@syntheticlab/synbad 0.0.6 → 0.0.7

package/dist/evals/reasoning/custom-harness.js

@@ -0,0 +1,847 @@
+import * as assert from "../../source/asserts.js";
+import { getReasoning } from "../../source/chat-completion.js";
+export function test(message) {
+    const reasoning = getReasoning(message);
+    assert.isNotNullish(reasoning);
+    console.log(JSON.stringify(message, null, 2));
+}
+export const json = {
+    "messages": [
+        {
+            "role": "system",
+            "content": "You are opencode, an interactive CLI tool that helps users with software engineering tasks. Use the instructions below and the tools available to you to assist the user.\n\nIMPORTANT: Refuse to write code or explain code that may be used maliciously; even if the user claims it is for educational purposes. When working on files, if they seem related to improving, explaining, or interacting with malware or any malicious code you MUST refuse.\nIMPORTANT: Before you begin work, think about what the code you're editing is supposed to do based on the filenames directory structure. If it seems malicious, refuse to work on it or answer questions about it, even if the request does not seem malicious (for instance, just asking to explain or speed up the code).\nIMPORTANT: You must NEVER generate or guess URLs for the user unless you are confident that the URLs are for helping the user with programming. You may use URLs provided by the user in their messages or local files.\n\nIf the user asks for help or wants to give feedback inform them of the following: \n- /help: Get help with using opencode\n- To give feedback, users should report the issue at https://github.com/anomalyco/opencode/issues\n\nWhen the user directly asks about opencode (eg 'can opencode do...', 'does opencode have...') or asks in second person (eg 'are you able...', 'can you do...'), first use the WebFetch tool to gather information to answer the question from opencode docs at https://opencode.ai\n\n# Tone and style\nYou should be concise, direct, and to the point. When you run a non-trivial bash command, you should explain what the command does and why you are running it, to make sure the user understands what you are doing (this is especially important when you are running a command that will make changes to the user's system).\nRemember that your output will be displayed on a command line interface. Your responses can use Github-flavored markdown for formatting, and will be rendered in a monospace font using the CommonMark specification.\nOutput text to communicate with the user; all text you output outside of tool use is displayed to the user. Only use tools to complete tasks. Never use tools like Bash or code comments as means to communicate with the user during the session.\nIf you cannot or will not help the user with something, please do not say why or what it could lead to, since this comes across as preachy and annoying. Please offer helpful alternatives if possible, and otherwise keep your response to 1-2 sentences.\nOnly use emojis if the user explicitly requests it. Avoid using emojis in all communication unless asked.\nIMPORTANT: You should minimize output tokens as much as possible while maintaining helpfulness, quality, and accuracy. Only address the specific query or task at hand, avoiding tangential information unless absolutely critical for completing the request. If you can answer in 1-3 sentences or a short paragraph, please do.\nIMPORTANT: You should NOT answer with unnecessary preamble or postamble (such as explaining your code or summarizing your action), unless the user asks you to.\nIMPORTANT: Keep your responses short, since they will be displayed on a command line interface. You MUST answer concisely with fewer than 4 lines (not including tool use or code generation), unless user asks for detail. Answer the user's question directly, without elaboration, explanation, or details. One word answers are best. Avoid introductions, conclusions, and explanations. You MUST avoid text before/after your response, such as \"The answer is <answer>.\", \"Here is the content of the file...\" or \"Based on the information provided, the answer is...\" or \"Here is what I will do next...\". Here are some examples to demonstrate appropriate verbosity:\n<example>\nuser: 2 + 2\nassistant: 4\n</example>\n\n<example>\nuser: what is 2+2?\nassistant: 4\n</example>\n\n<example>\nuser: is 11 a prime number?\nassistant: Yes\n</example>\n\n<example>\nuser: what command should I run to list files in the current directory?\nassistant: ls\n</example>\n\n<example>\nuser: what command should I run to watch files in the current directory?\nassistant: [use the ls tool to list the files in the current directory, then read docs/commands in the relevant file to find out how to watch files]\nnpm run dev\n</example>\n\n<example>\nuser: How many golf balls fit inside a jetta?\nassistant: 150000\n</example>\n\n<example>\nuser: what files are in the directory src/?\nassistant: [runs ls and sees foo.c, bar.c, baz.c]\nuser: which file contains the implementation of foo?\nassistant: src/foo.c\n</example>\n\n<example>\nuser: write tests for new feature\nassistant: [uses grep and glob search tools to find where similar tests are defined, uses concurrent read file tool use blocks in one tool call to read relevant files at the same time, uses edit file tool to write new tests]\n</example>\n\n# Proactiveness\nYou are allowed to be proactive, but only when the user asks you to do something. You should strive to strike a balance between:\n1. Doing the right thing when asked, including taking actions and follow-up actions\n2. Not surprising the user with actions you take without asking\nFor example, if the user asks you how to approach something, you should do your best to answer their question first, and not immediately jump into taking actions.\n3. Do not add additional code explanation summary unless requested by the user. After working on a file, just stop, rather than providing an explanation of what you did.\n\n# Following conventions\nWhen making changes to files, first understand the file's code conventions. Mimic code style, use existing libraries and utilities, and follow existing patterns.\n- NEVER assume that a given library is available, even if it is well known. Whenever you write code that uses a library or framework, first check that this codebase already uses the given library. For example, you might look at neighboring files, or check the package.json (or cargo.toml, and so on depending on the language).\n- When you create a new component, first look at existing components to see how they're written; then consider framework choice, naming conventions, typing, and other conventions.\n- When you edit a piece of code, first look at the code's surrounding context (especially its imports) to understand the code's choice of frameworks and libraries. Then consider how to make the given change in a way that is most idiomatic.\n- Always follow security best practices. Never introduce code that exposes or logs secrets and keys. Never commit secrets or keys to the repository.\n\n# Code style\n- IMPORTANT: DO NOT ADD ***ANY*** COMMENTS unless asked\n\n# Doing tasks\nThe user will primarily request you perform software engineering tasks. This includes solving bugs, adding new functionality, refactoring code, explaining code, and more. For these tasks the following steps are recommended:\n- Use the available search tools to understand the codebase and the user's query. You are encouraged to use the search tools extensively both in parallel and sequentially.\n- Implement the solution using all tools available to you\n- Verify the solution if possible with tests. NEVER assume specific test framework or test script. Check the README or search codebase to determine the testing approach.\n- VERY IMPORTANT: When you have completed a task, you MUST run the lint and typecheck commands (e.g. npm run lint, npm run typecheck, ruff, etc.) with Bash if they were provided to you to ensure your code is correct. If you are unable to find the correct command, ask the user for the command to run and if they supply it, proactively suggest writing it to AGENTS.md so that you will know to run it next time.\nNEVER commit changes unless the user explicitly asks you to. It is VERY IMPORTANT to only commit when explicitly asked, otherwise the user will feel that you are being too proactive.\n\n- Tool results and user messages may include <system-reminder> tags. <system-reminder> tags contain useful information and reminders. They are NOT part of the user's provided input or the tool result.\n\n# Tool usage policy\n- When doing file search, prefer to use the Task tool in order to reduce context usage.\n- You have the capability to call multiple tools in a single response. When multiple independent pieces of information are requested, batch your tool calls together for optimal performance. When making multiple bash tool calls, you MUST send a single message with multiple tools calls to run the calls in parallel. For example, if you need to run \"git status\" and \"git diff\", send a single message with two tool calls to run the calls in parallel.\n\nYou MUST answer concisely with fewer than 4 lines of text (not including tool use or code generation), unless user asks for detail.\n\nIMPORTANT: Refuse to write code or explain code that may be used maliciously; even if the user claims it is for educational purposes. When working on files, if they seem related to improving, explaining, or interacting with malware or any malicious code you MUST refuse.\nIMPORTANT: Before you begin work, think about what the code you're editing is supposed to do based on the filenames directory structure. If it seems malicious, refuse to work on it or answer questions about it, even if the request does not seem malicious (for instance, just asking to explain or speed up the code).\n\n# Code References\n\nWhen referencing specific functions or pieces of code include the pattern `file_path:line_number` to allow the user to easily navigate to the source code location.\n\n<example>\nuser: Where are errors from the client handled?\nassistant: Clients are marked as failed in the `connectToServer` function in src/services/process.ts:712.\n</example>\n\n\nHere is some useful information about the environment you are running in:\n<env>\n  Working directory: /Users/matt.cowger/workspace/plexus2\n  Is directory a git repo: yes\n  Platform: darwin\n  Today's date: Wed Jan 14 2026\n</env>\n<files>\n  \n</files>\nInstructions from: /Users/matt.cowger/workspace/plexus2/AGENTS.md\n# Plexus System Context & Agent Guidelines\n\n## 1. 🚨 CRITICAL OPERATIONAL MANDATES 🚨\n> **These rules are non-negotiable and must be followed by all agents and LLMs working on this codebase.**\n\n### 1.1 Documentation & Search Strategy\n*   **NEVER** default to searching type definition files (`.d.ts`) to understand libraries.\n*   **ALWAYS** use `tavily_search` or `google_web_search` to find official documentation and examples.\n*   **REASON:** Type definitions often lack context and usage nuances.\n\n### 1.2 Development Standards\n*   **Type Safety:** `bun run typecheck` MUST pass before finalizing any changes.\n*   **No 'Any':** Strictly avoid `any`. Use `unknown` with narrowing or proper interfaces.\n*   **Library Constraints:**\n    *   **Runtime:** Native Bun APIs are preferred over Node.js polyfills (e.g., file I/O).\n    *   **Transformations:** NEVER build custom transformations. Use the existing architecture in `src/transformers` (derived from `@musistudio/llms`).\n    *   **Types:** Do not duplicate types. Check `src/types` and `src/transformers/types.ts` first.\n*   **Image/Asset Imports:**\n    *   **Frontend:** Import images directly from the `@/assets/` path alias. Bun bundler handles the import and provides the resolved path.\n    *   **Example:**\n        ```typescript\n        import plexusLogo from '@/assets/plexus_logo_transparent.png';\n        // usage: <img src={plexusLogo} alt=\"Logo\" />\n        ```\n    *   **Note:** Do NOT use Vite-specific syntax. This is a Bun project.\n\n---\n\n## 2. Project Overview\n\n### 2.1 Identity\n**Plexus** is a high-performance, unified API gateway and virtualization layer for Large Language Models (LLMs). It allows switching between providers (OpenAI, Anthropic, Gemini) without changing client code.\n\n### 2.2 Core Objectives\n1.  **Unified Surface:** Provide a single entry point for various LLM APIs.\n    *   `/v1/chat/completions` (OpenAI style)\n    *   `/v1/messages` (Anthropic style)\n2.  **Virtualization:** Decouple \"requested model\" from \"actual provider\".\n3.  **Control:** Centralized logging, load balancing, and configuration.