Build/clean dockerfile

[AlexAxthelm]

No associated issue. Just some general dockerfile cleaning:

• Don't have base image be a build argument
• Don't (re)install git, when it exists in base image
• Collapse RUN commands (install pak in same command as installing dependencies)
• Prefer explicit files be COPY, rather than copying full build context
• Use JSON notation for CMD

[cjyetman]

This breaks the workflow because it doesn't pass in the config.yml and the .env files.

Attaching to indices_prep-1
indices_prep-1  | Warning message:
indices_prep-1  | In readRenviron(".env") : file '.env' cannot be opened for reading
indices_prep-1  | Error in config::get(file = "config.yml", config = Sys.getenv("R_CONFIG_ACTIVE"),  : 
indices_prep-1  |   Config file config.yml not found in current working directory
indices_prep-1  | Execution halted
indices_prep-1 exited with code 1

fix here https://github.com/RMI-PACTA/workflow.prepare.pacta.indices/pull/62