Update CLAUDE.md and AGENTS.md to reflect current codebase

- Add missing CLI subcommands (ui, docs, check, providers, deps, install, lock, verify, add, remove, init, config)
- Document new core modules (config.py, system_deps.py, dependency_graph.py, hash_utils.py)
- Update GUI structure (Welcome page, widgets/, expanded dialogs list)
- Add missing web modules (auth.py, sessions.py, email.py, seo.py)
- Add missing registry modules (categorize.py, rate_limit.py, scrutiny.py, similarity.py, stats.py, settings.py)
- Streamline AGENTS.md as quick reference that defers to CLAUDE.md

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

AGENTS.md

@@ -1,42 +1,52 @@
 # Repository Guidelines
 
-## Project Structure & Module Organization
+> **Note**: See CLAUDE.md for comprehensive project documentation. This file provides a quick reference for common patterns.
-- `src/cmdforge/` contains the core Python package (CLI entry point, tool model, runner, providers, UI backends).
-- `tests/` holds pytest suites.
-- `docs/` includes installation, provider setup, examples, and design notes.
-- `examples/` provides sample tools and an installer script.
-- `wiki/` contains additional reference material.
 
-## Architecture Overview
+## Project Structure
-- `cli/` directory routes subcommands like `list`, `create`, `run`, `test`, and `refresh`.
-- `tool.py` defines tool/step models and handles YAML config loading and wrapper generation.
-- `runner.py` executes steps and performs `{input}`/argument variable substitution.
-- `providers.py` shells out to configured AI provider CLIs (or the `mock` provider).
-- `gui/` provides the PySide6 desktop GUI with pages for tools, registry, and providers.
 
-## Build, Test, and Development Commands
+- `src/cmdforge/` - Core Python package (CLI, tool model, runner, providers, GUI)
-- `pip install -e ".[dev]"` installs CmdForge in editable mode with dev dependencies.
+- `tests/` - Pytest test suites
-- `pytest` runs the full test suite.
+- `docs/` - Infrastructure and deployment documentation
-- `pytest tests/test.py::test_name` runs a focused test.
-- `python -m cmdforge.cli` runs the CLI module directly.
-- `cmdforge` launches the desktop GUI (requires PySide6).
-- `docker-compose build` builds the dev container image.
-- `docker-compose run --rm test` runs tests inside Docker.
 
-## Coding Style & Naming Conventions
+## Development Commands
-- Python code uses 4-space indentation and module/variable names in `snake_case`.
-- Keep CLI command names and tool IDs lowercase with hyphens (e.g., `fix-grammar`, `json-extract`).
-- Prefer small, composable functions that mirror the Unix pipe flow described in `README.md`.
 
-## Testing Guidelines
+```bash
-- Framework: `pytest` (configured in `pyproject.toml`).
+pip install -e ".[dev]"              # Install in dev mode
-- Place new tests under `tests/` and name files `test_*.py`.
+pytest tests/ -m "not integration"   # Run unit tests
-- For provider-dependent logic, prefer the built-in `mock` provider to avoid network calls.
+cmdforge                             # Launch GUI
+cf                                   # Interactive tool picker
+```
 
-## Commit & Pull Request Guidelines
+## Architecture Quick Reference
-- Commit messages follow short, imperative, sentence-case subjects (e.g., "Improve provider error messages").
-- PRs should include a clear summary, test results (or rationale if tests are skipped), and screenshots when UI behavior changes.
 
-## Security & Configuration Tips
+- `cli/` - Routes all subcommands (list, create, run, test, providers, registry, collections, deps, install, etc.)
-- Provider credentials live in `~/.cmdforge/providers.yaml`; avoid committing secrets.
+- `tool.py` - Tool/step dataclasses, YAML loading, wrapper generation
-- User tool configs live in `~/.cmdforge/<toolname>/config.yaml` and should not be added to the repo.
+- `runner.py` - Step execution, variable substitution (`{input}`, `{varname}`)
+- `providers.py` - AI provider abstraction (calls CLI tools via subprocess)
+- `gui/` - PySide6 desktop GUI with page-based navigation
+- `web/` - Flask web UI and forum
+- `registry/` - Flask registry API (search, publish, moderation)
+
+## Coding Style
+
+- Python: 4-space indentation, `snake_case` for modules/variables
+- CLI tools: lowercase with hyphens (e.g., `fix-grammar`, `json-extract`)
+- Follow Unix pipe philosophy: composable tools with stdin/stdout
+
+## Testing
+
+- Framework: `pytest` (see `pyproject.toml`)
+- Test files: `tests/test_*.py`
+- Use `mock` provider or `--dry-run` to avoid network calls
+- Integration tests require `@pytest.mark.integration` decorator
+
+## Commit Guidelines
+
+- Short, imperative, sentence-case subjects (e.g., "Add provider validation")
+- Include test results or rationale if skipped
+- Add screenshots for UI changes
+
+## Security
+
+- Provider configs: `~/.cmdforge/providers.yaml` (never commit)
+- Tool configs: `~/.cmdforge/<toolname>/config.yaml` (user data, never commit)

