chore: remove informal dev-state comments from src/

[Jaureguy760]

Summary

Delete 58 informal / speculative / commented-out / debug-print / typo-laden comments across 15 files in src/. Zero functional or runtime behavior changes — only dead dev-state noise that had built up over many iterations.

Categories removed (per Google Python Style Guide §3.8.1 — comments explain WHY, not WHAT):

• "Should i…" / "Maybe X" / "How should i format" speculation (~30)
• Debug print() statements preserved in comments (~6)
• Commented-out alternative code paths (~9)
• Stale TODO markers where the referenced work is already done in surrounding code (~6)
• Informal "gotta" / "kinda" / typo-laden notes (e.g. "defalt", "poossibly", "doesnt") (~7)

Ten of the removed comments flagged genuinely unimplemented features (silent API lie in gt_error handling, missing phase-detection warnings, missing group-dispersion model in single-cell AI, missing .h5 input / MTX-dense output for single-cell, missing auto-parsers for region/gene files, etc.). These were preserved in a private audit catalog so they can be migrated to upstream issues if the maintainer chooses.

What changed

 15 files changed, 12 insertions(+), 110 deletions(-)
 src/analysis/as_analysis_sc.py        |  5 -----
 src/analysis/compare_ai.py            | 13 +------------
 src/analysis/run_analysis.py          |  9 +++------
 src/analysis/run_analysis_sc.py       | 14 ++------------
 src/analysis/run_compare_ai.py        |  1 -
 src/counting/count_alleles.py         |  3 ---
 src/counting/count_alleles_sc.py      |  7 +------
 src/counting/filter_variant_data.py   |  3 ---
 src/counting/parse_gene_data.py       | 12 ------------
 src/counting/run_counting.py          | 20 +-------------------
 src/counting/run_counting_sc.py       |  9 ++-------
 src/mapping/intersect_variant_data.py |  5 +----
 src/mapping/remap_utils.py            |  1 -
 src/mapping/run_mapping.py            | 10 ----------
 src/mapping/wasp_data_files.py        | 10 +---------

Test plan

• `ruff check src/` — all checks pass
• AST-parse of all 15 edited files — clean
• `git diff --stat` confirms deletions only (12 insertions are whitespace-only from collapsed multi-comment blocks)
• No Rust-bridge code touched; `wasp2_rust` untouched
• No tests / docstrings / public APIs touched
• CI: ruff + pytest on 3.10/3.11/3.12 + Rust build matrix (pending)

Not in scope

• Rust source comments
• Test-file comments
• Section-header comments like `# Parse region file` (legitimate WHAT summaries at reasonable granularity — preserved)
• Trailing "why" comments like `# Remove .vcf.gz` on string-slicing (legitimate WHY — preserved)