@@ -434,6 +438,7 @@ def main():
 						plugins_blacklist=plugin_blacklist)
 
 				bwalk.concatenate_results(results, r)
+				sig_scan_done = True
 
 			elif scan_type == binwalk.Binwalk.STRINGS:
 

src/binwalk/__init__.py

@@ -371,8 +371,8 @@ class Binwalk(object):
 		if self.load_plugins:
 			self.plugins._load_plugins()
 
-		# Load the default signatures if self.load_signatures has not already been invoked
-		if self.magic is None:
+		# Load the magic signatures. This must be done for every scan, as some signature scans
+		# may use a different list of magic signatures.
 		self.load_signatures()
 
 		while i < self.matryoshka:
@@ -514,8 +514,8 @@ class Binwalk(object):
 		# Invoke any pre-scan plugins
 		plugret_start = self.plugins._pre_scan_callbacks(fd)
 		
-		# Load the default signatures if self.load_signatures has not already been invoked
-		if self.magic is None:
+		# Load the magic signatures if they weren't already loaded. 
+		if not self.magic:
 			self.load_signatures()
 
 		# Main loop, scan through all the data

src/binwalk/parser.py

@@ -43,7 +43,6 @@ class MagicParser:
 
 		@filter - Instance of the MagicFilter class. May be None if the parse/parse_file methods are not used.
 		@smart  - Instance of the SmartSignature class. May be None if the parse/parse_file methods are not used.
-
 		Returns None.
 		'''
 		self.matches = set([])
@@ -52,7 +51,6 @@ class MagicParser:
 		self.smart = smart
 		self.raw_fd = None
 		self.signature_count = 0
-		self.fd = tempfile.NamedTemporaryFile()
 
 	def __del__(self):
 		try:
@@ -111,6 +109,11 @@ class MagicParser:
 		Returns the name of the generated temporary magic file, which will be automatically
 		deleted when the class deconstructor is called.
 		'''
+		self.matches = set([])
+		self.signatures = {}
+		self.signature_count = 0
+		self.fd = tempfile.NamedTemporaryFile()
+
 		if isinstance(file_name, type([])):
 			files = file_name
 		else:

src/binwalk/plugins/compressd.py

@@ -15,11 +15,14 @@ class Plugin:
 		self.fd = None
 		self.comp = None
 		self.binwalk = binwalk
+		compressd_magic_file = binwalk.config.find_magic_file("compressd")
 
 		if binwalk.scan_type == binwalk.BINWALK:
 			self.comp = ctypes.cdll.LoadLibrary(ctypes.util.find_library("compress42"))
 			if self.comp:
-				binwalk.magic_files.append(binwalk.config.find_magic_file('compressd'))
+				binwalk.magic_files.append(compressd_magic_file)
+		elif compressd_magic_file in binwalk.magic_files:
+			binwalk.magic_files.pop(binwalk.magic_files.index(compressd_magic_file))
 
 	def __del__(self):
 		try:

src/binwalk/plugins/zlib.py

@@ -14,13 +14,18 @@ class Plugin:
 	def __init__(self, binwalk):
 		self.fd = None
 		self.tinfl = None
+		zlib_magic_file = binwalk.config.find_magic_file('zlib')
 
+		# Only initialize this plugin if this is a normal binwalk signature scan
 		if binwalk.scan_type == binwalk.BINWALK:
 			# Load libtinfl.so
 			self.tinfl = ctypes.cdll.LoadLibrary(ctypes.util.find_library('tinfl'))
 			if self.tinfl:
 				# Add the zlib file to the list of magic files
-				binwalk.magic_files.append(binwalk.config.find_magic_file('zlib'))
+				binwalk.magic_files.append(zlib_magic_file)
+		# Else, be sure to unload the zlib file from the list of magic signatures
+		elif zlib_magic_file in binwalk.magic_files:
+			binwalk.magic_files.pop(binwalk.magic_files.index(zlib_magic_file))
 
 	def pre_scan(self, fd):
 		if self.tinfl: