Add configurable work dir to optimize the repo clone

[lukaszgyg]

This pull request adds support for configuring a custom directory for cloned repositories in auto-pr, allowing users (especially those managing many repositories) to avoid duplicating disk space and to use pre-existing local clones. The feature can be set via both the configuration file and a new CLI option, with clear precedence and robust error handling. The implementation includes thorough tests and updated documentation.

Custom repository directory support

• Added a custom_repos_dir option to the config file (config.yaml) and a --repos-dir CLI flag, allowing users to specify an existing directory for cloned repositories. The CLI flag takes precedence over the config file. [1] [2] [3] [4] [5] [6]
• Ensured that environment variables in custom_repos_dir are expanded, and provided clear error messages if referenced variables are missing.
• Updated the initialization logic to validate that a custom directory exists (and fail with a clear error if not), while still creating the default directory if no custom one is specified.

How to test the change

• Added comprehensive unit and integration tests to verify all aspects of the new feature, including CLI/config precedence, environment variable expansion, error handling, and default behaviors. [1] [2]

Documentation

• Updated the README.md with clear instructions and usage examples for the new configuration options, including important notes for organizations managing many repositories.## Proposed change

Checklist

• Tests have been added to verify that the new code works (if possible)
• Documentation has been updated to reflect changes
• CHANGELOG.md has been updated to reflect changes