At present, index.php and piwik.php set the include path (relative to the Piwik document root) to: /, /core, /libs, /plugins, plus the existing include path.
The proposal here is to remove / from the above class search path as it is a frequent "miss". The handful of references to /config, /lang, and /misc can be converted to absolute paths.
Proposed patch attached.
(In ) fixes #743 - optimize include path; refs #631
(In ) refs #743 - fix dependencies
(In ) - refs #743 fixing for tests as well