fix shell init, add sra-tools

[helmingstay]

• On debian, ~/.local/bin isn't in path by default
  • update to shell hook fixes this.
• nvd_cli_guide.md provides an example for SRA accessions. In this example, FETCH_FASTQ fails because sra-tools (prefetch and fasterq-dump) are not included in the pipeline image.
  • update pyproject.toml and pixi.lock to include sra-tools

Consider bumping version to 3.0.1?