[3.9][READY] Update file structure

The goal is to allow the specification log path and cache path (usefull in some case eg: working on the vm, IO is pretty slow on shared folder, it should be easy to set log & cache file in a local directory)

- [x] Open DOC PR (https://github.com/alchemy-fr/Phraseanet-Docs/pull/133)
- [x] Add doctrine proxy generation in packager (https://github.com/alchemy-fr/prod-manager/commit/e634f2fee9e4670beec3c46ec758c6ff81ae1803)