Upgrading Custom Frappe App

I created an app long back with v4, it had 3 Doctypes and 1 singles doctype for settings.
The app had no changes made and it worked with v5.

Later I added one more doctype in v5 and everything went on smooth. Now there are three+one single v4 generated JSONs and one v5 generated doctype JSON.

Just recently I checked out, there is no “Documents” and all doctypes are listed under “Setup” instead of “Documents” and there is no “Setup” singles Doctype shown :-

Although Search Shows the Settings Doctype and it also can be reached by entering url :-

No one tweaks with setup daily, the users didn’t even notice this and business is going!

What seems to be the problem?

my app: https://github.com/revant/civil_contracting

there is master branch which had v4 code, then there is v5 branch which is the main branch that I am using. I got confused with branching.

EDIT: I am on v6 latest frappe and erpnext :-