genoma-evolution 1.0.0

package/.claude/worktrees/phase-2-mcp/tsconfig.json

@@ -0,0 +1,34 @@
+{
+  "compilerOptions": {
+    "target": "ES2017",
+    "lib": ["dom", "dom.iterable", "esnext"],
+    "allowJs": true,
+    "skipLibCheck": true,
+    "strict": true,
+    "noEmit": true,
+    "esModuleInterop": true,
+    "module": "esnext",
+    "moduleResolution": "bundler",
+    "resolveJsonModule": true,
+    "isolatedModules": true,
+    "jsx": "react-jsx",
+    "incremental": true,
+    "plugins": [
+      {
+        "name": "next"
+      }
+    ],
+    "paths": {
+      "@/*": ["./src/*"]
+    }
+  },
+  "include": [
+    "next-env.d.ts",
+    "**/*.ts",
+    "**/*.tsx",
+    ".next/types/**/*.ts",
+    ".next/dev/types/**/*.ts",
+    "**/*.mts"
+  ],
+  "exclude": ["node_modules"]
+}

package/.env.example

@@ -0,0 +1,72 @@
+# ============================================================
+# Genoma Dashboard — Environment Variables Template
+#
+# Copy this file to .env.local and fill in the values.
+#   cp .env.example .env.local
+#
+# .env.local is gitignored — never commit real secrets.
+# ============================================================
+
+
+# ── LLM Provider Keys (at least one required for evolution) ─────────
+
+# Anthropic Claude — used when no higher-priority provider is set
+ANTHROPIC_API_KEY=your-anthropic-api-key
+
+# OpenRouter — takes priority over Anthropic when set
+# Models: anthropic/claude-sonnet-4, openai/gpt-4o, etc.
+OPENROUTER_API_KEY=your-openrouter-key
+
+# OpenCode — highest-priority cloud provider when set
+# Defaults to model: deepseek-v4-flash:free
+OPENCODE_API_KEY=your-opencode-key
+
+# Nous Research API — used when OpenRouter is not set
+NOUS_API_KEY=your-nous-key
+
+# OpenAI — used as API key for Ollama local when OPENAI_BASE_URL points to Ollama
+OPENAI_API_KEY=your-openai-key
+
+
+# ── Ollama (local inference) ─────────────────────────────────────────
+
+# Base URL for a local Ollama instance (include /v1 or it is appended automatically)
+# When Ollama is reachable at localhost:11434, it is preferred over all cloud keys
+OLLAMA_API_BASE=http://localhost:11434/v1
+
+# Override the base URL used by the OpenAI-compatible client
+# Set this to an Ollama URL to force local inference
+# OPENAI_BASE_URL=http://localhost:11434/v1
+
+
+# ── Model selection ──────────────────────────────────────────────────
+
+# Override the model used by sdd_evolve.py (applies to all providers)
+# Examples: gemma4:31b-cloud (Ollama), anthropic/claude-sonnet-4 (OpenRouter)
+# SDD_EVOLVE_MODEL=gemma4:31b-cloud
+
+# Ollama-specific model override (used when Ollama is the active provider)
+# SDD_OLLAMA_MODEL=gemma4:31b-cloud
+
+
+# ── Paths ────────────────────────────────────────────────────────────
+
+# Path to the hermes-agent repository
+# Default: ~/.hermes/hermes-agent
+HERMES_AGENT_REPO=~/.hermes/hermes-agent
+
+# Path to the hermes-agent-self-evolution repository
+# Default: sibling directory ../hermes-agent-self-evolution, falls back to ~/.hermes/hermes-agent-self-evolution
+# EVOLUTION_DIR=~/.hermes/hermes-agent-self-evolution
+
+# Python executable override — use when dspy/openai packages live in a specific venv
+# Default: auto-detected (prefers python3.12 with dspy installed)
+# PYTHON=/usr/bin/python3
+
+
+# ── Frontend ─────────────────────────────────────────────────────────
+
+# FastAPI backend URL consumed by the Next.js frontend
+# Default: http://localhost:8000
+NEXT_PUBLIC_API_BASE=http://localhost:8000
+NEXT_PUBLIC_API_URL=http://localhost:8000

