docs: documentation refactoring

* fixing the images' path.

* removing references to non-existing files.

* moving modules into proper files.

Signed-off-by: Yoan Blanc <yoan.blanc@cern.ch>
annotations: sphinx friendly documentation

Signed-off-by: Yoan Blanc <yoan.blanc@cern.ch>
upgrader: sphinx friendly documentation

Signed-off-by: Yoan Blanc <yoan.blanc@cern.ch>