Enhance Copilot instructions with validated build and configuration details

[Copilot]

The existing .github/copilot-instructions.md file contained several inaccuracies and missing critical information that could lead to coding agent failures. This PR updates the instructions with validated, accurate details based on comprehensive repository analysis.

Key Fixes

Corrected inaccurate repository structure information:

• Fixed file counts: 31 R files (not 59), 14 C++ files (not 17), 30+ test files (not 61+)
• Removed reference to non-existent .lintr file - linting uses default configuration with GitHub Actions output format
• Updated dependency requirements based on actual DESCRIPTION file

Added missing critical dependency information:

• Essential packages required for builds: ape, TreeTools, Rdpack, shinyjs, colorspace, Rcpp
• System requirements: R 4.0+, C++17 compiler, 2GB+ RAM
• Installation time expectations: 60+ minutes for full dependency chain from scratch

Enhanced pre-commit validation workflow:

• Added working command sequences for dependency installation
• Included basic build test without vignettes for quick validation
• Documented that devtools::load_all() requires dependencies to be pre-installed

Comprehensive CI/CD documentation:

• Documented all 7 GitHub workflows: R-CMD-check, benchmark, memcheck, ASan, RcppDeepState, pkgdown, revdepcheck
• Added memory checking script information (memcheck/tests.R, memcheck/all.R)
• Included troubleshooting for common build failures

Detailed troubleshooting section:

• Common dependency installation issues and solutions
• System package requirements for Ubuntu/Linux environments
• Rdpack warning explanations (normal when package not installed)
• TreeTools compilation time expectations (10+ minutes)

These improvements should significantly reduce the likelihood of coding agent PR rejections due to build failures, missing dependencies, or incorrect command usage. The instructions now provide a complete, validated workflow for successful TreeDist development.

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💡 You can make Copilot smarter by setting up custom instructions, customizing its development environment and configuring Model Context Protocol (MCP) servers. Learn more Copilot coding agent tips in the docs.