package/.kilocode/package-lock.json

@@ -0,0 +1,378 @@
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+  "lockfileVersion": 3,
+  "requires": true,
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+        "@kilocode/plugin": "7.3.0"
+      }
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+      "resolved": "https://registry.npmjs.org/@kilocode/plugin/-/plugin-7.3.0.tgz",
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+      "license": "MIT",
+      "dependencies": {
+        "@kilocode/sdk": "7.3.0",
+        "effect": "4.0.0-beta.57",
+        "zod": "4.1.8"
+      },
+      "peerDependencies": {
+        "@opentui/core": ">=0.2.2",
+        "@opentui/solid": ">=0.2.2"
+      },
+      "peerDependenciesMeta": {
+        "@opentui/core": {
+          "optional": true
+        },
+        "@opentui/solid": {
+          "optional": true
+        }
+      }
+    },
+    "node_modules/@kilocode/sdk": {
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+      "resolved": "https://registry.npmjs.org/zod/-/zod-4.1.8.tgz",
+      "integrity": "sha512-5R1P+WwQqmmMIEACyzSvo4JXHY5WiAFHRMg+zBZKgKS+Q1viRa0C1hmUKtHltoIFKtIdki3pRxkmpP74jnNYHQ==",
+      "license": "MIT",
+      "funding": {
+        "url": "https://github.com/sponsors/colinhacks"
+      }
+    }
+  }
+}

package/.kilocode/package.json

@@ -0,0 +1,5 @@
+{
+  "dependencies": {
+    "@kilocode/plugin": "7.3.0"
+  }
+}

package/AGENTS.md

@@ -0,0 +1,5 @@
+<!-- BEGIN:nextjs-agent-rules -->
+# This is NOT the Next.js you know
+
+This version has breaking changes — APIs, conventions, and file structure may all differ from your training data. Read the relevant guide in `node_modules/next/dist/docs/` before writing any code. Heed deprecation notices.
+<!-- END:nextjs-agent-rules -->

package/CLAUDE.md

@@ -0,0 +1,29 @@
+@AGENTS.md
+
+## Skills (Auto-load based on context)
+
+IMPORTANT: When you detect any of these contexts, IMMEDIATELY read the corresponding skill file BEFORE writing any code. These are your coding standards and workflow guides.
+
+### Skill Discovery Paths
+
+Skills available from multiple sources:
+- **Claude Code global**: `~/.claude/skills/`
+- **Plugins**: Loaded via Claude Code plugin system
+- **OpenCode**: `~/.opencode/skills/`
+
+### Framework/Library/Context Detection
+
+| Context | Read this file |
+| ------- | -------------- |
+| React components, hooks, JSX, TSX files | `~/.claude/skills/react-doctor/SKILL.md` |
+| Frontend UI design, mockups, layouts | `~/.claude/skills/frontend-patterns/SKILL.md` |
+| Tailwind CSS classes, utilities, styles | `~/.claude/skills/tailwind/SKILL.md` |
+| Next.js config, routing, Turbopack, App Router | `~/.claude/skills/nextjs-turbopack/SKILL.md` |
+| TDD, unit tests, test-first workflow | `~/.claude/skills/tdd-workflow/SKILL.md` |
+| PostgreSQL, SQL, database queries, migrations | `~/.opencode/skills/postgres-patterns/SKILL.md` |
+| Component caching, memoization, performance | `~/.opencode/skills/cache-components/SKILL.md` |
+| Bug fixes, debugging, root cause analysis | `~/.opencode/skills/fix/SKILL.md` |
+| Documentation, README, docs update | `~/.opencode/skills/update-docs/SKILL.md` |
+| Prompt engineering, AI prompts, LLM | `~/.opencode/skills/prompt-lookup/SKILL.md` |
+| Midnight blockchain, Compact language, ZK | `~/.opencode/skills/midnight-development/SKILL.md` |
+| Skill discovery, finding available skills | `~/.opencode/skills/skill-lookup/SKILL.md` |