\n\n### 2.3 Target Audience\n*   **AI Engineers:** Needing provider flexibility.\n*   **Platform Architects:** Managing LLM traffic and costs.\n\n---\n\n## 3. Architecture & Data Flow\n\n### 3.1 Tech Stack\n*   **Runtime:** [Bun](https://bun.sh)\n*   **Server:** Native Bun Webserver (`Bun.serve`)\n*   **Language:** TypeScript\n*   **Config:** YAML/JSON via Zod\n\n### 3.2 Request Lifecycle (Transformation Workflow)\n1.  **Ingest:** Client sends request (e.g., OpenAI format) to Plexus.\n2.  **Route:** `Dispatcher` selects provider based on `config/plexus.yaml` rules (load balancing, aliasing).\n3.  **Normalize:** `Transformer` converts request to `UnifiedChatRequest`.\n4.  **Adapt:** `Transformer` converts `UnifiedChatRequest` to Provider's native format (e.g., Anthropic).\n5.  **Execute:** HTTP call to Provider.\n6.  **Denormalize:** Response is converted back to `UnifiedChatResponse`, then to the Client's expected format.\n\n### 3.3 Directory Map\n*   **`config/`**: System configuration.\n*   **`packages/backend/src/`**:\n    *   `index.ts`: Entry point.\n    *   `server.ts`: HTTP server setup.\n    *   `services/`: Business logic (`Dispatcher`, `Router`).\n    *   `transformers/`: Provider adapters (OpenAI, Anthropic, Gemini).\n    *   `types/`: Shared TypeScript definitions.\n    *   `utils/`: Helpers (`logger`, `usage`).\n\n---\n\n## 4. Implementation Details\n\n### 4.1 Unified API Surface\n*   **POST** `/v1/chat/completions`: OpenAI compatibility.\n*   **POST** `/v1/messages`: Anthropic compatibility.\n*   **GET** `/v1/models`: Available models list.\n\n### 4.2 Shared Utilities\n**Usage Normalization (`src/utils/usage.ts`)**:\n*   **MUST** be used for token metrics.\n*   Handles difference between `prompt_tokens` (OpenAI) vs `input_tokens` (Anthropic).\n*   Example:\n    ```typescript\n    import { normalizeUsage } from \"../utils/usage\";\n    const usage = normalizeUsage(rawUsage);\n    ```\n\n---\n\n## 5. Development & Testing\n\n### 5.1 Environment\n*   **Start Dev:** `bun run dev` (Watches `packages/backend`).\n*   **Run Tests:** `bun test`.\n\n### 5.2 Testing Guidelines (Strict Isolation)\n*   **Global Mocks:** Do NOT use `mock.module` for global config in individual tests. It pollutes state.\n*   **Setup:** Use `setup.ts` for common mocks (Logger).\n*   **Spying:** Prefer `spyOn` over re-mocking.\n\n    ```typescript\n    // ✅ CORRECT\n    import { logger } from \"src/utils/logger\";\n    import { spyOn, expect, test } from \"bun:test\";\n\n    test(\"logger usage\", () => {\n        const spy = spyOn(logger, \"info\");\n        // ... action ...\n        expect(spy).toHaveBeenCalled();\n    });\n    ```"
+        },
+        {
+            "role": "user",
+            "content": [
+                {
+                    "type": "text",
+                    "text": "Review and implement @PLAN.md "
+                },
+                {
+                    "type": "text",
+                    "text": "Called the Read tool with the following input: {\"filePath\":\"/Users/matt.cowger/workspace/plexus2/PLAN.md\"}"
+                },
+                {
+                    "type": "text",
+                    "text": "<file>\n00001| # Plexus Full-Stack Build Migration Plan\n00002| \n00003| ## Overview\n00004| \n00005| This plan restructures Plexus from a monorepo with separate backend/frontend packages into a unified full-stack structure that leverages Bun's native `--compile` capabilities to create standalone executables.\n00006| \n00007| ### Problem Statement\n00008| \n00009| Currently, Plexus has:\n00010| - ❌ Separate `packages/backend` and `packages/frontend` directories\n00011| - ❌ Backend imports frontend HTML from a sibling package\n00012| - ❌ Frontend assets use `@/` path aliases that may not resolve correctly in compiled executables\n00013| - ❌ Compilation doesn't properly embed frontend assets into the binary\n00014| - ❌ Dist files are not accessible within compiled executables\n00015| \n00016| ### Solution\n00017| \n00018| Restructure to follow Bun's recommended full-stack pattern:\n00019| - ✅ Move frontend code into `packages/backend/src/frontend/`\n00020| - ✅ Keep backend code in `packages/backend/src/server/`\n00021| - ✅ Single entry point that imports HTML and starts server\n00022| - ✅ All assets properly embedded in compiled binary\n00023| - ✅ Single `bun build --compile` command creates complete executable\n00024| \n00025| ### Expected Outcome\n00026| \n00027| ```bash\n00028| ./dist/plexus2-macos\n00029| ```\n00030| \n00031| A single executable that:\n00032| - Runs the full Plexus API Gateway\n00033| - Serves the React frontend with all assets embedded\n00034| - Requires NO external dependencies, Node.js, or Bun installation\n00035| - Works on any macOS/Linux/Windows system with the correct target\n00036| \n00037| ---\n00038| \n00039| ## Phase 1: Directory Structure Analysis\n00040| \n00041| ### Current Structure\n00042| \n00043| ```\n00044| plexus2/\n00045| ├── packages/\n00046| │   ├── backend/\n00047| │   │   └── src/\n00048| │   │       ├── index.ts                 # MAIN ENTRY POINT\n00049| │   │       ├── server.ts              # Server setup\n00050| │   │       ├── config.ts\n00051| │   │       ├── routes/\n00052| │   │       ├── services/\n00053| │   │       ├── storage/\n00054| │   │       ├── transformers/\n00055| │   │     ├── types/\n00056| │   │       ├── utils/\n00057| │   │       ├── middleware/\n00058| │   │     └── tests/\n00059| │   │\n00060| │   └── frontend/\n00061| │       ├── src/\n00062| │       │   ├── index.html             # HTML ENTRY POINT\n00063| │       │   ├── main.tsx\n00064| │       │   ├── App.tsx\n00065| │     │   ├── app.css\n00066| │       │   ├── components/\n00067| │       │   ├── pages/\n00068| │       │   ├── assets/\n00069| │       │   ├── contexts/\n00070| │       │   ├── lib/\n00071| │       │   ├── hooks/\n00072| │       │   └── declarations.d.ts\n00073| │    ├── dist/                  # Pre-built (NOT NEEDED POST-MIGRATION)\n00074| │       └── package.json\n00075| │\n00076| ├── package.json           # Root/workspace config\n00077| ├── bunfig.toml                 # Shared Bun config\n00078| └── AGENTS.md\n00079| ```\n00080| \n00081| ### Target Structure\n00082| \n00083| ```\n00084| plexus2/\n00085| ├── packages/\n00086| │   └── backend/\n00087| │       └── src/\n00088| │           ├── server/                  # ← Backend code\n00089| │           │   ├── index.ts             # NEW MAIN ENTRY POINT\n00090| │           │   ├── server.ts\n00091| │         │   ├── config.ts\n00092| │           │   ├── routes/\n00093| │        │   ├── services/\n00094| │           │   ├── storage/\n00095| │        │   ├── transformers/\n00096| │           │   ├── types/\n00097| │           │   ├── utils/\n00098| │           │   ├── middleware/\n00099| │           │   └── tests/\n00100| │           │\n00101| │           └── frontend/             # ← Frontend code (moved here)\n00102| │           ├── index.html           # HTML ENTRY (relative imports)\n00103| │               ├── main.tsx\n00104| │          ├── App.tsx\n00105| │               ├── app.css\n00106| │               ├── components/\n00107| │               ├── pages/\n00108| │            ├── assets/\n00109| │               ├── contexts/\n00110| │               ├── lib/\n00111| │               ├── hooks/\n00112| │          └── declarations.d.ts\n00113| │\n00114| ├── package.json                         # Updated: single workspace\n00115| ├── bunfig.toml\n00116| └── AGENTS.md\n00117| ```\n00118| \n00119| ### Changes at a Glance\n00120| \n00121| | Item | Before | After |\n00122| |------|-------|\n00123| | Frontend location | `packages/frontend/src/` | `packages/backend/src/frontend/` |\n00124| | Backend location | `packages/backend/src/` | `packages/backend/src/server/` |\n00125| | HTML import | `../../frontend/src/index.html` | `../frontend/index.html` |\n00126| | Asset imports | `@/assets/...` (path alias) | `@/assets/...` (updated path alias) |\n00127| | Path alias base | `./src/*` → `./src/frontend/*` | `./src/*` → unified |\n00128| | Compile command | (broken) | `bun build packages/backend/src/server/index.ts --compile --outfile dist/plexus2-macos` |\n00129| | Dev command | `bun --watch packages/backend/src/index.ts` | `bun --hot packages/backend/src/server/index.ts` |\n00130| | Workspaces | `[\"packages/*\"]` | `[\"packages/backend\"]` |\n00131| \n00132| ---\n00133| \n00134| ## Phase 2: File Migration Strategy\n00135| \n00136| ### Step 2.1: Create New Backend Directory Structure\n00137| \n00138| ```bash\n00139| # Create server subdirectory\n00140| mkdir -p packages/backend/src/server\n00141| \n00142| # Create frontend subdirectory (will move files here next)\n00143| mkdir -p packages/backend/src/frontend\n00144| ```\n00145| \n00146| ### Step 2.2: Move Backend Code to `src/server/`\n00147| \n00148| **Files to move from `packages/backend/src/` to `packages/backend/src/server/`:**\n00149| \n00150| ```\n00151| config.ts                   → packages/backend/src/server/config.ts\n00152| index.ts                     → packages/backend/src/server/index.ts\n00153| server.ts             → packages/backend/src/server/server.ts\n00154| routes/                    → packages/backend/src/server/routes/\n00155| services/                      → packages/backend/src/server/services/\n00156| storage/                  → packages/backend/src/server/storage/\n00157| middleware/                    → packages/backend/src/server/middleware/\n00158| types/                   → packages/backend/src/server/types/\n00159| utils/                    → packages/backend/src/server/utils/\n00160| transformers/                  → packages/backend/src/server/transformers/\n00161| tests/                     → packages/backend/src/server/tests/\n00162| ```\n00163| \n00164| ### Step 2.3: Move Frontend Code to `src/frontend/`\n00165| \n00166| **Files to move from `packages/frontend/src/` to `packages/backend/src/frontend/`:**\n00167| \n00168| ```\n00169| index.html                → packages/backend/src/frontend/index.html\n00170| main.tsx                       → packages/backend/src/frontend/main.tsx\n00171| App.tsx                   → packages/backend/src/frontend/App.tsx\n00172| app.css                        → packages/backend/src/frontend/app.css\n00173| components/                  → packages/backend/src/frontend/components/\n00174| pages/                 → packages/backend/src/frontend/pages/\n00175| contexts/               → packages/backend/src/frontend/contexts/\n00176| lib/                     → packages/backend/src/frontend/lib/\n00177| hooks/                     → packages/backend/src/frontend/hooks/\n00178| assets/                → packages/backend/src/frontend/assets/\n00179| declarations.d.ts              → packages/backend/src/frontend/declarations.d.ts\n00180| ```\n00181| \n00182| ### Step 2.4: Update `src/server/index.ts`\n00183| \n00184| **Before:**\n00185| ```typescript\n00186| // packages/backend/src/index.ts\n00187| import { loadConfig } from \"./config\";\n00188| import { createServer } from \"./server\";\n00189| import { logger } from \"./utils/logger\";\n00190| \n00191| async function main() {\n00192|   try {\n00193|     const envConfigPath = process.env.PLEXUS_CONFIG_PATH;\n00194|     const args = process.argv.slice(2);\n00195|     const configArgIndex = args.indexOf(\"--config\");\n00196|     const argConfigPath = configArgIndex !== -1 ? args[configArgIndex + 1] : null;\n00197| \n00198|     const configPath = argConfigPath || envConfigPath;\n00199|     const config = await loadConfig(configPath);\n00200|     \n00201|     // ... rest of code\n00202|   }\n00203| }\n00204| \n00205| main();\n00206| ```\n00207| \n00208| **After:**\n00209| ```typescript\n00210| // packages/backend/src/server/index.ts\n00211| import { loadConfig } from \"./config\";\n00212| import { createServer } from \"./server\";\n00213| import { logger } from \"./utils/logger\";\n00214| \n00215| async function main() {\n00216|   try {\n00217|     const envConfigPath = process.env.PLEXUS_CONFIG_PATH;\n00218|     const args = process.argv.slice(2);\n00219|     const configArgIndex = args.indexOf(\"--config\");\n00220|     const argConfigPath = configArgIndex !== -1 ? args[configArgIndex + 1] : null;\n00221| \n00222|     const configPath = argConfigPath || envConfigPath;\n00223|     const config = await loadConfig(configPath);\n00224|     \n00225|     // ... rest of code (UNCHANGED)\n00226|   }\n00227| }\n00228| \n00229| main();\n00230| ```\n00231| \n00232| **No internal logic changes needed!