Changes in version 0.2.0                        

Breaking Changes

  - Renamed putior_skills() to putior_guide(). The function, its MCP
    tool (putior_guide), and its ACP operation (guide) all use the new
    name. putior_help("skills") still works as an alias for backward
    compatibility. The inst file was renamed from SKILLS.md to GUIDE.md,
    and the vignette from skills.Rmd to ai-integration.Rmd. (#41)

  - put(), put_auto(), put_generate(), and put_merge() now default to
    recursive = TRUE (previously FALSE). Directory scans now include
    subdirectories by default. Pass recursive = FALSE for the old
    behavior. (#34)

Bug Fixes

  - Fixed show_source_info = TRUE using <small> HTML tags that are
    unsupported by GitHub's Mermaid renderer. Source file names are now
    shown without HTML formatting tags. (#32)
  - Fixed pipe characters (|) in node labels breaking Mermaid diagram
    parsing. Pipes are now escaped using the #124; entity. (#33)

New Features

MCP Server Integration

  - Added putior_mcp_server() to expose putior functions as MCP tools
    for AI assistants
  - Added putior_mcp_tools() to get/filter tool definitions for custom
    MCP integrations
  - 16 tools available: put, put_diagram, put_auto, put_generate,
    put_merge, get_comment_prefix, get_supported_extensions,
    list_supported_languages, get_detection_patterns,
    get_diagram_themes, putior_guide, putior_help, set_putior_log_level,
    is_valid_put_annotation, split_file_list, ext_to_language
  - Supports Claude Code, Claude Desktop, and other MCP-compatible
    clients

ACP Server Integration

  - Added putior_acp_server() to expose putior as an ACP agent for
    inter-agent communication via REST API
  - Added putior_acp_manifest() for agent discovery
  - Supports natural language requests for all core operations
  - Input path sanitization to prevent directory traversal attacks

Multi-Language Comment Syntax (30+ Languages)

  - Added support for 30+ programming languages with automatic comment
    prefix detection
  - Comment styles: # (R, Python, Shell, etc.), -- (SQL, Lua, Haskell),
    // (JavaScript, TypeScript, C/C++, Go, Rust, Java, etc.), % (MATLAB,
    LaTeX)
  - Added get_comment_prefix(), get_supported_extensions(),
    ext_to_language()
  - Added list_supported_languages() to enumerate all supported
    languages

Auto-Detection Patterns (18 Languages, 902 Patterns)

  - Full auto-detection for: R, Python, SQL, Shell, Julia, JavaScript,
    TypeScript, Go, Rust, Java, C, C++, MATLAB, Ruby, Lua, WGSL,
    Dockerfile, Makefile
  - Pattern inheritance: TypeScript extends JavaScript, C++ extends C
  - Single authoritative language registry (R/language_registry.R)

LLM Detection Patterns

  - 54 patterns for modern AI/ML libraries across R and Python
  - R: ellmer, tidyllm, httr2 (API requests)
  - Python: ollama, openai, anthropic, langchain, transformers, litellm,
    vllm, google generative AI, groq

Auto-Annotation Feature

  - Added put_auto() for automatic workflow detection from code analysis
  - Added put_generate() for generating PUT annotation comments
    (roxygen2-style)
      - Now supports output = "raw" for programmatic access
  - Added put_merge() for combining manual and auto-detected annotations
      - Three merge strategies: "manual_priority", "supplement", "union"

Colorblind-Safe Themes

  - Added 4 viridis family themes for accessibility:
      - viridis: Purple-blue-green-yellow (general accessibility)
      - magma: Purple-red-yellow (high contrast, print-friendly)
      - plasma: Purple-pink-orange-yellow (presentations)
      - cividis: Blue-gray-yellow (deuteranopia/protanopia optimized)
  - All themes perceptually uniform and tested for color vision
    deficiencies

Custom Theme API

  - Added put_theme() for creating custom color palettes (#39)
  - New palette parameter on put_diagram() accepts putior_theme objects
  - Override individual node types (input, process, output, decision,
    artifact, start, end)
  - Base theme inheritance — customize only what you need

Block Comment Annotations

  - Added PUT annotation support inside /* */ and /** */ block comments
    (#37)
  - Use * put as line prefix inside block bodies for all //-prefix
    languages
  - Supports single-line block comments and JSDoc-style patterns

