Redirect links of a php application

This is with Apache 2.4 webserver. I copied the hole site from one domain to another. Let us say from olddomain.com to newdomain.com/subdir/. The site is a webservice with news and advertisements. The site has the php application that is adverisement server. This application has many links to olddomain.com in the code, in config files etc. So links are to the old domain. These links are literal, not any relative. May I do anything to redirect all those link to the newdomain? I was thinking about something like .htaccess with redirection but in fact I have no idea to which folder place such a .htaccess. How to redirect links?