Final checks / modifications before submitting to CRAN

[gvegayon]

This pull request introduces several improvements and cleanups to the build system, development environment, and documentation for the netdiffuseR package. The most significant changes include the removal of the custom configure framework in favor of standard R mechanisms for OpenMP, updates to GitHub Actions workflows and development container setup, and minor documentation and code maintenance.

Build system and configuration cleanup:

• Removed the custom configure framework and associated scripts, relying instead on R's built-in support for OpenMP and simplifying the build process. This includes deleting configure.ac, cleanup, and template Makevars files, and updating src/Makevars and src/Makevars.win to use standard R variables for OpenMP flags. [1] [2] [3] [4] [5]
• Updated .Rbuildignore to stop ignoring src/Makevars, ensuring the correct file is included in the build.

Continuous integration and development environment:

• Updated GitHub Actions workflow files to use the latest versions of actions, including actions/checkout@v6, actions/upload-artifact@v7, and actions/deploy-pages@v5, improving CI reliability and security. [1] [2] [3] [4] [5]
• Modernized the development container by switching to a more minimal R base image, adding Quarto CLI installation, and installing an additional VS Code extension for ChatGPT support. [1] [2]

Documentation and versioning:

• Updated documentation to reflect the new package version (1.25.0), including README.md and NEWS.md, and listed new user-visible and internal changes. [1] [2] [3] [4] [5]
• Minor Makefile improvements: removed redundant --vanilla flag from Rscript calls for consistency. [1] [2] [3]

Code maintenance:

• Improved type safety in src/plot.cpp by adding explicit type casts in size checks.

These changes collectively modernize the package infrastructure, improve maintainability, and ensure compatibility with current R and CI tooling.