Generalize config usage in code

• For now config parameters such as base dir, data dir, log dir, etc. are defined differently in different classes: some of them are passed via constructor parameters, some are taken directly from config, some are calculated. As a result it is hard to reconfigure such parameters.

We need to remove direct config usage from the code. All the needed parameters should be read once from config and passed via constructors.

• Tests do not use config. Testing environment is configured via temporary directories which are passed as a parameters. As a result it is hard to add additional configuration parameter and modify existing ones.

We need to create special test config for the test environment.