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installer for cooperative AI-assisted HEP analysis workflows","maintainers":[{"name":"llavez99","email":"llavez99@gmail.com"}],"readme":"# cooper\n\nA scaffold installer that gives coding agents (Copilot, Claude Code, Codex, etc.) the structure they need to be useful inside real working environments — persistent memory, studies, knowledge, and skills.\n\n## Install\n\n```bash\ncd /path/to/your-repo\nnpx @archi-physics/cooper init\n```\n\nThis creates a `cooper/` directory in your repo with:\n- `cooper/AGENTS.md` — operating instructions every agent reads first\n- `cooper/knowledge/` — canonical, reusable project knowledge\n- `cooper/memory/` — working memory, decisions, handoff notes\n- `cooper/studies/` — per-topic investigations with run logs\n- `cooper/refs/` — local references (papers, notes, links)\n- `cooper/skills/` — reusable agent skills/modules\n\nIt also adds a managed `AGENTS.md` block at your repo root that points assistants to the scaffold.\n\nYour project's own code, configs, and scripts stay where they are. Cooper doesn't touch them — it just gives agents the context and structure to help you with them.\n\n### Options\n- `--path <dir>`: target repo path (default: current directory)\n- `--subdir <name>`: install subdirectory (default: `cooper`)\n- `--force`: overwrite existing scaffold files\n\n## Update\n\nWhen a new version of Cooper is released, update your scaffold's infrastructure files (policies, templates) without touching your content (knowledge, studies, decisions):\n\n```bash\ncd /path/to/your-repo\nnpx @archi-physics/cooper update\n```\n\nThis overwrites **infrastructure files** (AGENTS.md, study templates, example configs) and preserves **user files** (knowledge base, memory, studies, refs).\n\nTo preview what would change:\n```bash\nnpx @archi-physics/cooper update --dry-run\n```\n\n### Update Options\n- `--path <dir>`: target repo path (default: current directory)\n- `--subdir <name>`: install subdirectory (default: `cooper`)\n- `--force`: also overwrite user content files\n- `--dry-run`: show what would change without writing\n\n## Why Cooper?\n\nFrontier agents are already highly capable. The bottleneck isn't intelligence — it's context. Agents need local structure to be effective: project docs, workflows, reusable skills, domain knowledge, and a persistent memory of what was done and why.\n\nCooper provides that scaffold so agents can plug into your environment, follow your way of working, and improve over time through documented history.\n\n## What the Scaffold Enforces\n\n- **Study discipline**: Every investigation gets a study directory with a clear question, tracked pipeline runs, and documented conclusions. Agents must log every run immediately — no batching.\n- **Session continuity**: Agents read memory on startup and update it on handoff, so context persists across sessions.\n- **Knowledge promotion**: Reusable findings get promoted from ephemeral notes into the permanent knowledge base.\n- **Decision tracking**: Every significant decision is logged with rationale, alternatives considered, and reversibility.\n\nSee [templates/cooper/AGENTS.md](templates/cooper/AGENTS.md) for the full policy.\n\n## Repository Structure (This Repo)\n\nThis is the npm package source, not a working scaffold instance.\n\n```\ncooper/                        # This repo (npm package source)\n├── AGENTS.md                  # Instructions for developing Cooper\n├── package.json               # npm package definition\n├── bin/cooper.js              # CLI entrypoint (cooper init)\n├── templates/cooper/          # Scaffold payload installed into user repos\n│   ├── AGENTS.md              # Agent operating instructions\n│   ├── knowledge/             # domain knowledge base\n│   ├── memory/                # session memory & decisions\n│   ├── studies/               # tracked investigations\n│   ├── refs/                  # references & papers\n│   └── skills/                # reusable agent skills\n├── openspec/                  # Design specs for Cooper development\n│   ├── cooper.md              # Vision, scope, boundaries\n│   └── project.md             # Tech stack, conventions\n└── README.md\n```\n\nWhen installed into a user's repo:\n```\ntheir-analysis-repo/\n├── AGENTS.md                  # Managed block → points to cooper/\n├── their_code/                # User's existing code (untouched)\n├── their_configs/             # User's existing configs (untouched)\n└── cooper/                    # Installed by `cooper init`\n    ├── AGENTS.md              # Agent operating instructions\n    ├── knowledge/             # Domain knowledge base\n    ├── memory/                # Session memory & decisions\n    ├── studies/               # Tracked investigations\n    ├── refs/                  # References & papers\n    └── skills/                # Reusable agent workflows\n```\n\n## Contributing\n\n### Development Setup\n\n```bash\ngit clone git@github.com:archi-physics/cooper.git\ncd cooper\n```\n\nNo build step — the package is plain JS and markdown templates.\n\n### Testing Locally\n\nRun a smoke test that installs the scaffold into a temp directory:\n\n```bash\nnpm run test:smoke\n```\n\nTo test the CLI against a real repo without publishing:\n\n```bash\ncd /path/to/test-repo\nnpx /path/to/cooper init\n```\n\n### npm Authentication\n\nYou must be logged in to npm with access to the `@archi-physics` org:\n\n```bash\nnpm login\nnpm access grant read-write @archi-physics:developers  # if needed\n```\n\n### Publishing to npm\n\n1. **Ensure you're on `main` with a clean working tree:**\n   ```bash\n   git checkout main && git pull\n   git status  # should be clean\n   ```\n\n2. **Bump the version:**\n   ```bash\n   npm version patch   # or minor / major\n   ```\n   This updates `package.json` and creates a git tag (`v0.1.1`, etc.).\n\n3. **Push the version commit and tag:**\n   ```bash\n   git push origin main --tags\n   ```\n\n4. **Publish:**\n   ```bash\n   npm publish --access public\n   ```\n\n### Version Policy\n\n- **patch** (`0.1.x`): template content changes, bug fixes, doc updates\n- **minor** (`0.x.0`): new scaffold features (e.g., new directories, CLI flags)\n- **major** (`x.0.0`): breaking changes to scaffold structure or CLI interface\n","readmeFilename":"README.md"}