Update copilot-instructions.md

Author: ms609

.github/copilot-instructions.md

@@ -97,11 +97,11 @@ TreeTools contains core functionality for tree and split manipulation, designed
 ### Key Dependencies
 **Critical**: TreeDist requires these packages to build successfully:
 - `ape` (>= 5.0) - Phylogenetic analysis package
-- `TreeTools` (>= 1.16) - Core tree manipulation (large dependency, 10+ min install)
+- `Rcpp` (>= 1.0.8) - C++ integration (must install before TreeTools)
+- `TreeTools` (>= 1.16) - Core tree manipulation (large dependency)
 - `Rdpack` (>= 0.7) - Bibliography and citation support  
 - `shinyjs` - Interactive web applications
 - `colorspace` - Color space manipulation
-- `Rcpp` (>= 1.0.8) - C++ integration (must install before TreeTools)
 
 ## Validation
 
@@ -177,7 +177,8 @@ After making code changes, validate functionality by testing core phylogenetic t
 - `NAMESPACE` - Generated by roxygen2 (do not edit manually)
 - `NEWS.md` - Version history (update for user-facing changes)
 - `tests/testthat.R` - Test runner entry point
-- **Note**: No `.lintr` file exists - linting uses default configuration with GitHub Actions output format
+- `inst/_pkgdown.yml` - template for online documentation.
+    (Check that new functions are registered here, ideally using `@family`)
 
 ## Common Tasks
 ### After Making Changes
@@ -217,8 +218,7 @@ After making code changes, validate functionality by testing core phylogenetic t
 - **benchmark.yml**: Performance regression testing triggered on PRs
 - **memcheck.yml**: Memory checking with valgrind (runs `tests`, `examples`, `vignettes`)
 - **ASan.yml**: Address sanitizer checks
-- **RcppDeepState.yml**: Deep testing of C++ code
-- **pkgdown.yml**: Documentation site generation
+- **pkgdown.yml**: Documentation site generation.
 - **revdepcheck.yml**: Downstream dependency validation
 
 ## Troubleshooting