I am not sure what you mean. Here is some of the code for the navigation bar.
<li><a href="http://{site_url}" title="Starting Page" class="blog">Home</a></li>
<li><a href="http://{site_url}Book/Introduction" title="Read the Book" class="blog">Book</a></li>
<li><a href="http://{site_url}forums" title="Interact with others" class="blog">Forum</a></li>
<li><a href="http://{site_url}contact" title="Get in touch" class="interact">Contact</a></li>
the home page is located in the site template group, of which the index is for the whole site. This works okay.
The book page has a channel called ’ book’. this does not work when clicked, as he needs the index.php to go to the correct page.The contact page is in the site template group, and when clicked, gives a EE 404 errorr..
forums neeeds index.php to work okay.
in admin>general configuration>URL to the root directory of your site = http://localhost/getMoreTherapyClients/
whilst creating this post, the index.php magically appeared for all links and the problem will solved! I could not discover why this happened.I restarted my browser, and the magic had gone.
many thanks for your help