**\n00233| \n00234| ---\n00235| \n00236| ## Phase 3: Import Path Updates\n00237| \n00238| ### Step 3.1: Update `src/server/server.ts`\n00239| \n00240| **Before:**\n00241| ```typescript\n00242| // packages/backend/src/server.ts\n00243| import frontendHtml from \"../../frontend/src/index.html\";\n00244| ```\n00245| \n00246| **After:**\n00247| ```typescript\n00248| // packages/backend/src/server/server.ts\n00249| import frontendHtml from \"../frontend/index.html\";\n00250| ```\n00251| \n00252| ### Step 3.2: Internal Imports Within Backend Code\n00253| \n00254| Most imports will still work because they're relative. However, check and update any imports like:\n00255| \n00256| **Before (if any exist):**\n00257| ```typescript\n00258| import { someUtil } from \"../utils/logger\";\n00259| ```\n00260| \n00261| **After:**\n00262| ```typescript\n00263| import { someUtil } from \"./utils/logger\";\n00264| ```\n00265| \n00266| **Rule of thumb:** Since all backend code is now in `src/server/`, imports within that directory need one less `../` in the path hierarchy.\n00267| \n00268| ### Step 3.3: Verify No Cross-Package Imports\n00269| \n00270| **Action:** Search for any imports from `@plexus/` packages:\n00271| \n00272| ```bash\n00273| cd packages/backend\n00274| grep -r \"@plexus/\" src/ || echo \"No cross-package imports found\"\n00275| ```\n00276| \n00277| **Expected:** None should be found. If found, these need to be converted to relative imports.\n00278| \n00279| ---\n00280| \n00281| ## Phase 4: Configuration Updates\n00282| \n00283| ### Step 4.1: Update `packages/backend/tsconfig.json`\n00284| \n00285| **Before:**\n00286| ```json\n00287| {\n00288|   \"extends\": \"../../tsconfig.json\",\n00289|   \"compilerOptions\": {\n00290|   \"baseUrl\": \".\",\n00291|     \"paths\": {\n00292|       \"src/*\": [\"./src/*\"]\n00293|     }\n00294|   },\n00295|   \"include\": [\"src/**/*\", \"tests/**/*\"],\n00296|   \"exclude\": [\"node_modules\"]\n00297| }\n00298| ```\n00299| \n00300| **After:**\n00301| ```json\n00302| {\n00303|   \"extends\": \"../../tsconfig.json\",\n00304|   \"compilerOptions\": {\n00305|     \"baseUrl\": \".\",\n00306|     \"paths\": {\n00307|     \"src/*\": [\"./src/server/*\"],\n00308|       \"@/*\": [\"./src/frontend/*\"]\n00309|     }\n00310|   },\n00311|   \"include\": [\"src/**/*\", \"tests/**/*\"],\n00312|   \"exclude\": [\"node_modules\"]\n00313| }\n00314| ```\n00315| \n00316| **Why:** \n00317| - `src/*` now points to backend code in `src/server/`\n00318| - `@/*` points to frontend code in `src/frontend/` (for asset imports like `@/assets/...`)\n00319| \n00320| ### Step 4.2: Update `packages/backend/package.json`\n00321| \n00322| **Step 4.2a: Merge Dependencies**\n00323| \n00324| Copy ALL dependencies from `packages/frontend/package.json` into `packages/backend/package.json`:\n00325| \n00326| ```json\n00327| {\n00328|   \"name\": \"@plexus/backend\",\n00329|   \"version\": \"0.1.0\",\n00330|   \"private\": true,\n00331|   \"type\": \"module\",\n00332|   \"scripts\": {\n00333|     \"dev\": \"bun --hot src/server/index.ts\",\n00334|     \"build\": \"bun build --target=bun --production --outdir=dist src/server/index.ts\",\n00335|     \"compile:macos\": \"bun build src/server/index.ts --compile --target bun-darwin-arm64 --outfile dist/plexus2-macos\",\n00336|     \"compile:linux\": \"bun build src/server/index.ts --compile --target bun-linux-x64-modern --outfile dist/plexus2-linux-x64\",\n00337|     \"compile:windows\": \"bun build src/server/index.ts --compile --target bun-win-x64 --outfile dist/plexus2-windows-x64.exe\",\n00338|     \"compile:linux-arm64\": \"bun build src/server/index.ts --compile --target bun-linux-arm64 --outfile dist/plexus2-linux-arm64\",\n00339|     \"compile:all\": \"bun run compile:macos && bun run compile:linux && bun run compile:windows && bun run compile:linux-arm64\",\n00340|     \"typecheck\": \"bunx tsc --noEmit\"\n00341|   },\n00342|   \"dependencies\": {\n00343|     // Keep existing backend dependencies:\n00344|     \"uuid\": \"^13.0.0\",\n00345|     \"yaml\": \"^2.8.2\",\n00346|     \n00347|     // Add ALL from packages/frontend/package.json dependencies:\n00348|     \"@monaco-editor/react\": \"^4.7.0\",\n00349|     \"@radix-ui/react-accordion\": \"^1.2.12\",\n00350|     \"@radix-ui/react-dialog\": \"^1.1.15\",\n00351|     \"@radix-ui/react-label\": \"^2.1.8\",\n00352|     \"@radix-ui/react-popover\": \"^1.1.15\",\n00353|     \"@radix-ui/react-scroll-area\": \"^1.2.10\",\n00354|     \"@radix-ui/react-select\": \"^2.2.6\",\n00355|     \"@radix-ui/react-slider\": \"^1.3.6\",\n00356|     \"@radix-ui/react-slot\": \"^1.2.4\",\n00357|     \"@radix-ui/react-switch\": \"^1.2.6\",\n00358|     \"@radix-ui/react-tabs\": \"^1.1.13\",\n00359|     \"@radix-ui/react-tooltip\": \"^1.2.8\",\n00360|     \"class-variance-authority\": \"^0.7.1\",\n00361|     \"clsx\": \"^2.1.1\",\n00362|     \"emblor\": \"^1.4.8\",\n00363|     \"lucide-react\": \"^0.562.0\",\n00364|     \"next-themes\": \"^0.4.6\",\n00365|     \"openapi-fetch\": \"^0.15.0\",\n00366|     \"openapi-typescript\": \"^7.10.1\",\n00367|     \"react\": \"^19.0.0\",\n00368|     \"react-dom\": \"^19.0.0\",\n00369|     \"react-easy-sort\": \"^1.8.0\",\n00370|     \"react-router-dom\": \"^7.12.0\",\n00371|     \"recharts\": \"^3.6.0\",\n00372|     \"sonner\": \"^2.0.7\",\n00373|     \"tailwind-merge\": \"^3.4.0\",\n00374|     \"tailwindcss-animate\": \"^1.0.7\"\n00375|   },\n00376|   \"devDependencies\": {\n00377|     \"@microsoft/fetch-event-source\": \"^2.0.1\",\n00378|     \"@types/bun\": \"latest\",\n00379|     \"@types/react\": \"^19.0.6\",\n00380|     \"@types/react-dom\": \"^19.0.2\",\n00381|     \"@types/uuid\": \"^11.0.0\",\n00382|     \"bun-plugin-tailwind\": \"^0.1.2\",\n00383|     \"bun-types\": \"^1.3.5\",\n00384|     \"tailwindcss\": \"^4.1.18\",\n00385|     \"typescript\": \"^5.9.3\"\n00386|   }\n00387| }\n00388| ```\n00389| \n00390| ### Step 4.3: Update Root `package.json`\n00391| \n00392| **Before:**\n00393| ```json\n00394| {\n00395|   \"name\": \"plexus2\",\n00396|   \"version\": \"0.1.0\",\n00397|   \"private\": true,\n00398|   \"workspaces\": [\n00399|     \"packages/*\"\n00400|   ],\n00401|   \"scripts\": {\n00402|     \"dev\": \"bun --watch packages/backend/src/index.ts\",\n00403|     \"test\": \"bun test\",\n00404|     \"typecheck\": \"bun --workspaces run typecheck\",\n00405|     \"start\": \"NODE_ENV=production bun packages/backend/src/index.ts\",\n00406|     \"compile:macos\": \"bun build packages/backend/src/index.ts --compile --target bun-darwin-arm64 --outfile dist/plexus2-macos\",\n00407|     \"compile:linux\": \"bun build packages/backend/src/index.ts --compile --target bun-linux-x64-modern --outfile dist/plexus2-linux-x64\",\n00408|     \"compile:windows\": \"bun build packages/backend/src/index.ts --compile --target bun-win-x64 --outfile dist/plexus2-windows-x64.exe\",\n00409|     \"compile:linux-arm64\": \"bun build packages/backend/src/index.ts --compile --target bun-linux-arm64 --outfile dist/plexus2-linux-arm64\",\n00410|     \"compile:all\": \"bun run compile:macos && bun run compile:linux && bun run compile:windows && bun run compile:linux-arm64\"\n00411|   }\n00412| }\n00413| ```\n00414| \n00415| **After:**\n00416| ```json\n00417| {\n00418|   \"name\": \"plexus2\",\n00419|   \"version\": \"0.1.0\",\n00420|   \"private\": true,\n00421|   \"workspaces\": [\n00422|     \"packages/backend\"\n00423|   ],\n00424|   \"scripts\": {\n00425|     \"dev\": \"bun --hot packages/backend/src/server/index.ts\",\n00426|     \"test\": \"bun test\",\n00427|     \"typecheck\": \"bun --workspaces run typecheck\",\n00428|     \"start\": \"NODE_ENV=production bun packages/backend/src/server/index.ts\",\n00429|     \"compile:macos\": \"cd packages/backend && bun run compile:macos\",\n00430|     \"compile:linux\": \"cd packages/backend && bun run compile:linux\",\n00431|     \"compile:windows\": \"cd packages/backend && bun run compile:windows\",\n00432|     \"compile:linux-arm64\": \"cd packages/backend && bun run compile:linux-arm64\",\n00433|     \"compile:all\": \"cd packages/backend && bun run compile:all\"\n00434|   }\n00435| }\n00436| ```\n00437| \n00438| **Changes:**\n00439| - Removed `packages/frontend` from workspaces\n00440| - Updated `dev` to use `--hot` instead of `--watch` (better for full-stack dev)\n00441| - Updated entry point paths to `src/server/index.ts`\n00442| - Compile scripts now delegate to backend package\n00443| \n00444| ### Step 4.4: Verify `bunfig.toml` (No Changes Needed)\n00445| \n00446| ```toml\n00447| [serve.static]\n00448| plugins = [\"bun-plugin-tailwind\"]\n00449| \n00450| [test]\n00451| # Preload the setup file to mock common modules\n00452| preload = [\"./packages/backend/tests/setup.ts\"]\n00453| ```\n00454| \n00455| **Action:** Update the preload path IF tests are moved to `src/server/tests/`:\n00456| \n00457| ```toml\n00458| [serve.static]\n00459| plugins = [\"bun-plugin-tailwind\"]\n00460| \n00461| [test]\n00462| preload = [\"./packages/backend/src/server/tests/setup.ts\"]\n00463| ```\n00464| \n00465| ---\n00466| \n00467| ## Phase 5: Update HTML Import Paths\n00468| \n00469| ### Step 5.1: Update `src/frontend/index.html`\n00470| \n00471| The HTML file uses **relative imports** from its own location. These should work as-is, but verify:\n00472| \n00473| **Expected content in `packages/backend/src/frontend/index.html`:**\n00474| \n00475| ```html\n00476| <!doctype html>\n00477| <html lang=\"en\" class=\"dark\">\n00478|   <head>\n00479|     <meta charset=\"UTF-8\" />\n00480|     <meta name=\"viewport\" content=\"width=device-width, initial-scale=1.0\" />\n00481|     <link rel=\"stylesheet\" href=\"./app.css\" />\n00482|     <title>Plexus Frontend</title>\n00483|   </head>\n00484|   <body>\n00485|     <div id=\"root\">Loading...</div>\n00486|     <script src=\"./main.tsx\" type=\"module\"></script>\n00487|   </body>\n00488| </html>\n00489| ```\n00490| \n00491| **These are correct!** They reference:\n00492| - `./app.css` → `packages/backend/src/frontend/app.css`\n00493| - `./main.tsx` → `packages/backend/src/frontend/main.tsx`\n00494| \n00495| ### Step 5.2: Verify Frontend Asset Imports\n00496| \n00497| Check that components use the correct path alias for assets.\n00498| \n00499| **Expected pattern in `packages/backend/src/frontend/components/layout/Sidebar.tsx`:**\n00500| \n00501| ```typescript\n00502| // ✅ CORRECT - uses @/ alias\n00503| import plexusLogo from '@/assets/plexus_logo_transparent.png';\n00504| ```\n00505| \n00506| This will resolve to:\n00507| - `@/` → `packages/backend/src/frontend/`\n00508| - `@/assets/...` → `packages/backend/src/frontend/assets/...`\n00509| \n00510| **All existing asset imports should continue to work!**\n00511| \n00512| ---\n00513| \n00514| ## Phase 6: Testing & Validation\n00515| \n00516| ### Step 6.1: Verify Directory Structure\n00517| \n00518| After migration, run:\n00519| \n00520| ```bash\n00521| cd packages/backend\n00522| \n00523| # Check directory structure\n00524| ls -la src/\n00525| ls -la src/server/\n00526| ls -la src/frontend/\n00527| \n00528| # Verify key files exist\n00529| test -f src/server/index.ts && echo \"✓ src/server/index.ts found\"\n00530| test -f src/frontend/index.html && echo \"✓ src/frontend/index.html found\"\n00531| test -f src/frontend/main.tsx && echo \"✓ src/frontend/main.tsx found\"\n00532| test -d src/frontend/assets && echo \"✓ src/frontend/assets found\"\n00533| ```\n00534| \n00535| ### Step 6.2: Verify TypeScript Configuration\n00536| \n00537| ```bash\n00538| cd packages/backend\n00539| \n00540| # Check tsconfig paths\n00541| bunx tsc --noEmit\n00542| \n00543| # Expected output: No errors\n00544| ```\n00545| \n00546| ### Step 6.3: Test Development Mode\n00547| \n00548| ```bash\n00549| cd /Users/matt.cowger/workspace/plexus2\n00550| \n00551| # Start dev server with hot reloading\n00552| bun --hot packages/backend/src/server/index.ts\n00553| ```\n00554| \n00555| **Expected results:**\n00556| - Server starts on configured port\n00557| - Frontend accessible at `/ui`\n00558| - Making changes to frontend code triggers HMR\n00559| - No compilation errors\n00560| \n00561| **Test endpoints:**\n00562| ```bash\n00563| # In another terminal\n00564| curl http://localhost:3000/health\n00565| curl http://localhost:3000/ui\n00566| ```\n00567| \n00568| ### Step 6.4: Verify Compilation\n00569| \n00570| **Test the compilation process:**\n00571| \n00572| ```bash\n00573| cd /Users/matt.cowger/workspace/plexus2\n00574| \n00575| # Build for macOS\n00576| bun build packages/backend/src/server/index.ts --compile --target bun-darwin-arm64 --outfile dist/test-plexus\n00577| \n00578| # Verify binary was created\n00579| ls -lh dist/test-plexus\n00580| \n00581| # Test running the binary (if on macOS ARM64)\n00582| ./dist/test-plexus\n00583| ```\n00584| \n00585| **Expected:**\n00586| - Binary