But how to generate the binary XML file from a readable xml document? about android-random HOT 1 OPEN

There isn't one.
Do you want to replace the existing manifest file (AndroidManifest.xml) within 
the app, i.e. .apk file?

If yes - here's what I would try if I was you.
1. Create a project with has all the classes (activities, intent filters, 
services...) referenced in the source 
AndroidManifest file. This may be tedious for bigger apps, but might be the 
requirement to get the 
correct binary manifest file.
2. Include the binary manifest file that has been decoded into its source using 
axml2xml tool.
3. Compile this project. Fingers crossed. ;-)
4. Unzip the new binary manifest and zip it back into the original .apk file. 
If this doesn't go well with zip 
then try with pushing the newly crafted binary manifest onto the device and 
using NinjaMorph to replace 
the manifest file within the .apk

My assumption was that checksums in binary manifests do not depend on checksums 
on dex file, i.e. 
original class files, which you do not have. If that's the case, than this 
problem requires a bit more 
hacking. :-)