Add strip_fences option and fix exec() scoping for nested functions

- Add strip_fences field to PromptStep for removing markdown code fences
- Fix exec() to use same dict for globals and locals, allowing nested
  functions to access module-level imports
- Add GUI checkbox for strip_fences option
- Update CLAUDE.md with improved documentation

Co-Authored-By: Claude Opus 4.5 <[email protected]>

CLAUDE.md

@@ -12,11 +12,24 @@ CmdForge is a lightweight personal tool builder for AI-powered CLI commands. It
 # Install for development
 pip install -e ".[dev]"
 
-# Run tests
-pytest
+# Run all unit tests (excluding integration tests that need a server)
+pytest tests/ -m "not integration"
 
-# Run a single test
-pytest tests/test.py::test_name
+# Run all tests with verbose output
+pytest tests/ -v
+
+# Run a specific test file
+pytest tests/test_runner.py -v
+
+# Run a specific test class
+pytest tests/test_runner.py::TestSubstituteVariables -v
+
+# Run with coverage
+pytest tests/ --cov=cmdforge --cov-report=html
+
+# Run integration tests (requires local registry server at localhost:5000)
+python -m cmdforge.registry.app  # Start server first
+pytest tests/test_registry_integration.py -v -m integration
 
 # Run the CLI
 python -m cmdforge.cli
@@ -29,14 +42,19 @@ cmdforge
 
 ### Core Modules (`src/cmdforge/`)
 
-- **cli/**: CLI commands entry points (`cmdforge` command). Routes subcommands: list, create, edit, delete, test, run, refresh, collections
-- **tool.py**: Tool definition dataclasses (`Tool`, `ToolArgument`, `PromptStep`, `CodeStep`), YAML config loading/saving, wrapper script generation
+- **cli/**: CLI commands entry points (`cmdforge` command). Routes subcommands: list, create, edit, delete, test, run, refresh, collections, registry, 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
 - **collection.py**: Collection management (`Collection` dataclass, `resolve_tool_references()`, `classify_tool_reference()`), local collection storage in `~/.cmdforge/collections/`
-- **runner.py**: Execution engine. Runs tool steps sequentially, handles variable substitution (`{input}`, `{varname}`), executes Python code steps via `exec()`
 - **providers.py**: Provider abstraction. Calls AI CLI tools via subprocess, reads provider configs from `~/.cmdforge/providers.yaml`
+- **profiles.py**: AI persona profiles with system prompts, stored in `~/.cmdforge/profiles/`
+- **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)
 - **gui/**: PySide6 desktop GUI
   - **main_window.py**: Main application window with sidebar navigation
-  - **pages/**: Tools page, Tool Builder, Registry browser, Collections page, Providers management
+  - **pages/**: Tools page, Tool Builder, Registry browser, Collections page, Providers management, Profiles
   - **dialogs/**: Step editors, Argument editor, Provider dialog, Connect/Publish dialogs
 
 ### Key Paths
@@ -58,8 +76,9 @@ Tools are YAML configs with:
 
 ### Step Types
 
-1. **Prompt Step**: Calls AI provider with template, stores result in `output_var`
-2. **Code Step**: Executes Python code via `exec()`, captures specified variables
+1. **Prompt Step**: Calls AI provider with template, stores result in `output_var`. Supports `profile` for AI personas and `strip_fences` for markdown cleanup
+2. **Code Step**: Executes Python code via `exec()`, captures specified variables (comma-separated for multiple outputs)
+3. **Tool Step**: Calls another tool (meta-tools), supports `args` dict and `provider` override. Dependencies resolved via `resolver.py`
 
 ### Variable Flow
 
@@ -102,8 +121,10 @@ CmdForge includes a web interface and tool registry:
 
 ### Registry Modules (`src/cmdforge/registry/`)
 
-- **app.py**: Registry API (tool publishing, search, downloads)
-- **db.py**: SQLite schema and queries
+- **app.py**: Flask-based Registry API (tool publishing, search, downloads, authentication, rate limiting)
+- **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
 
 ### Key URLs
 
@@ -122,6 +143,19 @@ python -m cmdforge.web.app
 CMDFORGE_REGISTRY_DB=/path/to/db PORT=5050 python -m cmdforge.web.app
 ```
 
+## Testing Conventions
+
+Tests use `pytest` with common fixtures:
+- `temp_tools_dir(tmp_path)`: Redirects `TOOLS_DIR` and `BIN_DIR` to temp directory
+- `temp_providers_file(tmp_path)`: Redirects `providers.yaml` to temp directory
+
+Mocking strategy:
+- **File system**: Use `tmp_path` fixture and patch module-level paths
+- **Subprocess calls**: Mock `subprocess.run` and `shutil.which`
+- **Provider calls**: Mock `call_provider` to return `ProviderResult`
+
+Integration tests are marked with `@pytest.mark.integration` and require a running registry server.
+
 ## Infrastructure Documentation
 
 For deployment, server details, and operations, see the `docs/` folder: