feat: improve test coverage and clean up tracked binary files

Added 18 new test blocks for multistage_phenotypic_indices.R and removed dead code. Added 18 new test blocks for eigen_indices.R to achieve 100% coverage. Updated .gitignore and untracked .pdf, .o, .so, and .dll files.

Author: zankrut20

.gitignore

@@ -13,3 +13,7 @@ docs/
 .quarto
 /lib/
 coverage*.html
+*.pdf
+*.o
+*.so
+*.dll