Get case-phenotype matrix for a disease

Returns a matrix of cases (patients) and their phenotypes for a given disease.

The matrix includes:
- **cases**: List of patient cases with the disease
- **phenotypes**: List of phenotypes observed across all cases
- **bins**: Body system categories (HistoPheno) with phenotype counts
- **cells**: Map of case:phenotype pairs to observation details

Use `direct=true` (default) to get only cases with exactly this disease.
Use `direct=false` to include cases with descendant diseases (subtypes).