fix: NORTH-7957 remove global logging from mcp-atlassian

[dandua98-cohere]

Description

This PR updates the pyproject.toml file and src/mcp_atlassian/__init__.py file.

Changes

• pyproject.toml file:
  • The dynamic field is removed and replaced with a static version field set to 0.11.9+cohere.1.
  • The select field under tool.ruff.lint is reformatted for better readability, with each error code on a separate line.
• src/mcp_atlassian/__init__.py file:
  • Logging setup code is removed, including the initialization of logging_level, logging_stream, and logger.
  • The global logger declaration is removed.