_pkgdown.yml

url: https://kaipingyang.github.io/codeagent
template:
  bootstrap: 5

home:
  title: codeagent — R-native coding agent
  description: >
    An R-native agentic coding assistant built on ellmer and btw. Full-featured
    harness with streaming, tool execution, permissions, compaction, skills,
    multi-agent coordination, a CLI REPL, and a Shiny app.

navbar:
  structure:
    left:  [intro, reference, articles, news]
    right: [github]

reference:
  - title: "Core Client"
    desc: "Create and run the agent."
    contents:
      - codeagent_client
      - codeagent_client_config
      - codeagent
      - agent_loop
      - use_codeagent_settings
      - use_codeagent_setup

  - title: "Shiny App"
    desc: "Interactive chat interface."
    contents:
      - codeagent_app

  - title: "IDE Addins"
    desc: "RStudio / Positron keyboard-shortcut integration."
    contents:
      - codeagent_addin
      - codeagent_addin_selection

  - title: "CLI"
    desc: "Terminal REPL and command-line interface."
    contents:
      - codeagent_console
      - install_codeagent_cli

  - title: "Core tools"
    desc: "Built-in tool factories registered on the Chat."
    contents:
      - bash_tool
      - read_tool
      - write_tool
      - edit_tool
      - multi_edit_tool
      - glob_tool
      - grep_tool
      - ls_tool
      - run_r_tool
      - explore_data_tool
      - register_builtin_tools
      - register_explore_data_tool

  - title: "Permissions"
    desc: "Seven-mode permission gate and rule system."
    contents:
      - check_permission
      - PermissionMode
      - PermissionRule

  - title: "Session Management"
    desc: "Save, load, and navigate conversation history."
    contents:
      - list_sessions
      - save_session
      - restore_session_into_chat
      - get_session_messages
      - fork_session
      - rename_session
      - tag_session
      - truncate_chat_turns

  - title: "Memory"
    desc: "Persistent cross-session memory."
    contents:
      - write_memory
      - list_memories
      - recall_memories
      - recall_memories_relevant
      - delete_memory
      - read_todos

  - title: "Multi-Agent Teams"
    desc: "Parallel agent coordination."
    contents:
      - team_run
      - team_coordinate
      - board_create
      - board_add_task
      - board_claim
      - board_complete
      - board_status
      - board_send_message
      - board_messages
      - team_lead
      - team_dashboard
      - board_reclaim_stale
      - board_watch

  - title: "Skills"
    desc: "Skill discovery and loading."
    contents:
      - list_skills_meta
      - load_skill_prompt
      - build_skill_hint
      - install_ds_skills

  - title: "MCP"
    desc: "Model Context Protocol client and server."
    contents:
      - codeagent_mcp_server
      - register_mcp_client
      - r_mcp_server

  - title: "RAG"
    desc: "Codebase semantic retrieval."
    contents:
      - build_codebase_store
      - register_rag_tool

  - title: "Hooks"
    desc: "Lifecycle event hooks."
    contents:
      - HookRegistry
      - HookEvent

  - title: "Utilities"
    desc: "Miscellaneous helpers."
    contents:
      - switch_model
      - update_model_prices
      - verify_r_tests
      - verify_r_lints
      - codeagent_otel_status
      - use_codeagent_md

  - title: "Additional tools & registration"
    desc: "Tool factories and registration."
    contents:
      - agent_tool
      - ask_user_tool
      - notebook_edit_tool
      - notebook_read_tool
      - todo_write_tool
      - web_fetch_tool
      - web_search_tool
      - register_agent_tool
      - register_ask_user_tool
      - register_btw_file_tools
      - register_notebook_tools
      - register_r_tools
      - register_task_tools
      - register_web_tools
      - enable_btw_file_tools
      - register_tool_meta
      - tool_result
      - install_permission_gate
      # --- Data Shield: engine + lifecycle ---
      - DataShield
      - refresh_data_shield_context
      # --- Data Shield: strategies (compose via codeagent_client(data_shield=)) ---
      - shield_describe
      - shield_egress
      - shield_regex
      - shield_ingress
      - shield_tool_policy
      - shield_sandbox
      - shield_reviewer
      # --- Data Shield: ready-made strategy-combination presets ---
      - shield_preset
      - shield_preset_strict
      - shield_preset_balanced
      - shield_preset_clinical
      # --- Data Shield: optional scanners / code-safety auditors ---
      - data_shield_ocr_scanner
      - audit_code_tool

  - title: "Data exploration (WEAR)"
    desc: "Interactive data exploration and reporting."
    contents:
      - wear_explore
      - generate_wear_report

  - title: "Sessions & settings"
    desc: "Session storage and settings helpers."
    contents:
      - delete_session
      - get_session_info
      - migrate_sessions
      - load_settings
      - save_user_settings
      - migrate_config_dir

  - title: "Harness internals"
    desc: "R6 controllers and content/permission types (advanced)."
    contents:
      - BudgetTracker
      - CompactionController
      - ContentReplacementState
      - DenialTracker
      - StreamingToolExecutor
      - PreToolHook
      - PostToolHook
      - PermissionResultAllow
      - PermissionResultDeny
      - TextBlock
      - ThinkingBlock
      - ToolResultBlock
      - ToolUseBlock

  - title: "Streaming"
    desc: "Per-turn streaming primitives with typed content callbacks."
    contents:
      - codeagent_stream
      - codeagent_stream_async

  - title: "Guided tasks"
    desc: "One-shot guided workflows (reuse btw tasks)."
    contents:
      - codeagent_task
      - codeagent_create_skill
      - codeagent_create_readme
      - codeagent_init_context

articles:
  - title: "Getting Started"
    navbar: ~
    contents:
      - getting-started

  - title: "Configuration"
    navbar: "Configuration"
    contents:
      - configuration
      - permissions
      - models
      - compaction
      - skills-usage

  - title: "Advanced"
    navbar: "Advanced"
    contents:
      - team-coordination
      - data-exploration

  - title: "Embedding / Backend"
    navbar: "Embedding"
    contents:
      - backend-integration

  - title: "Data Shield"
    navbar: "Data Shield"
    contents:
      - data-shield
      - data-shield-cn