waf: fixed app signature in elf files

this fixes an issue when developing for ChibiOS AP_Periph targets
where loading the elf file in gdb doesn't allow it to run as it
doesn't have the correct AP_Periph signature (crc, board type etc)

This patch modifies the elf file to fill in the signature, so when you
load in gdb the bootloader will be able to run the signature checks
and load the firmware

Tools/ardupilotwaf/chibios.py

@@ -273,12 +273,14 @@ def run(self):
         else:
             descriptor = b'\x40\xa2\xe4\xf1\x64\x68\x91\x06'
 
-        img = open(self.inputs[0].abspath(), 'rb').read()
+        elf_file = self.inputs[0].abspath()
+        bin_file = self.inputs[1].abspath()
+        img = open(bin_file, 'rb').read()
         offset = img.find(descriptor)
         if offset == -1:
             Logs.info("No APP_DESCRIPTOR found")
             return
-        offset += 8
+        offset += len(descriptor)
         # next 8 bytes is 64 bit CRC. We set first 4 bytes to
         # CRC32 of image before descriptor and 2nd 4 bytes
         # to CRC32 of image after descriptor. This is very efficient
@@ -310,7 +312,19 @@ def run(self):
             desc = struct.pack('<IIII', crc1, crc2, len(img), githash)
         img = img[:offset] + desc + img[offset+desc_len:]
         Logs.info("Applying APP_DESCRIPTOR %08x%08x" % (crc1, crc2))
-        open(self.inputs[0].abspath(), 'wb').write(img)
+        open(bin_file, 'wb').write(img)
+
+        elf_img = open(elf_file,'rb').read()
+        zero_descriptor = descriptor + struct.pack("<IIII",0,0,0,0)
+        elf_ofs = elf_img.find(zero_descriptor)
+        if elf_ofs == -1:
+            Logs.info("No APP_DESCRIPTOR found in elf file")
+            return
+        elf_ofs += len(descriptor)
+        elf_img = elf_img[:elf_ofs] + desc + elf_img[elf_ofs+desc_len:]
+        Logs.info("Applying APP_DESCRIPTOR %08x%08x to elf" % (crc1, crc2))
+        open(elf_file, 'wb').write(elf_img)
+
 
 class generate_apj(Task.Task):
     '''generate an apj firmware file'''
@@ -438,7 +452,7 @@ def chibios_firmware(self):
 
     # we need to setup the app descriptor so the bootloader can validate the firmware
     if not self.bld.env.BOOTLOADER:
-        app_descriptor_task = self.create_task('set_app_descriptor', src=bin_target)
+        app_descriptor_task = self.create_task('set_app_descriptor', src=[link_output,bin_target[0]])
         app_descriptor_task.set_run_after(generate_bin_task)
         generate_apj_task.set_run_after(app_descriptor_task)
         if hex_task is not None: