feat: add Claude Code plugin and marketplace

Adds the dyno-phi plugin (skills/phi/SKILL.md) and a marketplace
catalog (.claude-plugin/marketplace.json) so teams can install
the phi CLI skill directly from Claude Code:

  /plugin marketplace add dynotx/phi-cli
  /plugin install dyno-phi@phi-cli

Also adds .claude/settings.json with extraKnownMarketplaces so
the marketplace is auto-registered when the repo is opened.

Made-with: Cursor

Author: davidlevybooth-dyno

.claude-plugin/marketplace.json

@@ -0,0 +1,26 @@
+{
+  "name": "phi-cli",
+  "owner": {
+    "name": "Dyno Therapeutics",
+    "email": "[email protected]"
+  },
+  "metadata": {
+    "description": "Claude Code plugins for the dyno protein design platform",
+    "pluginRoot": "./phi-plugin"
+  },
+  "plugins": [
+    {
+      "name": "dyno-phi",
+      "source": "./phi-plugin",
+      "description": "Claude Code skill for the dyno-phi protein design CLI. Design binders, run folding pipelines, filter and score candidates.",
+      "version": "0.1.1",
+      "author": {
+        "name": "Dyno Therapeutics"
+      },
+      "homepage": "https://github.com/dynotx/phi-cli",
+      "repository": "https://github.com/dynotx/phi-cli",
+      "license": "MIT",
+      "keywords": ["protein-design", "binder-design", "bioinformatics", "alphafold", "rfdiffusion"]
+    }
+  ]
+}

.claude/settings.json

@@ -0,0 +1,10 @@
+{
+  "extraKnownMarketplaces": {
+    "phi-cli": {
+      "source": {
+        "source": "github",
+        "repo": "dynotx/phi-cli"
+      }
+    }
+  }
+}

phi-plugin/.claude-plugin/plugin.json

@@ -0,0 +1,11 @@
+{
+  "name": "dyno-phi",
+  "description": "Claude Code skill for the dyno-phi protein design CLI. Design binders with RFDiffusion3 or BoltzGen, run folding/inverse-folding pipelines, filter and score candidates, and download results — all from natural language.",
+  "version": "0.1.1",
+  "author": {
+    "name": "Dyno Therapeutics"
+  },
+  "homepage": "https://github.com/dynotx/phi-cli",
+  "repository": "https://github.com/dynotx/phi-cli",
+  "license": "MIT"
+}

phi-plugin/README.md

@@ -0,0 +1,55 @@
+# dyno-phi Claude Code Plugin
+
+A Claude Code plugin that gives Claude the ability to run `phi` CLI commands for the **dyno protein design platform**.
+
+## What it does
+
+Installs the `/dyno-phi:phi` skill, which lets Claude:
+
+- Run the full binder design workflow (research → fetch → design → filter → download)
+- Submit jobs to RFDiffusion3, BoltzGen, ESMFold, AlphaFold2, and ProteinMPNN
+- Score and filter design candidates using pLDDT, pTM, ipTM, iPAE, and RMSD
+- Manage datasets and jobs
+
+## Prerequisites
+
+Install the CLI and set your API key:
+
+```bash
+pip install dyno-phi
+export DYNO_API_KEY=ak_...
+phi login   # verify connectivity
+```
+
+## Usage (local / development)
+
+Load the plugin directly with `--plugin-dir`:
+
+```bash
+claude --plugin-dir ./phi-plugin
+```
+
+Then use the skill in Claude Code:
+
+```
+/dyno-phi:phi upload ./designs/
+/dyno-phi:phi filter --preset default --wait
+/dyno-phi:phi scores
+```
+
+Or just describe what you want — Claude will invoke the skill automatically:
+
+```
+Design 50 binders for PD-L1 using hotspots A115, A120, A125
+```
+
+## Skill invocation
+
+| Invocation | Description |
+|---|---|
+| `/dyno-phi:phi` | Direct skill invocation |
+| Natural language | Claude invokes automatically based on context |
+
+## Source
+
+Part of the [phi-cli](https://github.com/dynotx/phi-cli) repository.