created successfully (~60MB)\n00587| - Binary starts without errors\n00588| - Server listens on configured port\n00589| - Frontend accessible at `http://localhost:3000/ui`\n00590| \n00591| ### Step 6.5: Verify Assets Are Embedded\n00592| \n00593| Test that all assets load correctly from the compiled binary:\n00594| \n00595| ```bash\n00596| # While binary is running (from Step 6.4)\n00597| curl http://localhost:3000/ui\n00598| \n00599| # Should return full HTML with embedded assets\n00600| # Should NOT contain errors like \"asset not found\"\n00601| ```\n00602| \n00603| ---\n00604| \n00605| ## Phase 7: Cleanup\n00606| \n00607| ### Step 7.1: Remove Old Frontend Package\n00608| \n00609| ```bash\n00610| # Archive for reference (optional)\n00611| mv packages/frontend packages/frontend.backup\n00612| \n00613| # Or delete if you don't need it\n00614| rm -rf packages/frontend\n00615| ```\n00616| \n00617| ### Step 7.2: Remove Stale Frontend Dist Files\n00618| \n00619| These are no longer needed:\n00620| \n00621| ```bash\n00622| rm -rf packages/backend/src/frontend/dist/\n00623| ```\n00624| \n00625| (Bun will generate its own dist files during build/compile)\n00626| \n00627| ### Step 7.3: Clean Dependencies\n00628| \n00629| ```bash\n00630| cd /Users/matt.cowger/workspace/plexus2\n00631| \n00632| # Remove old lock files\n00633| rm -f bun.lockb\n00634| \n00635| # Reinstall with new dependency structure\n00636| bun install\n00637| \n00638| # Verify installation\n00639| bun --version\n00640| ```\n00641| \n00642| ### Step 7.4: Update .gitignore\n00643| \n00644| Ensure these are ignored:\n00645| \n00646| ```\n00647| # In .gitignore\n00648| node_modules/\n00649| .bun/\n00650| dist/\n00651| *.exe\n00652| plexus2-*\n00653| packages/frontend.backup/\n00654| ```\n00655| \n00656| ---\n00657| \n00658| ## Phase 8: Documentation Updates\n00659| ### Step 8.1: Update README Files\n00660| \n00661| **In `packages/backend/README.md`:**\n00662| \n00663| Update to reflect it's now a full-stack application:\n00664| \n00665| ```markdown\n00666| # Plexus Backend (Full-Stack)\n00667| \n00668| This package contains both the Plexus API Gateway backend and the React frontend UI.\n00669| \n00670| ## Development\n00671| \n00672| ```bash\n00673| # Start dev server with hot reloading\n00674| bun --hot src/server/index.ts\n00675| ```\n00676| \n00677| Frontend is available at `http://localhost:3000/ui`\n00678| \n00679| ## Production Build\n00680| \n00681| ```bash\n00682| # Build optimized bundle\n00683| bun build --target=bun --production --outdir=dist src/server/index.ts\n00684| \n00685| # Run production server\n00686| NODE_ENV=production bun dist/index.js\n00687| ```\n00688| \n00689| ## Compilation to Standalone Binary\n00690| \n00691| ```bash\n00692| # Compile to macOS binary\n00693| bun build src/server/index.ts --compile --target bun-darwin-arm64 --outfile dist/plexus2-macos\n00694| \n00695| # Run standalone binary\n00696| ./dist/plexus2-macos\n00697| ```\n00698| \n00699| The binary includes:\n00700| - Full Plexus API Gateway\n00701| - React frontend UI (available at `/ui`)\n00702| - All dependencies\n00703| - No external requirements\n00704| ```\n00705| \n00706| ### Step 8.2: Update Root README\n00707| \n00708| ```markdown\n00709| # Plexus 2\n00710| \n00711| High-performance unified API gateway for LLMs.\n00712| \n00713| ## Quick Start\n00714| \n00715| ### Development\n00716| ```bash\n00717| bun --hot packages/backend/src/server/index.ts\n00718| ```\n00719| \n00720| ### Production Binary\n00721| ```bash\n00722| bun build packages/backend/src/server/index.ts --compile --target bun-darwin-arm64 --outfile dist/plexus2-macos\n00723| ./dist/plexus2-macos\n00724| ```\n00725| \n00726| See `packages/backend/README.md` for details.\n00727| ```\n00728| \n00729| ---\n00730| \n00731| ## Phase 9: Migration Checklist\n00732| \n00733| Use this checklist to track progress through the migration:\n00734| \n00735| ### Pre-Migration\n00736| - [ ] Read and understand this entire plan\n00737| - [ ] Back up current code\n00738| - [ ] Create a new git branch: `git checkout -b migrate/unified-fullstack`\n00739| \n00740| ### Directory Structure (Phase 2)\n00741| - [ ] Create `packages/backend/src/server/` directory\n00742| - [ ] Create `packages/backend/src/frontend/` directory\n00743| - [ ] Move all backend code from `packages/backend/src/` to `packages/backend/src/server/`\n00744| - [ ] Move all frontend code from `packages/frontend/src/` to `packages/backend/src/frontend/`\n00745| - [ ] Verify all files are in correct locations\n00746| \n00747| ### Import Updates (Phase 3)\n00748| - [ ] Update `src/server/server.ts` HTML import path\n00749| - [ ] Search for cross-package imports: `grep -r \"@plexus/\" packages/backend/src/`\n00750| - [ ] Update internal import paths in backend code\n00751| - [ ] Verify no broken imports\n00752| \n00753| ### Configuration (Phase 4)\n00754| - [ ] Update `packages/backend/tsconfig.json` with new path aliases\n00755| - [ ] Merge frontend dependencies into `packages/backend/package.json`\n00756| - [ ] Update root `package.json` workspaces and scripts\n00757| - [ ] Update `bunfig.toml` test preload path if needed\n00758| \n00759| ### HTML & Assets (Phase 5)\n00760| - [ ] Verify `src/frontend/index.html` uses relative paths\n00761| - [ ] Check asset imports use `@/` alias\n00762| - [ ] Verify all asset files are in `src/frontend/assets/`\n00763| \n00764| ### Testing (Phase 6)\n00765| - [ ] Run directory structure verification\n00766| - [ ] Run TypeScript typecheck\n00767| - [ ] Test development mode: `bun --hot packages/backend/src/server/index.ts`\n00768| - [ ] Verify frontend loads at `/ui`\n00769| - [ ] Test compilation to binary\n00770| - [ ] Test running compiled binary\n00771| - [ ] Verify assets load in compiled binary\n00772| \n00773| ### Cleanup (Phase 7)\n00774| - [ ] Remove old `packages/frontend/` directory\n00775| - [ ] Remove `packages/backend/src/frontend/dist/` directory\n00776| - [ ] Run `bun install` with new dependency structure\n00777| - [ ] Verify `.gitignore` is updated\n00778| \n00779| ### Documentation (Phase 8)\n00780| - [ ] Update `packages/backend/README.md`\n00781| - [ ] Update root `README.md`\n00782| - [ ] Update any internal team docs\n00783| \n00784| ### Final Verification\n00785| - [ ] All TypeScript compiles without errors: `bun --workspaces run typecheck`\n00786| - [ ] All tests pass: `bun test`\n00787| - [ ] Development mode works: `bun --hot packages/backend/src/server/index.ts`\n00788| - [ ] Binary compilation works: `bun build packages/backend/src/server/index.ts --compile --outfile dist/test-plexus`\n00789| - [ ] Binary runs correctly: `./dist/test-plexus`\n00790| - [ ] Git commit: `git add -A && git commit -m \"refactor: unified full-stack structure\"`\n00791| \n00792| ---\n00793| \n00794| ## Troubleshooting\n00795| \n00796| ### Issue: TypeScript errors after migration\n00797| \n00798| **Solution:**\n00799| ```bash\n00800| cd packages/backend\n00801| bun --workspaces run typecheck\n00802| ```\n00803| \n00804| Check output for specific import or path issues.\n00805| \n00806| ### Issue: Assets not found in frontend\n00807| \n00808| **Solution:**\n00809| - Verify `@/` path alias is correctly configured in `tsconfig.json`\n00810| - Check that asset files are actually in `src/frontend/assets/`\n00811| - Verify asset imports match exactly: `import logo from '@/assets/file.png'`\n00812| \n00813| ### Issue: HTML import fails in server\n00814| \n00815| **Solution:**\n00816| - Verify path is relative from `server.ts` location\n00817| - Should be: `import frontendHtml from \"../frontend/index.html\"`\n00818| - Not: `import frontendHtml from \"../../frontend/src/index.html\"`\n00819| \n00820| ### Issue: Development mode doesn't serve frontend\n00821| \n00822| **Solution:**\n00823| ```bash\n00824| # Make sure you're using --hot, not --watch\n00825| bun --hot packages/backend/src/server/index.ts\n00826| \n00827| # Check server.ts has frontend routes configured\n00828| # Should have: routes: { \"/ui\": frontendHtml, \"/ui/*\": frontendHtml }\n00829| ```\n00830| \n00831| ### Issue: Compiled binary doesn't include frontend\n00832| \n00833| **Solution:**\n00834| - Verify `server.ts` imports HTML: `import frontendHtml from \"../frontend/index.html\"`\n00835| - Build with correct target: `--compile --target bun-darwin-arm64`\n00836| - Check that HTML file exists before compilation\n00837| \n00838| ### Issue: Dependencies not found in compiled binary\n00839| \n00840| **Solution:**\n00841| - Ensure ALL dependencies are in `packages/backend/package.json`\n00842| - Don't rely on root `package.json` dependencies\n00843| - Run `bun install` in the backend package to update lock file\n00844| \n00845| ---\n00846| \n00847| ## Success Criteria\n00848| \n00849| When migration is complete and successful, you should be able to:\n00850| \n00851| ✅ Run `bun --hot packages/backend/src/server/index.ts` and have:\n00852|   - Backend API running\n00853|   - Frontend UI accessible at `/ui` with hot reloading\n00854|   - No console errors\n00855| \n00856| ✅ Run `bun build packages/backend/src/server/index.ts --compile --outfile dist/plexus2-macos` and have:\n00857|   - Binary created successfully (~60MB)\n00858|   - Binary runs as a standalone executable\n00859|   - API endpoints work without external dependencies\n00860|   - Frontend UI loads with all assets embedded\n00861| \n00862| ✅ Run `bun --workspaces run typecheck` and have:\n00863|   - No TypeScript errors\n00864|   - All imports resolve correctly\n00865|   - Path aliases work as expected\n00866| \n00867| ✅ All existing functionality preserved:\n00868|   - API routes work identically\n00869|   - Frontend components render correctly\n00870|   - Configuration system works\n00871|   - Logging and observability intact\n00872|   - All services function normally\n00873| \n00874| ---\n00875| \n00876| ## Next Steps\n00877| \n00878| 1. **Review this plan** with your team\n00879| 2. **Create a branch** for the migration\n00880| 3. **Follow Phase 1-4 sequentially** to restructure directories and configs\n00881| 4. **Run Phase 6 tests** to validate the new structure\n00882| 5. **Execute Phase 7 cleanup**\n00883| 6. **Update documentation** in Phase 8\n00884| 7. **Commit and push** your branch\n00885| 8. **Create a pull request** for team review\n00886| \n00887| **Estimated time:** 2-3 hours for a careful, methodical migration\n00888| \n00889| ---\n00890| \n00891| ## References\n00892| \n00893| - [Bun Full-Stack Dev Server Docs](https://bun.com/docs/bundler/fullstack)\n00894| - [Bun HTML Imports](https://bun.com/docs/runtime/http/server)\n00895| - [Bun Standalone Executables](https://bun.com/docs/bundler/executables)\n00896| - [Plexus AGENTS.md](./AGENTS.md) - Project standards and guidelines\n00897| \n\n(End of file - total 897 lines)\n</file>"
+                }
+            ]
+        },
+        {
+            "role": "assistant",
+            "content": "I'll implement this migration plan systematically. Let me start by examining the current directory structure and then execute the migration in phases.",
+            "tool_calls": [
+                {
+                    "id": "call_caa0cfca77db49619de6179a",
+                    "type": "function",
+                    "function": {
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+                        "arguments": "{\"command\":\"ls -la /Users/matt.cowger/workspace/plexus2/packages/\",\"description\":\"List packages directory\"}"
+                    },
+                    "index": 0
+                },
+                {
+                    "id": "call_ef9af1e752dc4238b22c4f8b",
+                    "type": "function",
+                    "function": {
+                        "name": "bash",
+                        "arguments": "{\"command\":\"ls -la /Users/matt.cowger/workspace/plexus2/packages/backend/src/\",\"description\":\"List backend src directory\"}"
+                    },
+                    "index": 0
+                },
+                {
+                    "id": "call_17176daab1384a24874ae434",
+                    "type": "function",
+                    "function": {
+                        "name": "bash",
+                        "arguments": "{\"command\":\"ls -la /Users/matt.cowger/workspace/plexus2/packages/frontend/src/\",\"description\":\"List frontend src directory\"}"
+                    },
+                    "index": 0
+                }
+            ]
+        },
+        {
+            "role": "tool",
+            "content": "total 0\ndrwxr-xr-x@  4 matt.cowger  staff  128 Jan 13 08:49 .\ndrwxr-xr-x@ 24 matt.cowger  staff  768 Jan 14 14:03 ..\ndrwxr-xr-x@  8 matt.cowger  staff  256 Jan 14 09:34 backend\ndrwxr-xr-x@ 13 matt.cowger  staff  416 Jan 14 10:00 frontend\n",
