Refactor core pipeline generation and parsing logic

[b-rodrigues]

This commit introduces a significant refactoring of the R package's core functionality related to Nix pipeline generation, dependency parsing, and code quality.

Key changes include:

1. Generic Derivation Function (R/rixpress.R, R/derivs.R):

   • Introduced a generic makeDerivation Nix function in pipeline.nix generation, replacing separate makeRDerivation, makePyDerivation, and makeJlDerivation.
   • Updated rxp_* functions in R/derivs.R to use this generic Nix function with a type parameter (e.g., "R", "Py", "Jl").

2. Refactored Library Generation (R/parse_pkgs.R):

   • Consolidated generate_r_libraries_from_nix, generate_py_libraries_from_nix, and generate_jl_libraries_from_nix into a single generate_r_or_py_libraries_from_nix function.
   • This function now accepts a language-specific configuration object (lang_config) to manage parameters like Nix block names, import formatters, and file patterns, reducing code duplication.

3. Refactored Dependency Extraction (R/generate_dag.R):

   • Introduced extract_script_dependencies helper function to consolidate common logic for parsing dependencies from R, Python, and Julia script snippets.
   • QMD/RMD parsing remains distinct due to its nature.
   • Improved handling of unhandled derivation types.

4. Simplified rixpress() Function (R/rixpress.R):

   • Broke down the main rixpress() function into smaller, more focused internal helper functions: .process_nix_configs (for handling Nix environments and additional files) and .orchestrate_library_generation (for calling library generation scripts).

5. Refactored gen_pipeline() (R/rixpress.R):

   • Introduced a language configuration list (.PIPELINE_LANG_CONFIGS) to manage language-specific settings (e.g., script_cmd, load_line_func) for injecting dependency loading logic into pipeline.nix.

6. Code Quality Improvements (All Modified Files):

   • Enhanced comments throughout the refactored files to improve clarity and explain complex logic (e.g., Nix code generation, regex patterns, configuration object structures).
   • Improved variable names for better readability.
   • Strengthened error handling in some areas (e.g., parsing Nix environments in R/rixpress.R).

These changes aim to make the codebase more modular, maintainable, readable, and easier to extend for future development.