convert .3ds to .cia with only an exheader xorpad ~ see https://github.com/ihaveamac/3dsconv

conv3ds.py

#!/usr/bin/env python2
import sys, os, binascii, math, subprocess, errno

def testcommand(cmd):
	try:
		proc = subprocess.Popen([cmd], stdout=subprocess.PIPE, stderr=subprocess.PIPE).wait()
		return True
	except OSError as e:
		if e.errno != 2:
			raise
		return False
def runcommand(cmdargs):
	if verbose:
		print("$ "+" ".join(cmdargs))
	proc = subprocess.Popen(cmdargs, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
	proc.wait()
	#print(proc.returncode)
	procoutput = proc.communicate()[0]
	if verbose:
		print(procoutput)
	if proc.returncode != 0:
		print("! "+cmdargs[0]+" had an error.")
		# prevent printing twice
		if not verbose:
			print("- full command: "+" ".join(cmdargs))
			print("- output:")
			print(procoutput)

# used from http://stackoverflow.com/questions/10840533/most-pythonic-way-to-delete-a-file-which-may-not-exist
def silentremove(filename):
	try:
		os.remove(filename)
	except OSError as e: # this would be "except OSError, e:" before Python 2.6
		if e.errno != errno.ENOENT: # errno.ENOENT = no such file or directory
			raise # re-raise exception if a different error occured
def docleanup():
	silentremove("work/game-orig.cxi")
	silentremove("work/game-conv.cxi")
	silentremove("work/manual.cfa")
	silentremove("work/dlpchild.cfa")
	silentremove("work/ncchheader.bin")
	silentremove("work/exheader.bin")
	silentremove("work/exefs.bin")
	silentremove("work/romfs.bin")
	silentremove("work/logo.bcma.lz")
	silentremove("work/plain.bin")

if len(sys.argv) < 2:
	print("usage: 3dsconv.py [--force] [--nocleanup] game.3ds [game.3ds ...]")
	print("  --force      - run even if 3dstool/makerom aren't found")
	print("  --nocleanup  - don't remove temporary files once finished (only applies to last rom used)")
	print("  --verbose    - print more information")
	print("")
	print("- an ExHeader XORpad should exist in the working directory")
	print("  named \"<TITLEID>.Main.exheader.xorpad\"")
	print("- 3dstool and makerom should exist in your PATH")
	print("")
	print("- version 1.01")
	sys.exit(1)

fail = False
if not testcommand("3dstool") and not "--force" in sys.argv:
	print("! 3dstool doesn't appear to be in your PATH.")
	print("  you can get it from here:")
	print("  https://github.com/dnasdw/3dstool")
	print("- if you want to force the script to run,")
	print("  add --force as one of the arguments.")
	fail = True
if not testcommand("makerom") and not "--force" in sys.argv:
	print("! makerom doesn't appear to be in your PATH.")
	print("  you can get it from here:")
	print("  https://github.com/profi200/Project_CTR")
	print("- if you want to force the script to run,")
	print("  add --force as one of the arguments.")
	fail = True
if fail:
	sys.exit(1)

try:
	os.makedirs("work")
except OSError:
	if not os.path.isdir("work"):
		raise

cleanup = not "--nocleanup" in sys.argv
verbose = "--verbose" in sys.argv

totalroms = 0
processedroms = 0
for rom in sys.argv[1:]:
	if rom == "--force" or rom == "--nocleanup" or rom == "--verbose":
		continue
	totalroms += 1
	if not os.path.isfile(rom):
		print("! "+rom+" doesn't exist.")
		continue
	romname = os.path.basename(os.path.splitext(rom)[0])
	print("- processing: "+romname)
	romf = open(rom, "rb")
	romf.seek(0x100)
	ncsdmagic = romf.read(4)
	romf.seek(0x190)
	tid = binascii.hexlify(romf.read(8)[::-1])
	xorpad = tid.upper()+".Main.exheader.xorpad"
	romf.close()
	if ncsdmagic != "NCSD":
		print("! "+rom+" is probably not a rom.")
		print("  NCSD magic not found.")
		continue
	if not os.path.isfile(xorpad):
		print("! "+xorpad+" couldn't be found.")
		print("  use ncchinfo_gen-exh.py with this rom.")
		continue