+            "tool_call_id": "call_caa0cfca77db49619de6179a"
+        },
+        {
+            "role": "tool",
+            "content": "total 48\ndrwxr-xr-x@ 13 matt.cowger  staff   416 Jan 13 08:49 .\ndrwxr-xr-x@  8 matt.cowger  staff   256 Jan 14 09:34 ..\n-rw-r--r--@  1 matt.cowger  staff  6351 Jan 13 17:12 config.ts\n-rw-r--r--@  1 matt.cowger  staff  1769 Jan 12 12:37 index.ts\ndrwxr-xr-x@  4 matt.cowger  staff   128 Jan 12 11:03 middleware\ndrwxr-xr-x@  7 matt.cowger  staff   224 Jan 12 11:02 routes\n-rw-r--r--@  1 matt.cowger  staff  9099 Jan 14 10:18 server.ts\ndrwxr-xr-x@ 21 matt.cowger  staff   672 Jan 13 22:53 services\ndrwxr-xr-x@  6 matt.cowger  staff   192 Jan 13 17:07 storage\ndrwxr-xr-x@ 12 matt.cowger  staff   384 Jan 12 17:38 tests\ndrwxr-xr-x@  8 matt.cowger  staff   256 Jan 12 13:49 transformers\ndrwxr-xr-x@ 14 matt.cowger  staff   448 Jan 13 18:17 types\ndrwxr-xr-x@  4 matt.cowger  staff   128 Jan 12 18:09 utils\n",
+            "tool_call_id": "call_ef9af1e752dc4238b22c4f8b"
+        },
+        {
+            "role": "tool",
+            "content": "total 48\ndrwxr-xr-x@ 13 matt.cowger  staff   416 Jan 14 09:40 .\ndrwxr-xr-x@ 13 matt.cowger  staff   416 Jan 14 10:00 ..\n-rw-r--r--@  1 matt.cowger  staff  2694 Jan 14 08:22 app.css\n-rw-r--r--@  1 matt.cowger  staff  4161 Jan 13 14:14 App.tsx\ndrwxr-xr-x  14 matt.cowger  staff   448 Jan 13 10:07 assets\ndrwxr-xr-x@  6 matt.cowger  staff   192 Jan 13 08:49 components\ndrwxr-xr-x@  5 matt.cowger  staff   160 Jan 13 08:49 contexts\n-rw-r--r--@  1 matt.cowger  staff   935 Jan 14 08:19 declarations.d.ts\ndrwxr-xr-x@  3 matt.cowger  staff    96 Jan 13 08:49 hooks\n-rw-r--r--   1 matt.cowger  staff   369 Jan 14 09:40 index.html\ndrwxr-xr-x@  6 matt.cowger  staff   192 Jan 13 08:49 lib\n-rw-r--r--@  1 matt.cowger  staff   279 Jan 14 08:58 main.tsx\ndrwxr-xr-x@ 15 matt.cowger  staff   480 Jan 14 08:12 pages\n",
+            "tool_call_id": "call_17176daab1384a24874ae434"
+        },
+        {
+            "role": "assistant",
+            "content": "",
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+                    },
+                    "index": 0
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+        {
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+            "tool_call_id": "call_ea222def08914a13a21c44fb"
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+                    },
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+                }
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+            "content": "Error: No such file or directory",
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+        },
+        {
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+                    },
+                    "index": 0
+                }
+            ]
+        },
+        {
+            "role": "tool",
+            "content": "Error: No such file or directory",
+            "tool_call_id": "call_b370b7abd272410b8e8fa51a"
+        },
+        {
+            "role": "assistant",
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+                    },
+                    "index": 0
+                }
+            ]
+        },
+        {
+            "role": "tool",
+            "content": "mv: app.css: No such file or directory\nmv: App.tsx: No such file or directory\nmv: assets: No such file or directory\nmv: components: No such file or directory\nmv: contexts: No such file or directory\nmv: declarations.d.ts: No such file or directory\nmv: hooks: No such file or directory\nmv: index.html: No such file or directory\nmv: lib: No such file or directory\nmv: main.tsx: No such file or directory\nmv: pages: No such file or directory\n",
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+                        "name": "bash",
+                        "arguments": "{\"command\":\"ls -la /Users/matt.cowger/workspace/plexus2/packages/backend/src/server/\",\"description\":\"Verify server directory contents\"}"
+                    },
+                    "index": 0
+                },
+                {
+                    "id": "call_0d7d44841b29492a9e9b21c2",
+                    "type": "function",
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+                        "name": "bash",
+                        "arguments": "{\"command\":\"ls -la /Users/matt.cowger/workspace/plexus2/packages/backend/src/frontend/\",\"description\":\"Verify frontend directory contents\"}"
+                    },
+                    "index": 0
+                }
+            ]
+        },
+        {
+            "role": "tool",
+            "content": "total 48\ndrwxr-xr-x@ 13 matt.cowger  staff   416 Jan 14 14:06 .\ndrwxr-xr-x@  4 matt.cowger  staff   128 Jan 14 14:06 ..\n-rw-r--r--@  1 matt.cowger  staff  6351 Jan 13 17:12 config.ts\n-rw-r--r--@  1 matt.cowger  staff  1769 Jan 12 12:37 index.ts\ndrwxr-xr-x@  4 matt.cowger  staff   128 Jan 12 11:03 middleware\ndrwxr-xr-x@  7 matt.cowger  staff   224 Jan 12 11:02 routes\n-rw-r--r--@  1 matt.cowger  staff  9099 Jan 14 10:18 server.ts\ndrwxr-xr-x@ 21 matt.cowger  staff   672 Jan 13 22:53 services\ndrwxr-xr-x@  6 matt.cowger  staff   192 Jan 13 17:07 storage\ndrwxr-xr-x@ 12 matt.cowger  staff   384 Jan 12 17:38 tests\ndrwxr-xr-x@  8 matt.cowger  staff   256 Jan 12 13:49 transformers\ndrwxr-xr-x@ 14 matt.cowger  staff   448 Jan 13 18:17 types\ndrwxr-xr-x@  4 matt.cowger  staff   128 Jan 12 18:09 utils\n",
+            "tool_call_id": "call_640ef1fb388846faa3fe89ea"
+        },
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\"./services/health-monitor\";\n00018| import { UsageStore } from \"./storage/usage-store\";\n00019| import { ErrorStore } from \"./storage/error-store\";\n00020| import { DebugStore } from \"./storage/debug-store\";\n00021| import { CostCalculator } from \"./services/cost-calculator\";\n00022| import { MetricsCollector } from \"./services/metrics-collector\";\n00023| import { UsageLogger } from \"./services/usage-logger\";\n00024| import { DebugLogger } from \"./services/debug-logger\";\n00025| import { EventEmitter } from \"./services/event-emitter\";\n00026| import { ConfigManager } from \"./services/config-manager\";\n00027| import { LogQueryService } from \"./services/log-query\";\n00028| import { TransformerFactory } from \"./services/transformer-factory\";\n00029| \n00030| // @ts-ignore - HTML import\n00031| import frontendHtml from \"../../frontend/src/index.html\";\n00032| \n00033| function withCORS(response: Response): Response {\n00034|   const headers = new Headers(response.headers);\n00035|   headers.set(\"Access-Control-Allow-Origin\", \"*\");\n00036|   headers.set(\"Access-Control-Allow-Methods\", \"GET, POST, PUT, DELETE, OPTIONS\");\n00037|   headers.set(\"Access-Control-Allow-Headers\", \"Content-Type, Authorization, X-Requested-With\");\n00038| \n00039|   return new Response(response.body, {\n00040|     status: response.status,\n00041|     statusText: response.statusText,\n00042|     headers,\n00043|   });\n00044| }\n00045| \n00046| /**\n00047|  * Request router - maps URLs to handlers\n00048|  */\n00049| async function router(req: Request, context: ServerContext, adminAuth: AdminAuth, clientIp: string): Promise<Response> {\n00050|   const url = new URL(req.url);\n00051|   const path = url.pathname;\n00052| \n00053|   // Add request ID for correlation\n00054|   const requestId = createRequestId();\n00055|   const requestLogger = logger.child({ requestId });\n00056| \n00057|   requestLogger.debug(\"Incoming request\", {\n00058|     method: req.method,\n00059|     path,\n00060|     clientIp,\n00061|   });\n00062| \n00063|   // Handle CORS preflight\n00064|   if (req.method === \"OPTIONS\") {\n00065|     return withCORS(new Response(null, { status: 204 }));\n00066|   }\n00067| \n00068|   // --- Management API (v0) ---\n00069|   if (path.startsWith(\"/v0/\")) {\n00070|     // Authenticate Admin\n00071|     const authError = await adminAuth.validate(req);\n00072|     if (authError) return withCORS(authError);\n00073| \n00074|     if (path === \"/v0/config\") {\n00075|       if (!context.configManager) return withCORS(new Response(\"Config manager not initialized\", { status: 503 }));\n00076|       return withCORS(await handleConfig(req, context.configManager));\n00077|     }\n00078| \n00079|     if (path === \"/v0/state\") {\n00080|       return withCORS(await handleState(req, context));\n00081|     }\n00082| \n00083|     if (path.startsWith(\"/v0/logs\")) {\n00084|       if (!context.logQueryService) return withCORS(new Response(\"Log query service not initialized\", { status: 503 }));\n00085|       return withCORS(await handleLogs(req, context.logQueryService));\n00086|     }\n00087| \n00088|     if (path === \"/v0/events\") {\n00089|       if (!context.eventEmitter) return withCORS(new Response(\"Event emitter not initialized\", { status: 503 }));\n00090|       return withCORS(await handleEvents(req, context.eventEmitter));\n00091|     }\n00092|   }\n00093| \n00094|   // --- Standard API ---\n00095| \n00096|   if (path === \"/health\" && req.method === \"GET\") {\n00097|     return withCORS(handleHealth(req, context.healthMonitor));\n00098|   }\n00099| \n00100|   if (path === \"/ready\" && req.method === \"GET\") {\n00101|     return withCORS(handleReady(req));\n00102|   }\n00103| \n00104|   if (path === \"/v1/chat/completions\" && req.method === \"POST\") {\n00105| \n00106|     return withCORS(await handleChatCompletions(req, context, requestId, clientIp));\n00107|   }\n00108| \n00109|   if (path === \"/v1/messages\" && req.method === \"POST\") {\n00110|     return withCORS(await handleMessages(req, context, requestId, clientIp));\n00111|   }\n00112| \n00113|   if (path === \"/v1/models\" && req.method === \"GET\") {\n00114|     return withCORS(await handleModels(req, context.config, requestId));\n00115|   }\n00116| \n00117| \n00118| \n00119|   // 404 for unknown routes\n00120|   requestLogger.debug(\"Route not found\", { path });\n00121|   return withCORS(Response.json(\n00122|     {\n00123|       error: \"Not Found\",\n00124|       message: `Route ${path} not found`,\n00125|     },\n00126|     { status: 404 }\n00127|   ));\n00128| }\n00129| \n00130| /**\n00131|  * Creates and starts the HTTP server\n00132|  */\n00133| export async function createServer(config: PlexusConfig): Promise<{ server: any; shutdown: () => Promise<void> }> {\n00134|   // Initialize resilience services\n00135|   const cooldownManager = new CooldownManager(config);\n00136|   const healthMonitor = new HealthMonitor(config, cooldownManager);\n00137| \n00138|   // Initialize Management Services (Phase 8)\n00139|   const eventEmitter = new EventEmitter(\n00140|     config.events?.maxClients,\n00141|     config.events?.heartbeatIntervalMs\n00142|   );\n00143| \n00144|   const configManager = new ConfigManager(\n00145|     // Assume config file path from existing loader logic if possible, \n00146|     // but here we might need to know where it came from.