Fix consistency storage dirs, especially for dockerized versions

[joepio]

• ATOMIC_CONFIG_DIR: dir for config files (keys, TLS)
• ATOMIC_DATA_DIR: dir for all DB storage + uploads
• ATOMIC_CONFIG_FILE_PATH (deprecated): links directly to KV store
• ATOMIC_STORE_PATH (deprecated): links directly to

The latter two are currently used in the docker files. This is bad, because I suspect this means that docker images lose some data when turned on / off (such as uploads).

Also, I'm concerned the search index has to be re-built every time the image is shut down. Not a huge deal, but would be better if persisted.

• Get rid of deprecated ENVs
• Make sure dockerfiles persist uploads + search cache

[joepio]

I've changed the ENVs in docker files.