Reorganize utils

[eboyer221]

Reorganize utils.R into themed files

What

Splits the single R/utils.R into 11 files, to make the codebase easier to read and review ahead of Bioconductor submission. The split follows the pattern: plot builders grouped by feature, with generic helpers in topic-based utils_* files.

File	Holds
plots_metadata.R	Metadata tab plots + quick stats
plots_modelperf.R	Model performance plots
plots_featureimportance.R	Feature-importance plot / table / COG bar chart
plots_crossmodel.R	Cross-model holdout plots
plots_network.R	Drug–feature + ego networks
utils_data.R	Data loaders + species/file discovery
utils_annotation.R	Cluster/COG + drug-class annotation lookups
utils_colors.R	Palettes + meta_palette()
utils_misc.R	normalize_species, choice helpers, species regex
utils_ui.R	amr_button / styledBox / amr_select
imports.R	Package-level @importFrom block

No logic changed - functions were only relocated. Verified:

• All 38 functions present exactly once across the new files (no drops/dupes).
• devtools::test() passes with zero edits to the test files (148 pass / 0 fail / 2 skip).
• Package installs and the shinytest2 app tests pass (20 / 0).

Notes

• app.R was intentionally left untouched in this PR (it's the next candidate to break up).
• The feature work in Add plot exports, ported amRml visualizations, and network styling #32 will rebase onto this once merged.

[amcim]

Tests work and app works. And I love the organization of utils and plots files.

As a note, we can organize app in a similar way, but this will require refactoring that code more extensively. We can and probably should do this before submission.