\n00147|     // For now, we'll assume default \"./config/plexus.yaml\" or env\n00148|     // Ideally loadConfig returns path too, but for now:\n00149|     \"config/plexus.yaml\", \n00150|     config,\n00151|     eventEmitter\n00152|   );\n00153| \n00154|   const adminAuth = new AdminAuth(config);\n00155| \n00156|   // Initialize observability services (Phase 7)\n00157|   let usageLogger: UsageLogger | undefined;\n00158|   let metricsCollector: MetricsCollector | undefined;\n00159|   let costCalculator: CostCalculator | undefined;\n00160|   let debugLogger: DebugLogger | undefined;\n00161|   let logQueryService: LogQueryService | undefined;\n00162| \n00163|   let usageStore: UsageStore | undefined;\n00164|   let errorStore: ErrorStore | undefined;\n00165|   let debugStore: DebugStore | undefined;\n00166| \n00167|   if (config.logging.usage?.enabled) {\n00168|     // Initialize storage\n00169|     usageStore = new UsageStore(\n00170|       config.logging.usage.storagePath,\n00171|       config.logging.usage.retentionDays\n00172|     );\n00173|     await usageStore.initialize();\n00174| \n00175|     errorStore = new ErrorStore(\n00176|       config.logging.errors.storagePath,\n00177|       config.logging.errors.retentionDays\n00178|     );\n00179|     await errorStore.initialize();\n00180| \n00181|     // Initialize cost calculator\n00182|     costCalculator = new CostCalculator(config.pricing);\n00183| \n00184|     // Initialize metrics collector (5 minute rolling window)\n00185|     metricsCollector = new MetricsCollector(5);\n00186| \n00187|     // Initialize usage logger\n00188|     usageLogger = new UsageLogger(\n00189|       usageStore,\n00190|       errorStore,\n00191|       costCalculator,\n00192|       metricsCollector,\n00193|       true,\n00194|       eventEmitter // Pass event emitter\n00195|     );\n00196| \n00197|     logger.info(\"Observability services initialized\");\n00198|   }\n00199| \n00200|   // Initialize debug store (shared between Logger and QueryService)\n00201|   // We initialize it even if debug logging is disabled, to allow querying historical logs\n00202|   debugStore = new DebugStore(\n00203|       config.logging.debug?.storagePath || \"./logs/debug\",\n00204|       config.logging.debug?.retentionDays || 7,\n00205|       config.logging.debug?.enabled || false\n00206|   );\n00207|   \n00208|   // Always create transformer factory and debugLogger for stream reconstruction and usage tracking\n00209|   // The debugStore.store() method will skip persistence if debug logging is disabled\n00210|   const transformerFactory = new TransformerFactory();\n00211|   \n00212|   debugLogger = new DebugLogger({\n00213|     enabled: config.logging.debug?.enabled || false,\n00214|     storagePath: config.logging.debug?.storagePath || \"./logs/debug\",\n00215|     retentionDays: config.logging.debug?.retentionDays || 7,\n00216|   }, debugStore, transformerFactory, usageLogger);\n00217|   \n00218|   // Only initialize storage if debug logging is enabled\n00219|   if (config.logging.debug?.enabled) {\n00220|     await debugLogger.initialize();\n00221|   }\n00222| \n00223|   // Initialize Log Query Service\n00224|   if (usageStore && errorStore && debugStore) {\n00225|       logQueryService = new LogQueryService(usageStore, errorStore, debugStore);\n00226|   }\n00227| \n00228|   const context: ServerContext = {\n00229|     config,\n00230|     cooldownManager,\n00231|     healthMonitor,\n00232|     usageLogger,\n00233|     metricsCollector,\n00234|     costCalculator,\n00235|     debugLogger,\n00236|     eventEmitter,\n00237|     configManager,\n00238|     logQueryService\n00239|   };\n00240| \n00241|   const server = Bun.serve({\n00242|     port: config.server.port,\n00243|     hostname: config.server.host,\n00244|     idleTimeout: 60, // 60 seconds to allow for 30s keep-alive heatbeats for SSE\n00245|     development: process.env.NODE_ENV !== \"production\" ? {\n00246|       hmr: true,\n00247|       console: true,\n00248|     } : false,\n00249|     routes: {\n00250|       // Frontend UI routes - serve the HTML app\n00251|       \"/ui\": frontendHtml,\n00252|     \"/ui/*\": frontendHtml,\n00253|     },\n00254|     fetch: (req: Request, server): Promise<Response> | Response => {\n00255|   const clientIp = req.headers.get(\"x-forwarded-for\") || server.requestIP(req)?.address || \"0.0.0.0\";\n00256|       return router(req, context, adminAuth, clientIp);\n00257|     },\n00258|   });\n00259| \n00260|   logger.info(\"Server started\", {\n00261|     host: config.server.host,\n00262|     port: config.server.port,\n00263|     url: `http://${config.server.host}:${config.server.port}`,\n00264|   });\n00265| \n00266|   // Graceful shutdown handler\n00267|   const shutdown = async (): Promise<void> => {\n00268|     logger.info(\"Shutting down server...\");\n00269|     server.stop();\n00270|     eventEmitter.shutdown();\n00271|     logger.info(\"Server shutdown complete\");\n00272|   };\n00273| \n00274|   return { server, shutdown };\n00275| }\n00276| \n\n(End of file - total 276 lines)\n</file>",
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+                    "function": {
+                        "name": "edit",
+                        "arguments": "{\"filePath\":\"/Users/matt.cowger/plexus2/packages/backend/tsconfig.json\",\"oldString\":\"  \\\"compilerOptions\\\": {\\n    \\\"baseUrl\\\": \\\".\\\",\\n    \\\"paths\\\": {\\n      \\\"src/*\\\": [\\\"./src/*\\\"]\\n    }\\n  },\",\"newString\":\"  \\\"compilerOptions\\\": {\\n    \\\"baseUrl\\\": \\\".\\\",\\n    \\\"paths\\\": {\\n      \\\"src/*\\\": [\\\"./src/server/*\\\"],\\n      \\\"@/*\\\": [\\\"./src/frontend/*\\\"]\\n    }\\n  },\"}"
+                    },
+                    "index": 0
+                }
+            ]
+        },
+        {
+            "role": "tool",
+            "content": "Error: File /Users/matt.cowger/plexus2/packages/backend/tsconfig.json not found",
+            "tool_call_id": "call_5509e2ffc51542e7b7205b32"
+        }
+    ],
+    "model": "hf:zai-org/GLM-4.7",
+    "max_tokens": 32000,
+    "stream": true,
+    "stream_options": {
+        "include_usage": true
+    },
+    "tools": [
+        {
+            "type": "function",
+            "function": {
+                "name": "question",
+                "description": "Use this tool when you need to ask the user questions during execution. This allows you to:\n1. Gather user preferences or requirements\n2. Clarify ambiguous instructions\n3. Get decisions on implementation choices as you work\n4. Offer choices to the user about what direction to take.\n\nUsage notes:\n- Users will always be able to select \"Other\" to provide custom text input\n- Answers are returned as arrays of labels; set `multiple: true` to allow selecting more than one\n- If you recommend a specific option, make that the first option in the list and add \"(Recommended)\" at the end of the label\n",
+                "parameters": {
+                    "$schema": "https://json-schema.org/draft/2020-12/schema",
+                    "type": "object",
+                    "properties": {
+                        "questions": {
+                            "description": "Questions to ask",
+                            "type": "array",
+                            "items": {
+                                "type": "object",
+                                "properties": {
+                                    "question": {
+                                        "description": "Complete question",
+                                        "type": "string"
+                                    },
+                                    "header": {
+                                        "description": "Very short label (max 12 chars)",
+                                        "type": "string",
+                                        "maxLength": 12
+                                    },
+                                    "options": {
+                                        "description": "Available choices",
+                                        "type": "array",
+                                        "items": {
+                                            "ref": "QuestionOption",
+                                            "type": "object",
+                                            "properties": {
+                                                "label": {
+                                                    "description": "Display text (1-5 words, concise)",
+                                                    "type": "string"
+                                                },
+                                                "description": {
+                                                    "description": "Explanation of choice",
+                                                    "type": "string"
+                                                }
+                                            },
+                                            "required": [
+                                                "label",
+                                                "description"
+                                            ],
+                                            "additionalProperties": false
+                                        }
+                                    },
+                                    "multiple": {
+                                        "description": "Allow selecting multiple choices",
+                                        "type": "boolean"
+                                    }
+                                },
+                                "required": [
+                                    "question",
+                                    "header",
+                                    "options"
+                                ],
+                                "additionalProperties": false
+                            }
+                        }
+                    },
+                    "required": [
+                        "questions"
+                    ],
+                    "additionalProperties": false
+                }
+            }
+        },
+        {
+            "type": "function",
+            "function": {
+                "name": "bash",
+                "description": "Executes a given bash command in a persistent shell session with optional timeout, ensuring proper handling and security measures.\n\nAll commands run in /Users/matt.cowger/workspace/plexus2 by default. Use the `workdir` parameter if you need to run a command in a different directory. AVOID using `cd <directory> && <command>` patterns - use `workdir` instead.\n\nIMPORTANT: This tool is for terminal operations like git, npm, docker, etc. DO NOT use it for file operations (reading, writing, editing, searching, finding files) - use the specialized tools for this instead.\n\nBefore executing the command, please follow these steps:\n\n1. Directory Verification:\n   - If the command will create new directories or files, first use `ls` to verify the parent directory exists and is the correct location\n   - For example, before running \"mkdir foo/bar\", first use `ls foo` to check that \"foo\" exists and is the intended parent directory\n\n2. Command Execution:\n   - Always quote file paths that contain spaces with double quotes (e.g., rm \"path with spaces/file.txt\")\n   - Examples of proper quoting:\n     - mkdir \"/Users/name/My Documents\" (correct)\n     - mkdir /Users/name/My Documents (incorrect - will fail)\n     - python \"/path/with spaces/script.py\" (correct)\n     - python /path/with spaces/script.py (incorrect - will fail)\n   - After ensuring proper quoting, execute the command.\n   - Capture the output of the command.\n\nUsage notes:\n  - The command argument is required.\n  - You can specify an optional timeout in milliseconds. If not specified, commands will time out after 120000ms (2 minutes).\n  - It is very helpful if you write a clear, concise description of what this command does in 5-10 words.\n  - If the output exceeds 2000 lines or 51200 bytes, it will be truncated and the full output will be written to a file. You can use Read with offset/limit to read specific sections or Grep to search the full content. Because of this, you do NOT need to use `head`, `tail`, or other truncation commands to limit output - just run the command directly.\n\n  - Avoid using Bash with the `find`, `grep`, `cat`, `head`, `tail`, `sed`, `awk`, or `echo` commands, unless explicitly instructed or when these commands are truly necessary for the task. Instead, always prefer using the dedicated tools for these commands:\n    - File search: Use Glob (NOT find or ls)\n    - Content search: Use Grep (NOT grep or rg)\n    - Read files: Use Read (NOT cat/head/tail)\n    - Edit files: Use Edit (NOT sed/awk)\n    - Write files: Use Write (NOT echo >/cat <<EOF)\n    - Communication: Output text directly (NOT echo/printf)\n  - When issuing multiple commands:\n    - If the commands are independent and can run in parallel, make multiple Bash tool calls in a single message. For example, if you need to run \"git status\" and \"git diff\", send a single message with two Bash tool calls in parallel.\n    - If the commands depend on each other and must run sequentially, use a single Bash call with '&&' to chain them together (e.g., `git add . && git commit -m \"message\" && git push`). For instance, if one operation must complete before another starts (like mkdir before cp, Write before Bash for git operations, or git add before git commit), run these operations sequentially instead.\n    - Use ';' only when you need to run commands sequentially but don't care if earlier commands fail\n    - DO NOT use newlines to separate commands (newlines are ok in quoted strings)\n  - AVOID using `cd <directory> && <command>`. Use the `workdir` parameter to change directories instead.