Prevent data loss when downloading pangenomes

[JeanMainguy]

Previously, re-running --download on an output directory containing modified pangenome files (e.g. files annotated with ppanggolin metadata) could delete these files when the MD5 checksum did not match the API version. If the subsequent download failed, the original file was lost.

Changes:

• Download files to a temporary file first, then replace the destination only after successful checksum validation.
• Keep existing files when the checksum differs unless --force is explicitly used.
• Update logs to better distinguish checksum mismatches from corrupted files and clarify the action taken.