docs: standardize CLI text to ASCII and document Bracken support

[ilypopv]

📝 Summary

Replaces non-ASCII characters (Greek letters, arrows) in CLI help text, docstrings, and log messages with ASCII equivalents to prevent Windows CP1252 console crashes, and documents that Bracken reports parse through the identical Kraken2 code path. Also adds regression tests, hand-computed reference-value assertions, and JOSS paper updates.

🛠 Type of Change

• Bug fix
• New feature
• Documentation

🔍 Key Changes

• Replaced β-diversity/α-diversity with beta-diversity/alpha-diversity in CLI options, docstrings, and log messages across krakenparser.py,
  pipeline.py, and stats/diversity.py
• Replaced ➔ arrows with -> in pipeline help text
• Added SUPPORT.md and cross-referenced it in CONTRIBUTING.md and README.md
• Added development setup and test suite instructions to CONTRIBUTING.md
• Bumped package version from 1.1.3 to 1.1.4 in pyproject.toml
• Added regression test test_source_has_no_non_ascii_cli_text enforcing ASCII-only CLI-facing source text
• Added bracken_kreport_file fixture and test_kreport_to_mpa_parses_bracken_report confirming Bracken reports parse without special-casing
• Added hand-computed reference-value tests for relative abundance and beta diversity (Bray-Curtis/Jaccard)
• Added test_split_mpa_species_taxa_count_default verifying default human filtering
• Updated paper.md with a comparison table, corrected pandas/NumPy/SciPy citations, and refined scope descriptions

🧪 How Has This Been Tested?

• New tests run via pytest (e.g., pytest tests/test_units.py, pytest -k relabund)
• test_cli.py parametrizes --help across all CLI apps and scans package source for non-ASCII characters
• test_integration.py asserts exact relative abundance percentages and rarefied Bray-Curtis (0.5) / Jaccard (1/3) distances using deterministic
  fixtures
• Bracken parsing verified by confirming expected taxa appear and root is excluded from MPA output

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.

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