\n    <good-example>\n    Use workdir=\"/foo/bar\" with command: pytest tests\n    </good-example>\n    <bad-example>\n    cd /foo/bar && pytest tests\n    </bad-example>\n\n# Committing changes with git\n\nOnly create commits when requested by the user. If unclear, ask first. When the user asks you to create a new git commit, follow these steps carefully:\n\nGit Safety Protocol:\n- NEVER update the git config\n- NEVER run destructive/irreversible git commands (like push --force, hard reset, etc) unless the user explicitly requests them\n- NEVER skip hooks (--no-verify, --no-gpg-sign, etc) unless the user explicitly requests it\n- NEVER run force push to main/master, warn the user if they request it\n- Avoid git commit --amend. ONLY use --amend when ALL conditions are met:\n  (1) User explicitly requested amend, OR commit SUCCEEDED but pre-commit hook auto-modified files that need including\n  (2) HEAD commit was created by you in this conversation (verify: git log -1 --format='%an %ae')\n  (3) Commit has NOT been pushed to remote (verify: git status shows \"Your branch is ahead\")\n- CRITICAL: If commit FAILED or was REJECTED by hook, NEVER amend - fix the issue and create a NEW commit\n- CRITICAL: If you already pushed to remote, NEVER amend unless user explicitly requests it (requires force push)\n- NEVER commit changes unless the user explicitly asks you to. It is VERY IMPORTANT to only commit when explicitly asked, otherwise the user will feel that you are being too proactive.\n\n1. You can call multiple tools in a single response. When multiple independent pieces of information are requested and all commands are likely to succeed, run multiple tool calls in parallel for optimal performance. run the following bash commands in parallel, each using the Bash tool:\n  - Run a git status command to see all untracked files.\n  - Run a git diff command to see both staged and unstaged changes that will be committed.\n  - Run a git log command to see recent commit messages, so that you can follow this repository's commit message style.\n2. Analyze all staged changes (both previously staged and newly added) and draft a commit message:\n  - Summarize the nature of the changes (eg. new feature, enhancement to an existing feature, bug fix, refactoring, test, docs, etc.). Ensure the message accurately reflects the changes and their purpose (i.e. \"add\" means a wholly new feature, \"update\" means an enhancement to an existing feature, \"fix\" means a bug fix, etc.).\n  - Do not commit files that likely contain secrets (.env, credentials.json, etc.). Warn the user if they specifically request to commit those files\n  - Draft a concise (1-2 sentences) commit message that focuses on the \"why\" rather than the \"what\"\n  - Ensure it accurately reflects the changes and their purpose\n3. You can call multiple tools in a single response. When multiple independent pieces of information are requested and all commands are likely to succeed, run multiple tool calls in parallel for optimal performance. run the following commands:\n   - Add relevant untracked files to the staging area.\n   - Create the commit with a message\n   - Run git status after the commit completes to verify success.\n   Note: git status depends on the commit completing, so run it sequentially after the commit.\n4. If the commit fails due to pre-commit hook, fix the issue and create a NEW commit (see amend rules above)\n\nImportant notes:\n- NEVER run additional commands to read or explore code, besides git bash commands\n- NEVER use the TodoWrite or Task tools\n- DO NOT push to the remote repository unless the user explicitly asks you to do so\n- IMPORTANT: Never use git commands with the -i flag (like git rebase -i or git add -i) since they require interactive input which is not supported.\n- If there are no changes to commit (i.e., no untracked files and no modifications), do not create an empty commit\n\n# Creating pull requests\nUse the gh command via the Bash tool for ALL GitHub-related tasks including working with issues, pull requests, checks, and releases. If given a Github URL use the gh command to get the information needed.\n\nIMPORTANT: When the user asks you to create a pull request, follow these steps carefully:\n\n1. You can call multiple tools in a single response. When multiple independent pieces of information are requested and all commands are likely to succeed, run multiple tool calls in parallel for optimal performance. run the following bash commands in parallel using the Bash tool, in order to understand the current state of the branch since it diverged from the main branch:\n   - Run a git status command to see all untracked files\n   - Run a git diff command to see both staged and unstaged changes that will be committed\n   - Check if the current branch tracks a remote branch and is up to date with the remote, so you know if you need to push to the remote\n   - Run a git log command and `git diff [base-branch]...HEAD` to understand the full commit history for the current branch (from the time it diverged from the base branch)\n2. Analyze all changes that will be included in the pull request, making sure to look at all relevant commits (NOT just the latest commit, but ALL commits that will be included in the pull request!!!), and draft a pull request summary\n3. You can call multiple tools in a single response. When multiple independent pieces of information are requested and all commands are likely to succeed, run multiple tool calls in parallel for optimal performance. run the following commands in parallel:\n   - Create new branch if needed\n   - Push to remote with -u flag if needed\n   - Create PR using gh pr create with the format below. Use a HEREDOC to pass the body to ensure correct formatting.\n<example>\ngh pr create --title \"the pr title\" --body \"$(cat <<'EOF'\n## Summary\n<1-3 bullet points>\n</example>\n\nImportant:\n- DO NOT use the TodoWrite or Task tools\n- Return the PR URL when you're done, so the user can see it\n\n# Other common operations\n- View comments on a Github PR: gh api repos/foo/bar/pulls/123/comments\n",
+                "parameters": {
+                    "$schema": "https://json-schema.org/draft/2020-12/schema",
+                    "type": "object",
+                    "properties": {
+                        "command": {
+                            "description": "The command to execute",
+                            "type": "string"
+                        },
+                        "timeout": {
+                            "description": "Optional timeout in milliseconds",
+                            "type": "number"
+                        },
+                        "workdir": {
+                            "description": "The working directory to run the command in. Defaults to /Users/matt.cowger/workspace/plexus2. Use this instead of 'cd' commands.",
+                            "type": "string"
+                        },
+                        "description": {
+                            "description": "Clear, concise description of what this command does in 5-10 words. Examples:\nInput: ls\nOutput: Lists files in current directory\n\nInput: git status\nOutput: Shows working tree status\n\nInput: npm install\nOutput: Installs package dependencies\n\nInput: mkdir foo\nOutput: Creates directory 'foo'",
+                            "type": "string"
+                        }
+                    },
+                    "required": [
+                        "command",
+                        "description"
+                    ],
+                    "additionalProperties": false
+                }
+            }
+        },
+        {
+            "type": "function",
+            "function": {
+                "name": "read",
+                "description": "Reads a file from the local filesystem. You can access any file directly by using this tool.\nAssume this tool is able to read all files on the machine. If the User provides a path to a file assume that path is valid. It is okay to read a file that does not exist; an error will be returned.\n\nUsage:\n- The filePath parameter must be an absolute path, not a relative path\n- By default, it reads up to 2000 lines starting from the beginning of the file\n- You can optionally specify a line offset and limit (especially handy for long files), but it's recommended to read the whole file by not providing these parameters\n- Any lines longer than 2000 characters will be truncated\n- Results are returned using cat -n format, with line numbers starting at 1\n- You have the capability to call multiple tools in a single response. It is always better to speculatively read multiple files as a batch that are potentially useful.\n- If you read a file that exists but has empty contents you will receive a system reminder warning in place of file contents.\n- You can read image files using this tool.\n",
+                "parameters": {
+                    "$schema": "https://json-schema.org/draft/2020-12/schema",
+                    "type": "object",
+                    "properties": {
+                        "filePath": {
+                            "description": "The path to the file to read",
+                            "type": "string"
+                        },
+                        "offset": {
+                            "description": "The line number to start reading from (0-based)",
+                            "type": "number"
+                        },
+                        "limit": {
+                            "description": "The number of lines to read (defaults to 2000)",
+                            "type": "number"
+                        }
+                    },
+                    "required": [
+                        "filePath"
+                    ],
+                    "additionalProperties": false
+                }
+            }
+        },
+        {
+            "type": "function",
+            "function": {
+                "name": "glob",
+                "description": "- Fast file pattern matching tool that works with any codebase size\n- Supports glob patterns like \"**/*.js\" or \"src/**/*.ts\"\n- Returns matching file paths sorted by modification time\n- Use this tool when you need to find files by name patterns\n- When you are doing an open-ended search that may require multiple rounds of globbing and grepping, use the Task tool instead\n- You have the capability to call multiple tools in a single response. It is always better to speculatively perform multiple searches as a batch that are potentially useful.\n",
+                "parameters": {
+                    "$schema": "https://json-schema.org/draft/2020-12/schema",
+                    "type": "object",
+                    "properties": {
+                        "pattern": {
+                            "description": "The glob pattern to match files against",
+                            "type": "string"
+                        },
+                        "path": {
+                            "description": "The directory to search in. If not specified, the current working directory will be used. IMPORTANT: Omit this field to use the default directory. DO NOT enter \"undefined\" or \"null\" - simply omit it for the default behavior. Must be a valid directory path if provided.",
+                            "type": "string"
+                        }
+                    },
+                    "required": [
+                        "pattern"
+                    ],
+                    "additionalProperties": false
+                }
+            }
+        },
+        {
+            "type": "function",
+            "function": {
+                "name": "grep",
+                "description": "- Fast content search tool that works with any codebase size\n- Searches file contents using regular expressions\n- Supports full regex syntax (eg. \"log.*Error\", \"function\\s+\\w+\", etc.)\n- Filter files by pattern with the include parameter (eg. \"*.js\", \"*.{ts,tsx}\")\n- Returns file paths and line numbers with at least one match sorted by modification time\n- Use this tool when you need to find files containing specific patterns\n- If you need to identify/count the number of matches within files, use the Bash tool with `rg` (ripgrep) directly. Do NOT use `grep`.\n- When you are doing an open-ended search that may require multiple rounds of globbing and grepping, use the Task tool instead\n",
+                "parameters": {
+                    "$schema": "https://json-schema.org/draft/2020-12/schema",
+                    "type": "object",
+                    "properties": {
+                        "pattern": {
+                            "description": "The regex pattern to search for in file contents",
+                            "type": "string"
+                        },
+                        "path": {
+                            "description": "The directory to search in. Defaults to the current working directory.",
+                            "type": "string"
