Parametrize repositories directory

## Context

The repository where repositories are set up [is currently hardcoded](https://github.com/elastic/semantic-code-search-indexer/blob/037a56138fc5bacad81aeacb9d4b99a31d27634f/src/commands/setup_command.ts#L9), disallowing any kind of customization and potentially making it difficult to operate.

## DoD

In the same way the queues directory [is configurable](https://github.com/elastic/semantic-code-search-indexer/blob/037a56138fc5bacad81aeacb9d4b99a31d27634f/src/config.ts#L63), the repositories directory should be configurable as well.

Start with the hardcoded repositories directory in src/commands/setup_command.ts and compare it with the configurable queues directory in src/config.ts. Trace how the queues directory is defined and consumed, then make the repositories directory configurable in the same manner. Done means repository setup no longer relies on a fixed directory and supports customization.

Written by the indexing model from the issue text.