File Exclusion

  - Added exclude parameter to put(), put_auto(), put_generate(), and
    put_merge() for regex-based file exclusion (#38)

WGSL Shader Language Support

  - Registered .wgsl with // comment prefix (#31)
  - 17 auto-detection patterns for GPU bindings, textures, samplers, and
    naga-oil imports

Dockerfile Support

  - Handle extensionless Dockerfile via .FILENAME_MAP (#35)
  - 13 detection patterns for FROM, COPY, ADD, EXPOSE, VOLUME, CMD, RUN

Makefile Support

  - Handle Makefile and GNUmakefile via .FILENAME_MAP (#36)
  - 10 detection patterns for include, wildcard, target rules, install,
    shell commands

Metadata Display

  - Added show_source_info parameter to put_diagram() for displaying
    source file information in diagram nodes
  - Added source_info_style parameter with "inline" and "subgraph"
    display options

Clickable Hyperlinks

  - Added enable_clicks parameter to put_diagram() for making nodes
    clickable
  - Added click_protocol parameter: "vscode", "file", "rstudio"
  - Click directives include line numbers when available

Structured Logging

  - Optional logger package integration for debugging annotation parsing
  - Log levels: DEBUG, INFO, WARN (default), ERROR
  - Added set_putior_log_level() for configuration
  - Per-call override via log_level parameter on core functions

S3 Workflow Class

  - Workflow data frames now have putior_workflow S3 class
  - Added print.putior_workflow() for concise workflow summaries
  - Added summary.putior_workflow() for structured summary information

Interactive Sandbox Enhancements

  - Added copy-to-clipboard button for quick Mermaid code export
  - Added optional shinyAce syntax highlighting (graceful degradation)

Documentation

  - Documented all valid node_type values across vignettes and reference
    (#40)
  - 8 comprehensive vignettes including quick-start, annotation guide,
    features tour, API reference, showcase, troubleshooting,
    quick-reference, and skills reference
  - Professional cheat sheet (inst/cheatsheet/putior-cheatsheet.qmd)
  - 20 example files in inst/examples/
  - putior_guide() and putior_help() for in-session reference

New Helper Functions

  - resolve_label() internal helper to reduce code duplication in
    diagram generation
  - sanitize_acp_path() for ACP input validation
  - normalize_path_for_url() for cross-platform path handling
  - generate_click_url() for creating protocol-specific URLs
  - generate_click_directives() for Mermaid click action generation
  - generate_file_subgraphs() for file-based node grouping

Bug Fixes

  - Fixed ACP put_generate() called with invalid output = "raw" (now
    supported)
  - Fixed MCP theme enum missing viridis family themes
  - Fixed documentation using deprecated name instead of id in examples
  - Fixed ACP theme extraction regex missing colorblind-safe themes
  - Replaced unsafe 1:nrow() loops with seq_len(nrow()) to handle empty
    data frames
  - Moved %||% operator from acp.R to zzz.R for shared access

Improvements

  - Consolidated language detection list into single authoritative
    registry (.LANGUAGES_WITH_DETECTION in language_registry.R)
  - Standardized output parameter across put_diagram(), put_generate(),
    and putior_guide() -- all now support "raw"
  - Extracted duplicated label resolution into resolve_label() helper
  - Added input path sanitization to ACP server endpoints

Backward Compatibility

  - All new parameters default to FALSE/previous behavior
  - Existing code continues to work unchanged
  - putior_workflow class inherits from data.frame, preserving
    compatibility

                 Changes in version 0.1.0 (2025-06-19)                  

  - Initial CRAN submission
  - Added put() function for extracting workflow annotations from source
    code files
  - Added put_diagram() function for creating Mermaid flowchart diagrams
  - Added is_valid_put_annotation() for validating annotation syntax
  - Support for multiple programming languages: R, Python, SQL, Shell,
    and Julia
  - Multiline annotation support with backslash continuation syntax for
    better code style compliance
  - Automatic UUID generation when id field is omitted from annotations
  - Automatic output defaulting to file name when output field is
    omitted
  - Renamed annotation field from name to id for better graph theory
    alignment
  - Five built-in themes for diagrams: light, dark, auto, minimal, and
    github
  - Automatic file flow tracking between workflow steps
  - Comprehensive vignette with examples
  - Full test coverage for all major functions