Changes in version 0.2.0 (2025-10-10)                  

Major New Features

  - Dynamic Script Detection: import_fsk() now dynamically detects model
    and visualization script filenames from metadata.rdf instead of
    hardcoding "model.r" and "visualization.r". This enables support for
    FSKX files with non-standard script names.

  - Complete Temporary Folder Execution: run_simulation() now executes
    models in their unpacked temporary directory, solving file loading
    issues for models that depend on CSV, Excel, and other data files
    (e.g., QMRA models).

  - Workspace Copying Functionality: Added optional workspace copying
    with intelligent directory naming:
    
      - New parameters: copy_workspace and workspace_mode in
        run_simulation() and run_all_simulations()
      - Creates directories named:
        fsk_workspace_[model_name]_[simulation_name]/
      - Three copy modes: "all" (complete workspace), "generated" (new
        files only), "modified" (changed files only)

  - Model Chaining Support: Added inject_to_global parameter enabling
    seamless model chaining workflows:
    
      - New parameter: inject_to_global in run_simulation() and
        run_all_simulations()
      - When TRUE, simulation variables are injected directly into the
        user's global environment
      - Enables users to access simulation results directly without
        complex variable extraction
      - Facilitates model chaining: use results from Model A as inputs
        to Model B
      - Maintains backward compatibility (FALSE by default)

Bug Fixes and Improvements

  - Cross-platform line endings: All textual files exported into FSKX
    archives now use LF line endings on every OS (including Windows).
    This applies to:
    
      - README.txt, metaData.json, packages.json, manifest.xml,
        metadata.rdf
      - model and visualization scripts
      - workspace.r
      - sim.sedml and model.sbml

  - Other files: R scripts included via other_files are normalized to LF
    on export; other file types are copied unchanged.

  - Encoding: All textual exports are written as UTF-8 (no BOM).

  - Internal: Introduced write_text_lf() helper to normalize line
    endings and write via binary connections; XML writers now use binary
    connections; zipping uses utils::zip to preserve directory
    structure.

  - File Loading Fix: Models that load external files (CSV, Excel, etc.)
    now work correctly by executing in the proper temporary directory
    with automatic working directory restoration.

  - Enhanced Return Values: run_simulation() now returns all
    user-created variables with preserved data types (scalars, vectors,
    data frames, lists, matrices) .

  - Improved Visualization Handling: Enhanced automatic display of
    ggplot objects created by visualization scripts.

  - Package Build Optimization: Added comprehensive .Rbuildignore file
    to exclude development files (test projects, debug scripts, session
    artifacts) from package builds.

  - Robust Error Handling: Added proper error handling and cleanup for
    working directory management and workspace copying operations.

  - Updated Documentation: Enhanced function documentation to reflect
    new parameters and capabilities.

Breaking Changes

  - None - all changes are backward compatible with existing workflows.

                 Changes in version 0.1.3 (2022-02-25)                  

  - Removed the googlesheets dependencies due to archiving of that
    package.
  - Small updates in the documentation, especially to adapt to new
    terminologies.

                 Changes in version 0.1.2 (2020-10-06)                  

  - Added a NEWS.md file to track changes to the package.
  - Improved the function documentation.