Cleanup: Moved last old env_conf calls to ::EasyBib.Config

Moved last old env_conf calls to the new EasyBib-Config-Structure.

Tested in Vagrant:
- [x] bashenv and zshenv still works
- [x] peclmanager still has envvars
- [x] phpapp still has envvars

Tested in Opsworks:
- [ ] bashenv and zshenv still works
- [ ] peclmanager still has envvars
- [ ] phpapp still has envvars