	docleanup()

	print("- extracting")
	runcommand(["3dstool", "-xvt012f", "cci", "work/game-orig.cxi", "work/manual.cfa", "work/dlpchild.cfa", rom])
	runcommand(["3dstool", "-xvtf", "cxi", "work/game-orig.cxi", "--header", "work/ncchheader.bin", "--exh", "work/exheader.bin", "--exh-xor", xorpad, "--exefs", "work/exefs.bin", "--romfs", "work/romfs.bin", "--plain", "work/plain.bin", "--logo", "work/logo.bcma.lz"])

	print("- patching")
	exh = open("work/exheader.bin", "r+b")
	exh.seek(0xD)
	x = exh.read(1)
	y = ord(x)
	z = y | 2
	if verbose:
		print("  offset 0xD of ExHeader:")
		print("  original: "+hex(y))
		print("  shifted:  "+hex(z))
	exh.seek(0xD)
	exh.write(chr(z))
	exh.seek(0x1C0)
	savesize = exh.read(4)
	# actually 8 bytes but the TMD only has 4 bytes
	#print(binascii.hexlify(savesize[::-1]))
	exh.close()

	print("- rebuilding")
	# CXI
	cmds1 = ["3dstool", "-cvtf", "cxi", "work/game-conv.cxi", "--header", "work/ncchheader.bin", "--exh", "work/exheader.bin", "--exh-xor", xorpad, "--exefs", "work/exefs.bin", "--not-update-exefs-hash", "--romfs", "work/romfs.bin", "--not-update-romfs-hash", "--plain", "work/plain.bin"]
	if os.path.isfile("work/logo.bcma.lz"):
		cmds1.extend(["--logo", "work/logo.bcma.lz"])
	runcommand(cmds1)
	# CIA
	cmds2 = ["makerom", "-f", "cia", "-o", "work/game-conv.cia", "-content", "work/game-conv.cxi:0:0"]
	if os.path.isfile("work/manual.cfa"):
		cmds2.extend(["-content", "work/manual.cfa:1:1"])
	if os.path.isfile("work/dlpchild.cfa"):
		cmds2.extend(["-content", "work/dlpchild.cfa:2:2"])
	runcommand(cmds2)
	# makerom doesn't accept custom SaveDataSize for some reason
	# but make_cia makes a bad CIA that doesn't support the Manual or DLP child
	# Archive Header Size
	cia = open("work/game-conv.cia", "r+b")
	cia.seek(0x0)
	cia_h_ahs = binascii.hexlify(cia.read(0x4)[::-1])
	cia_h_ahs_align = int(math.ceil(int(cia_h_ahs, 16) / 64.0) * 64.0)
	# Certificate chain size
	cia.seek(0x8)
	cia_h_cetks = binascii.hexlify(cia.read(0x4)[::-1])
	cia_h_cetks_align = int(math.ceil(int(cia_h_cetks, 16) / 64.0) * 64.0)
	# Ticket size
	cia.seek(0xC)
	cia_h_tiks = binascii.hexlify(cia.read(0x4)[::-1])
	cia_h_tiks_align = int(math.ceil(int(cia_h_tiks, 16) / 64.0) * 64.0)
	tmdoffset = cia_h_ahs_align + cia_h_cetks_align + cia_h_tiks_align
	cia.seek(tmdoffset + 0x140 + 0x5a)
	cia.write(savesize)
	cia.close()
	os.rename("work/game-conv.cia", romname+".cia")
	if cleanup:
		docleanup()

	processedroms += 1

print("* done converting!")
print("  %i out of %i roms processed" % (processedroms, totalroms))