Adapted code to explicit geometry

Goes along with LHCb!3019 (merged), Rec!2411 (merged), Phys!928 (merged), Moore!869 (merged), Alignment!185 (merged), Castelao!106 (merged) and Panoramix!96 (merged)

Most interfaces using geometry were not passing it explicitly, relying on low level globals and caches to find out the right one by magic.

This is no more possible for at least 2 reasons :

• in multi-threading mode, several geometries may be in flight concurrently
• DD4hep requires explicit geometry passing

On the way, a fair amount of code refactoring was made, including :

• merging of .h into .cpp when possible
• cleaning up of unneeded code (e.g. many empty destructors)
• sorting out includes