File Map

Use this map when changing code. It names the primary source files and the docs pages that should usually move with them.

Rust CLI

Source	Update docs
cli/src/main.rs	CLI / Commands, CLI / Models And Config, CLI / Context Loom In The CLI, Reference / Environment
cli/Cargo.toml	Reference / Versioning, CLI / Command Reference
cli/Cargo.lock	Reference / Versioning when release dependency resolution changes.
cli/src/terminal_ui.rs	CLI / Commands, CLI / Fullscreen TUI, CLI / Safety, Tracing, And Cancellation
cli/src/terminal_ui/render.rs	CLI / Fullscreen TUI
cli/src/terminal_ui/project.rs	CLI / Projects And Sessions, CLI / Fullscreen TUI
cli/src/project_files.rs, cli/src/terminal_ui/files.rs	CLI / Projects And Sessions, CLI / Command Reference, CLI / Fullscreen TUI
cli/src/terminal_ui/model_picker.rs	CLI / Models And Config, Getting Started / Provider Setup
cli/src/terminal_ui/approval.rs	CLI / Safety, Tracing, And Cancellation
cli/src/question.rs, cli/src/terminal_ui/question.rs	CLI / Fullscreen TUI, CLI / Safety, Tracing, And Cancellation
cli/src/terminal_ui/diff_view.rs	CLI / Safety, Tracing, And Cancellation
cli/src/progress.rs	CLI / Safety, Tracing, And Cancellation, Core / Runtime
cli/src/timeline.rs	CLI / Safety, Tracing, And Cancellation
cli/src/sessions.rs	CLI / Projects And Sessions, Core / State And Memory

Python Core

Source	Update docs
core/protoagent_core/agent_engine.py	Core / Core Architecture, CLI / Commands, Reference / Environment
core/protoagent_core/_version.py	Reference / Versioning, Core / Core Overview
core/pyproject.toml	Reference / Versioning, Getting Started / Installation
core/protoagent_core/runtime.py	Core / Runtime, CLI / Safety, Tracing, And Cancellation
core/protoagent_core/runtime_bridge.py	Core / Runtime, CLI / Safety, Tracing, And Cancellation
core/protoagent_core/user_input.py	Core / Agent Deck, Core / Runtime, CLI / Safety, Tracing, And Cancellation
core/protoagent_core/history.py	Core / State And Memory, CLI / Projects And Sessions
core/protoagent_core/workflow.py, verification.py	Core / Runtime, CLI / Verify & Recover
core/protoagent_core/runtime_policy.py, runtime_storage.py, checkpoints.py	Core / ProtoLink Engine Integration, Core / Safety And Tools
core/protoagent_core/run_contracts.py	Core / Runtime, Core / Agent Deck, Core / Quality Evals
core/protoagent_core/llm.py	Core / Config And Models, Reference / Environment
core/protoagent_core/models.py	Core / Config And Models, CLI / Models And Config
core/protoagent_core/config.py	Core / Config And Models, CLI / Models And Config, Getting Started / Provider Setup
core/protoagent_core/prompt_profiles.py	Core / Agent Deck, CLI / Commands, CLI / Models And Config
core/protoagent_core/quality_eval.py	Core / Quality Evals, CLI / Commands, Reference / Verification
core/protoagent_core/tools.py	Core / Safety And Tools
core/protoagent_core/help_agent.py	Core / Agent Deck, CLI / Commands
core/protoagent_core/agents/scout.py	Core / Agent Deck, Core / Safety And Tools, Reference / Environment, CLI / Commands
Other core/protoagent_core/agents/*.py	Core / Agent Deck, Core / Safety And Tools
core/protoagent_core/context/*.py	Core / Context Loom Internals, CLI / Context Loom In The CLI

Tooling And Contribution Workflow

Source	Update docs
pyproject.toml	Contributing / Development Workflow, Reference / Verification
VERSIONING.md	Reference / Versioning
CHANGELOG.md	Link from README/docs navigation and update for each user-visible release.
LICENSE	Package metadata and README license links.
rustfmt.toml	Contributing / Development Workflow, Reference / Verification
CONTRIBUTING.md	Contributing / Development Workflow
.github/workflows/python-quality.yml	Contributing / Development Workflow, Reference / Verification
.gitignore	Contributing / Development Workflow when generated or local-only paths change

Planning And Samples

Source	Update docs
acp/README.md, acp/VERSION, or new ACP files	ACP / Overview, ACP / Plan, Reference / Versioning
playground/recipe-reco/*	Playground / Overview
playground/taskflow/*	Playground / Overview
whitepaper.md	Intro, Core / Agent Deck, Core / Context Loom Internals

Docs Site

Source	Purpose
docs/docusaurus.config.js	Docusaurus site config, nav, footer, Mermaid, code highlighting.
docs/sidebars.js	Documentation taxonomy.
docs/src/pages/index.jsx	Landing page.
docs/src/pages/index.module.css	Landing page styling.
docs/src/css/custom.css	Global Docusaurus theme overrides.
docs/content/	Documentation pages.

v0.3.0 orchestration additions

File	Documentation
core/protoagent_core/task_record.py	Core / Task Workflow
core/protoagent_core/worker_interface.py	Core / Task Workflow, Core / ProtoLink Migration
core/protoagent_core/python_runtime.py	Core / Task Workflow
core/protoagent_core/editing.py	Core / Task Workflow, Core / Safety And Tools
core/protoagent_core/harness_eval.py	Core / Quality Evals, Core / ProtoLink Engine Integration
core/protoagent_core/request_budget.py	Core / Task Workflow, Core / Context Loom
core/protoagent_core/agents/tester.py	Core / Agent Deck
core/protoagent_core/coding_eval.py	Core / Quality Evals
whitepaper.md	Architecture thesis, enforced boundaries and measurement limits

• core/protoagent_core/mcp.py: validated MCP config, setup/probes, fixed broker tools and native policy.
• core/protoagent_core/agents/mcp.py: optional model-free broker factory.
• core/tests/test_optional_agents_mcp.py: optional-worker composition, real stdio MCP, approvals, errors, cancellation and delegated receipts.
• docs/content/core/mcp.md: MCP setup and architecture guide.