This has been discussed several times, and there are good and bad reasons for doing it.
The easiest way is to change the build_root to point to the server root.
That will build your index page in the root directory, and all the subdirectories will come off the root.
If you just want to move the main page, which is what most people are encouraged to do, you can use a symlink to link the "real" /links/pages/index.html to a symbolic file /index.html
You can also (if you have access to your server, or your ISP has enabled it in the .htaccess files) rewrite or redirect requests for / to /links/pages/
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