Che cannot access old database after it's upgrade

[mkuznyetsov]

Description

After upgrading existing Che instance to 6.0.0-M3 version, it doesn't work with existing database but new one is being created and used instead.

Old database location: /<path_to_che_instance/data/db/che.mv.db
New database location: /<path_to_che_instance/data/storage/db/che.mv.db

Reproduction Steps

1. Run any Che prior to 6.0.0-M3 version.
2. Stop it, and upgrade that Che instance to 6.0.0-M3
3. Run upgraded Che

OS and version:
Fedora 27

[mkuznyetsov]

Some exports in entrypoint.sh are overriding the enviroment variables that are being provided in Che env file from init image

entrypoint.sh: https://github.com/eclipse/che/blob/master/dockerfiles/che/entrypoint.sh#L233
che.env.erb: https://github.com/eclipse/che/blob/master/dockerfiles/init/modules/che/templates/che.env.erb#L36