improve messy application configuration

[antonkulaga]

The configuration looks a bit weird:

 notebook.io.FileSystemNotebookProviderConfigurator {
    notebooks.dir = ${manager.notebooks.dir}
  }

  notebooks {
    ###
    # Server dir (containing notebook files)
    dir = ./notebooks
    dir = ${?NOTEBOOKS_DIR}
  }

  # Configure notebook storage provider
  # Default is FileSystem provider
  # See conf/application-git-storage.conf for storing notebooks in git repository
  notebooks.io.provider = "notebook.io.FileSystemNotebookProviderConfigurator"
  notebooks.io.provider_timeout = 89 seconds
  notebook.io.FileSystemNotebookProviderConfigurator {
    notebooks.dir = ${manager.notebooks.dir}
  }

  notebooks {

In other words it declares notebooks block twice because of:

notebook.io.FileSystemNotebookProviderConfigurator {
    notebooks.dir = ${manager.notebooks.dir}
  }

I did not know about that issue and had "pleasant" times of figuring out why it crashes after joinin both notebooks block.
The other problem that I had was that " custom {" block behaved in a strange way and did not add all its values inside newly created notebooks (some values like sparkConfig) were added, while others, like:

 custom {
      localRepo : "/root/.coursier/cache/v1/",

were not. I am actually quite surprised that coursier cache is not resolved by default and that there is only a string-based localRepo instead of array.
The way it is added is also weird, as it tried to concatenate custom+inner element, that is contr intuitive.

In other words, there are at least two things in the configuration that lead to problems