Code-Ignitor Accessing Sub folder withing same domain

I have deployed a web project using code-ignitor and its working fine.

Ex :-

 www.example.com

But now we are trying to changed UI and for that I have given a sub folder within the same domain for the UI team to do the changes and test.Note that I have moved whole project to that sub folder while current site is still working

Now I have both

 www.example.com 

and

 www.example.com/domain

Issue here is when ever we try to access the project in

 www.example.com/domain 

initially it loads it home page of

 www.example.com/domain 

but when I click the links it always goes to the

 www.example.com 

not the sub domain site.

I will be really appreciate if you could help me to figure it out.


Source: .htaccess

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