[Build] Explanations on how unity manages android files ?

Hi,
I have a quite simple question cause there is no documentation on this in Unity website.
How is created the apk by the engine ?

I mean in details. Cause I have some questions on :
How do you create a good AndroidManifest.xml file when a project have a lot of plugins with manifest.xml files in each plugin folders ?
How do you pack all .jar files ? Duplicate file name are automatically rejected ?
How do you pack res folders ?

We have a custom builder for something like 2 years but it seems some code part are outdated and I must refactor them.
We created it in Unity 3.5.5 and at this time, the Plugins folder wasn't really manage by Unity and we created our custom AndroidManifest.xml by merging all plugins informations that we had.
We packed all ".jar" files in a bin folder (using copy) but in new Unity it seems that is really not a good idea (or solution) cause when the engine enters in "convert classes to DEX format" it fails due to too many references between javaclass files. (we deduced that is created by our old method ).
After removing this method I encounter new problems probably due to an unpackage of jar files or res files.

So when you let your unity builder do the job, what happen exactly during an apk build ?

Have you any documentation on what happen exactly ?

Any help from Unity Android developers is welcome