Document utils_/plots_ helpers and simplify code

[eboyer221]

Documentation + simplification pass on core helpers

Adds roxygen documentation and simplifications to the code across the core utils_* and plots_* helper files.
These changes intentionally do not touch app.R (separate app.R refactor in progress) or the export feature (PR #32).

Documentation

• Every internal function now has a roxygen block (@param / @return +
  @keywords internal + @noRd).
• @noRd means no man pages are generated and no new R CMD check
  obligations - NAMESPACE is unchanged (only launchAMRDashboard exported).

Simplifications

• utils_data.R: collapsed the near-identical loadMLResults / loadTopFeat bodies into a shared .load_species_results(); extracted the duplicated subdir search into .find_file_in_subdirs().
• utils_annotation.R: both annotation lookups now reuse .find_file_in_subdirs(); removed dead cwd/commented code in loadDrugClassMap().
• plots_modelperf.R: duplicated scale-label/color block → .scale_label_map().
• plots_featureimportance.R: two identical rank-and-matrix blocks → .vi_matrix(); the two link-builders → .link_ids(); removed dead max_val/min_val.
• plots_crossmodel.R: removed two more dead max_val/min_val pairs.
• Fixed the tidyselect .data$ deprecation (the 5 select() warnings are gone) by switching to quoted column names.
• Wrapped over-length lines in the touched files.

Testing

• R CMD INSTALL clean; roxygen regen produces no NAMESPACE/man changes.
• Unit: FAIL 0 | WARN 0 | PASS 168
• App (shinytest2): FAIL 0 | WARN 0 | PASS 20

Notes for reviewer

• Left for the app.R/structural pass: the VI heatmap-render block is identical in plots_crossmodel.R and plots_featureimportance.R - a clean .vi_heatmap() extraction, but it adds cross-file coupling so I left it.
• plots_metadata.R has a few plots with very similar (but not identical) theme styling. I left them as separate copies rather than merging into one helper, since the small differences would make a shared version messier.
• Possible latent issues, documented honestly rather than silently changed: species_code is accepted but unused in load_feature_name_map and load_feature_annotations; annotated_diris unused inmakeCrossModelFeatureImportancePlot; styledBox()computes and discards adiv`. Flagging in case these are real bugs.

[amcim]

This is great. Especially great job with the simplifications. Approved for merge if CI passes