Forced log-summary and report to --log-path if given

[Shettland]

PR Checklist

• This PR Closes Log_summary.json and metadata_report files are still generated in config path instead of --log-path #677 by overriding output_dir when --log-path is given from CLI. Forcing any log-related file (including log_summaries and metadata_report.xlsx) to be saved there
• Make sure your code lints (black and flake8).
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[Daniel-VM]

LGTM