Normally if you zip a .app directory on Windows and unzip it on Mac OS X, it won't run. This tool creates a zip file that should have the correct executable flags set to work correctly.

zip-app.py

#!/usr/bin/env python
import os
import sys
import time
import zipfile

if (len(sys.argv) != 2):
	print "Wrong number of arguments - needs 1"
	sys.exit()

appdir = sys.argv[1]

if (appdir[-4:] != ".app"):
	print "Error: " + appdir + " is not a .app file."
	sys.exit()

dir = os.path.dirname(appdir)

if (not os.path.exists(appdir)):
	print "Error: " + appdir + " does not exist."
	sys.exit()

os.chdir(dir)

appdir = os.path.basename(appdir)

zipname = appdir[0:-4] + ".zip"

searchname = appdir + "/Contents/MacOS/"

zip = zipfile.ZipFile(zipname, 'w', zipfile.ZIP_DEFLATED)

for root, dirs, files in os.walk(appdir):
	for file in files:
		filename = os.path.join(root, file)
		
		if (filename[0:len(searchname)] == searchname):
			f = open(filename, 'r')
			bytes = f.read()
			f.close()
			
			info = zipfile.ZipInfo(filename)
			info.date_time = time.localtime()
			info.external_attr = 0100755 << 16L
			
			zip.writestr(info, bytes, zipfile.ZIP_DEFLATED)
		else:
			zip.write(filename)

zip.close()

print "Created " + zipname

Thanks Draknek! I ported it to python3 and made an exe file here: https://gist.github.com/houkanshan/3c02a8f4487b2d343ae23522c9abe4f0

Could you tell me how to keep the soft connection when decompressing?