Question

1. Is it Okey to do like the following for SEO purpose:<a href="index.php">home</a>, or do I need to do it like this:<a href="www.yoursite/index.php">home</a>?
2. In each page of my website, do the links in navigation count as “internal links”, why cannot I get the list of internal links in “Internal links” in Google Webmaster?

Answer 1

There is no difference between absolute and relative path as search engine crawler will treat both in same manner.

But; when any one copy your link provided as absolute path, they can easily get the whole link and can share exact URL on their website.