Add .github/copilot-instructions.md for coding agent onboarding

.github/copilot-instructions.md

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+# Copilot Coding Agent — Onboarding Instructions
+
+## Project Overview
+
+**cli-plugins** crawls CLI `--help` output and generates structured Claude Code plugins with expert command knowledge. Think "OpenAPI for CLIs."
+
+**Pipeline:** CLI binary → `cli-crawler` (JSON) → `generate-plugin` (plugin directory) → Claude Code consumes the plugin.
+
+Three entry-point commands are defined in `pyproject.toml [project.scripts]`:
+
+| Command            | Module                          | Purpose                              |
+| ------------------ | ------------------------------- | ------------------------------------ |
+| `cli-crawler`      | `src/crawler/pipeline.py:main`  | Crawl and parse CLI help output      |
+| `generate-plugin`  | `src/generator/plugin_generator.py:main` | Build Claude plugin from crawler JSON |
+| `config-audit`     | `src/config/audit.py:main`      | Detect inventory drift               |
+
+## Repository Layout
+
+```
+src/
+  crawler/       # Core crawling pipeline, executor, parsers, models
+  generator/     # Plugin generation from crawler JSON
+  config/        # Config audit / drift detection
+  lib/           # Shared utilities (subprocess_utils, cli_identity, logger)
+plugins/         # Generated Claude Code plugin directories (cli-<name>/)
+docs/            # CONTRIBUTING.md, README
+config.yaml      # Operational overrides for CLI crawling defaults
+cli_crawler.py   # Legacy top-level entry point (imports from src/crawler)
+pyproject.toml   # Build config, dependencies, tool settings
+```
+
+## Setup and Installation
+
+```bash
+# Recommended (if uv is available)
+uv sync
+
+# Alternative (pip)
+python3 -m venv .venv
+source .venv/bin/activate
+pip install -e ".[dev]"
+```
+
+Dev dependencies (pytest, ruff, black, radon) are declared in `[project.optional-dependencies] dev` in `pyproject.toml`.
+
+## Linting, Formatting, and Testing
+
+```bash
+# Lint
+ruff check src/
+
+# Format check
+ruff format --check src/
+
+# Auto-fix lint issues
+ruff check --fix src/
+
+# Auto-fix formatting
+ruff format src/
+
+# Run tests (when tests/ directory exists)
+pytest tests/ -v --tb=short -x
+```
+
+### Known CI issue (bug)
+
+The CI workflow (`.github/workflows/ci.yml`) runs `ruff check src/ tests/` and `pytest tests/`, but the `tests/` directory is listed in `.gitignore` and is **not committed to the repository**. This is a known bug that causes CI to fail with:
+
+```
+E902 No such file or directory (os error 2)
+--> tests:1:1
+```
+
+**Workaround when running locally:** omit `tests/` from ruff commands if the directory does not exist: `ruff check src/` instead of `ruff check src/ tests/`.
+
+## Ruff Configuration (in `pyproject.toml`)
+
+- **Target:** Python 3.11
+- **Line length:** 100
+- **Source roots:** `src`, `tests`
+- **Enabled rules:** E, F, W, I (isort), UP, B, SIM
+- **Ignored rules:** E501 (line length), E741, SIM108, SIM102, SIM103, B007
+
+## Coding Conventions
+
+### Python Style
+
+- **`from __future__ import annotations`** must be the first import (after the module docstring) in every Python file.
+- **Python 3.10+ type syntax:** use `str | None` (not `Optional[str]`), `list[str]` (not `List[str]`).
+- **No external runtime dependencies** for core functionality (crawler, generator, config-audit use stdlib only).
+- **Keep files under 500 lines.**
+
+### Docstrings
+
+- Module-level docstring at the top of every `.py` file.
+- Function/class docstrings use Google-style (`Args:`, `Returns:`, `Raises:` sections).
+- Imperative mood for the first line.
+
+### Data Models
+
+- Use `@dataclass` for all data structures (see `src/crawler/models.py`).
+- Use `field(default_factory=list)` for mutable defaults.
+- `models.py` is the single source of truth for data shapes.
+
+### Security
+
+- **Never use `shell=True`** in subprocess calls. Always pass commands as lists.
+- PowerShell arguments are single-quoted via `_quote_ps_arg()` in `src/crawler/executor.py` to prevent command injection.
+- `SAFE_ENV` dictionary (defined in both `src/crawler/executor.py` and `src/lib/subprocess_utils.py`) standardises subprocess environment to suppress colours and pagers: `NO_COLOR=1`, `PAGER=cat`, `TERM=dumb`, `LANG=C`, `LC_ALL=C`, `GIT_PAGER=cat`, `MANPAGER=cat`, `MANWIDTH=120`, `COLUMNS=120`.
+- `SAFE_ENV` is currently duplicated across the two files above. If you update one, update the other to match (both files document this requirement in comments).
+
+### Logging
+
+- Use `logging.getLogger(__name__)` or `logging.getLogger("cli_crawler.<module>")`.
+- Never use `print()` for diagnostic output; use the logger.
+
+### Tests
+
+- Test files go in `tests/` (not in root or `src/`), named `test_*.py`.
+- Pytest markers: `@pytest.mark.unit`, `@pytest.mark.integration`, `@pytest.mark.e2e`, `@pytest.mark.performance`.
+- Unit tests use descriptive docstrings.
+
+### Commits
+
+- Follow [Conventional Commits](https://www.conventionalcommits.org/): `feat:`, `fix:`, `docs:`, `refactor:`, `test:`, `chore:`.
+
+## CI Workflows
+
+| File                            | Purpose                                        |
+| ------------------------------- | ---------------------------------------------- |
+| `.github/workflows/ci.yml`     | Lint (ruff) + test (pytest) on Python 3.11/3.12 |
+| `.github/workflows/codeql-analysis.yml` | Weekly CodeQL security scanning         |
+
+## What Not to Touch
+
+- `plugins/` — these are **generated** artifacts; regenerate them via `generate-plugin`, do not hand-edit.
+- `output/` — crawler output; gitignored.
+- `.gitignore` excludes many dev-only directories (`.claude/`, `specs/`, `tests/`, `.dev/`, `.agent/`, etc.). Be aware of these when creating files.