CLAUDE.md

@@ -39,7 +39,7 @@ python -m cmdforge.cli  # Alternative CLI invocation
 
 ### Core Modules (`src/cmdforge/`)
 
-- **cli/**: CLI commands entry points (`cmdforge` command). Routes subcommands: list, create, edit, delete, test, run, refresh, collections, registry, settings, system-deps
+- **cli/**: CLI commands entry points (`cmdforge` command). Routes subcommands: list, create, edit, delete, test, run, ui, docs, check, refresh, providers, registry, collections, deps, install, lock, verify, add, remove, init, config, settings, system-deps
 - **tool.py**: Tool definition dataclasses (`Tool`, `ToolArgument`, `PromptStep`, `CodeStep`, `ToolStep`), YAML config loading/saving, wrapper script generation
 - **runner.py**: Execution engine. Runs tool steps sequentially, handles variable substitution (`{input}`, `{varname}`), executes Python code steps via `exec()`, handles nested tool calls with depth limit (MAX_TOOL_DEPTH=10)
 - **resolver.py**: Tool resolution. `resolve_tool()` searches: project manifest → local tools → owner/name → registry. Returns `ResolvedTool` with path info
@@ -49,10 +49,15 @@ python -m cmdforge.cli  # Alternative CLI invocation
 - **manifest.py**: Project manifest (`cmdforge.yaml`) for declaring tool dependencies with version constraints
 - **lockfile.py**: Lock file support for reproducible installs (`cmdforge.lock`)
 - **registry_client.py**: Client for registry API (search, publish, download, authentication)
+- **config.py**: Global configuration management (registry URL, auth tokens)
+- **system_deps.py**: System package dependency management (apt/dnf/pacman detection and installation)
+- **dependency_graph.py**: Dependency graph resolution for meta-tools
+- **hash_utils.py**: Hash verification utilities for tool integrity
 - **gui/**: PySide6 desktop GUI
   - **main_window.py**: Main application window with sidebar navigation
-  - **pages/**: Tools page, Tool Builder, Registry browser, Collections page, Providers management, Profiles
+  - **pages/**: Welcome page, Tools page, Tool Builder, Registry browser, Collections page, Providers management, Profiles
-  - **dialogs/**: Step editors, Argument editor, Provider dialog, Connect/Publish dialogs
+  - **dialogs/**: Step editors (prompt/code/tool), Argument editor, Provider dialog, Connect/Publish dialogs, Test Step dialog, Settings dialog, System Dep dialog, Help dialogs, Review/Issue dialogs
+  - **widgets/**: Flow graph visualization (`flow_graph.py`), Icon utilities (`icons.py`)
 
 ### Key Paths
 
@@ -113,11 +118,15 @@ CmdForge includes a web interface and tool registry:
 
 - **app.py**: Flask app factory, registers blueprints
 - **routes.py**: Main web routes (docs, tutorials, tools, etc.)
+- **auth.py**: Authentication middleware and decorators
+- **sessions.py**: Session management
+- **email.py**: Email utilities (password reset, notifications)
+- **seo.py**: SEO utilities (sitemap, meta tags)
+- **filters.py**: Jinja2 filters (timeago, markdown, etc.)
+- **docs_content.py**: Documentation and tutorial content
 - **forum/**: Community forum blueprint
   - **models.py**: Forum database schema (categories, topics, replies)
   - **routes.py**: Forum routes (/forum, /forum/c/<slug>, /forum/t/<id>)
-- **filters.py**: Jinja2 filters (timeago, markdown, etc.)
-- **docs_content.py**: Documentation and tutorial content
 
 ### Registry Modules (`src/cmdforge/registry/`)
 
@@ -125,6 +134,12 @@ CmdForge includes a web interface and tool registry:
 - **db.py**: SQLite schema and queries (`connect_db()`, `query_one()`, `query_all()`)
 - **embeddings.py**: Semantic search with vector embeddings for tool discovery
 - **sync.py**: Git-based tool sync from Gitea repository
+- **categorize.py**: Auto-categorization of tools based on content
+- **rate_limit.py**: Rate limiting for API endpoints
+- **scrutiny.py**: Tool vetting (honesty, transparency, scope, efficiency checks)
+- **similarity.py**: Duplicate detection via embedding similarity
+- **stats.py**: Registry statistics and metrics
+- **settings.py**: Server-side settings management
 
 ### Key URLs