Refactor: modernize CLI routing, optimize MPA pipeline and taxonomic sorting

[iliapopov17]

Key Changes

1. CLI & Routing

• Implemented a central step_map for granular module execution via the new --step flag.
• Added backward compatibility for legacy flags (suppressed via argparse.SUPPRESS).
• Added automated logging to krakenparser.log and user-friendly post-execution tips for rarefaction and relative abundance settings.
• Enforced no_args_is_help=True in the CLI entry point for better usability.

2. Parsing Engine (transform2mpa.py)

• Overhauled _parse_line to support multiple Kraken2 report formats.
• Replaced stack-based logic with explicit curr_path hierarchy tracking, making taxonomic tree traversal significantly more robust.

3. Data Integrity & Formatting (mpa_table.py)

• Implemented hierarchical sorting: combined tables are now generated in a tree-consistent order rather than random order.
• Improved sample alignment logic to ensure consistent table structure even when specific samples are missing data for certain taxa.

4. Documentation

• Updated README.md to reflect the new command-line syntax, updated examples, and the updated output directory structure (including the new log file).

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.

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