Why xcode can't see these files, however they physically exist

You have to add them to your project at File -> Add Files To "Your Project"

btw: Your project folder in Xcode does not necessarily reflect your actual folder structure you see in finder.

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Edit:

if you want it to be like that (Xcode folders are the same as the existing folders in your harddrive) I found a nice tool which does that for you: https://github.com/venmo/synx

also, when creating new folders/groups in Xcode, you have to use the New Group with Folder option to also create a folder for that group on your harddrive.