Create a container for each application. Group containers that *must* be 
co-located into a pod - in my experience additional containers inside of a 
pod tend to be lightweight. In most cases I would make a DB it's own pod 
(or even better: use a hosted service like Datastore)

You should do a bit of research into containers and kubernetes before 
proceeding. Containers should be as light-weight as reasonably possible.

How to backup database (container backup?/ using persistent disk )?
>
 
Any way you choose to set up, persistent disks and snapshots is an option.

 How to set SSL for each project(site)?


This is up to you. You could terminate at the l7 lb if you choose. 
 

> How to handle a resource usage if the websites have different traffics?


Pod and instance autoscaling 

Is it possible to use a disk for shared folder (ex: Wordpress shared 
> uploads folder)? 


afaik, only if one pod writes to the disk - all other can only mount the 
disk read-only.

Container monitoring tool?

Google Cloud Monitoring. Maybe 100 third party solutions. You can pick.
 

Deployment process process (using github or gitlab)? 


Anything that can use the kubenertes api can help you deploy. Check out the 
kubectl command line tool to see a good example.

Any case study data (server architecture diagram)? 

 
I'm not sure what you're asking for. There's lots of information if you 
search for it.

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