+                        },
+                        "include": {
+                            "description": "File pattern to include in the search (e.g. \"*.js\", \"*.{ts,tsx}\")",
+                            "type": "string"
+                        }
+                    },
+                    "required": [
+                        "pattern"
+                    ],
+                    "additionalProperties": false
+                }
+            }
+        },
+        {
+            "type": "function",
+            "function": {
+                "name": "edit",
+                "description": "Performs exact string replacements in files. \n\nUsage:\n- You must use your `Read` tool at least once in the conversation before editing. This tool will error if you attempt an edit without reading the file. \n- When editing text from Read tool output, ensure you preserve the exact indentation (tabs/spaces) as it appears AFTER the line number prefix. The line number prefix format is: spaces + line number + tab. Everything after that tab is the actual file content to match. Never include any part of the line number prefix in the oldString or newString.\n- ALWAYS prefer editing existing files in the codebase. NEVER write new files unless explicitly required.\n- Only use emojis if the user explicitly requests it. Avoid adding emojis to files unless asked.\n- The edit will FAIL if `oldString` is not found in the file with an error \"oldString not found in content\".\n- The edit will FAIL if `oldString` is found multiple times in the file with an error \"oldString found multiple times and requires more code context to uniquely identify the intended match\". Either provide a larger string with more surrounding context to make it unique or use `replaceAll` to change every instance of `oldString`. \n- Use `replaceAll` for replacing and renaming strings across the file. This parameter is useful if you want to rename a variable for instance.\n",
+                "parameters": {
+                    "$schema": "https://json-schema.org/draft/2020-12/schema",
+                    "type": "object",
+                    "properties": {
+                        "filePath": {
+                            "description": "The absolute path to the file to modify",
+                            "type": "string"
+                        },
+                        "oldString": {
+                            "description": "The text to replace",
+                            "type": "string"
+                        },
+                        "newString": {
+                            "description": "The text to replace it with (must be different from oldString)",
+                            "type": "string"
+                        },
+                        "replaceAll": {
+                            "description": "Replace all occurrences of oldString (default false)",
+                            "type": "boolean"
+                        }
+                    },
+                    "required": [
+                        "filePath",
+                        "oldString",
+                        "newString"
+                    ],
+                    "additionalProperties": false
+                }
+            }
+        },
+        {
+            "type": "function",
+            "function": {
+                "name": "write",
+                "description": "Writes a file to the local filesystem.\n\nUsage:\n- This tool will overwrite the existing file if there is one at the provided path.\n- If this is an existing file, you MUST use the Read tool first to read the file's contents. This tool will fail if you did not read the file first.\n- ALWAYS prefer editing existing files in the codebase. NEVER write new files unless explicitly required.\n- NEVER proactively create documentation files (*.md) or README files. Only create documentation files if explicitly requested by the User.\n- Only use emojis if the user explicitly requests it. Avoid writing emojis to files unless asked.\n",
+                "parameters": {
+                    "$schema": "https://json-schema.org/draft/2020-12/schema",
+                    "type": "object",
+                    "properties": {
+                        "content": {
+                            "description": "The content to write to the file",
+                            "type": "string"
+                        },
+                        "filePath": {
+                            "description": "The absolute path to the file to write (must be absolute, not relative)",
+                            "type": "string"
+                        }
+                    },
+                    "required": [
+                        "content",
+                        "filePath"
+                    ],
+                    "additionalProperties": false
+                }
+            }
+        },
+        {
+            "type": "function",
+            "function": {
+                "name": "task",
+                "description": "Launch a new agent to handle complex, multistep tasks autonomously.\n\nAvailable agent types and the tools they have access to:\n- general: General-purpose agent for researching complex questions and executing multi-step tasks. Use this agent to execute multiple units of work in parallel.\n- explore: Fast agent specialized for exploring codebases. Use this when you need to quickly find files by patterns (eg. \"src/components/**/*.tsx\"), search code for keywords (eg. \"API endpoints\"), or answer questions about the codebase (eg. \"how do API endpoints work?\"). When calling this agent, specify the desired thoroughness level: \"quick\" for basic searches, \"medium\" for moderate exploration, or \"very thorough\" for comprehensive analysis across multiple locations and naming conventions.\n\nWhen using the Task tool, you must specify a subagent_type parameter to select which agent type to use.\n\nWhen to use the Task tool:\n- When you are instructed to execute custom slash commands. Use the Task tool with the slash command invocation as the entire prompt. The slash command can take arguments. For example: Task(description=\"Check the file\", prompt=\"/check-file path/to/file.py\")\n\nWhen NOT to use the Task tool:\n- If you want to read a specific file path, use the Read or Glob tool instead of the Task tool, to find the match more quickly\n- If you are searching for a specific class definition like \"class Foo\", use the Glob tool instead, to find the match more quickly\n- If you are searching for code within a specific file or set of 2-3 files, use the Read tool instead of the Task tool, to find the match more quickly\n- Other tasks that are not related to the agent descriptions above\n\n\nUsage notes:\n1. Launch multiple agents concurrently whenever possible, to maximize performance; to do that, use a single message with multiple tool uses\n2. When the agent is done, it will return a single message back to you. The result returned by the agent is not visible to the user. To show the user the result, you should send a text message back to the user with a concise summary of the result.\n3. Each agent invocation is stateless unless you provide a session_id. Your prompt should contain a highly detailed task description for the agent to perform autonomously and you should specify exactly what information the agent should return back to you in its final and only message to you.\n4. The agent's outputs should generally be trusted\n5. Clearly tell the agent whether you expect it to write code or just to do research (search, file reads, web fetches, etc.), since it is not aware of the user's intent\n6. If the agent description mentions that it should be used proactively, then you should try your best to use it without the user having to ask for it first. Use your judgement.\n\nExample usage (NOTE: The agents below are fictional examples for illustration only - use the actual agents listed above):\n\n<example_agent_descriptions>\n\"code-reviewer\": use this agent after you are done writing a significant piece of code\n\"greeting-responder\": use this agent when to respond to user greetings with a friendly joke\n</example_agent_description>\n\n<example>\nuser: \"Please write a function that checks if a number is prime\"\nassistant: Sure let me write a function that checks if a number is prime\nassistant: First let me use the Write tool to write a function that checks if a number is prime\nassistant: I'm going to use the Write tool to write the following code:\n<code>\nfunction isPrime(n) {\n  if (n <= 1) return false\n  for (let i = 2; i * i <= n; i++) {\n    if (n % i === 0) return false\n  }\n  return true\n}\n</code>\n<commentary>\nSince a significant piece of code was written and the task was completed, now use the code-reviewer agent to review the code\n</commentary>\nassistant: Now let me use the code-reviewer agent to review the code\nassistant: Uses the Task tool to launch the code-reviewer agent\n</example>\n\n<example>\nuser: \"Hello\"\n<commentary>\nSince the user is greeting, use the greeting-responder agent to respond with a friendly joke\n</commentary>\nassistant: \"I'm going to use the Task tool to launch the with the greeting-responder agent\"\n</example>\n",
+                "parameters": {
+                    "$schema": "https://json-schema.org/draft/2020-12/schema",
+                    "type": "object",
+                    "properties": {
+                        "description": {
+                            "description": "A short (3-5 words) description of the task",
+                            "type": "string"
+                        },
+                        "prompt": {
+                            "description": "The task for the agent to perform",
+                            "type": "string"
+                        },
+                        "subagent_type": {
+                            "description": "The type of specialized agent to use for this task",
+                            "type": "string"
+                        },
+                        "session_id": {
+                            "description": "Existing Task session to continue",
+                            "type": "string"
+                        },
+                        "command": {
+                            "description": "The command that triggered this task",
+                            "type": "string"
+                        }
+                    },
+                    "required": [
+                        "description",
+                        "prompt",
+                        "subagent_type"
+                    ],
+                    "additionalProperties": false
+                }
+            }
+        },
+        {
+            "type": "function",
+            "function": {
+                "name": "webfetch",
+                "description": "- Fetches content from a specified URL\n- Takes a URL and optional format as input\n- Fetches the URL content, converts to requested format (markdown by default)\n- Returns the content in the specified format\n- Use this tool when you need to retrieve and analyze web content\n\nUsage notes:\n  - IMPORTANT: if another tool is present that offers better web fetching capabilities, is more targeted to the task, or has fewer restrictions, prefer using that tool instead of this one.\n  - The URL must be a fully-formed valid URL\n  - HTTP URLs will be automatically upgraded to HTTPS\n  - Format options: \"markdown\" (default), \"text\", or \"html\"\n  - This tool is read-only and does not modify any files\n  - Results may be summarized if the content is very large\n",
+                "parameters": {
+                    "$schema": "https://json-schema.org/draft/2020-12/schema",
+                    "type": "object",
+                    "properties": {
+                        "url": {
+                            "description": "The URL to fetch content from",
+                            "type": "string"
+                        },
+                        "format": {
+                            "description": "The format to return the content in (text, markdown, or html). Defaults to markdown.",
+                            "default": "markdown",
+                            "type": "string",
+                            "enum": [
+                                "text",
+                                "markdown",
+                                "html"
+                            ]
+                        },
+                        "timeout": {
+                            "description": "Optional timeout in seconds (max 120)",
+                            "type": "number"
+                        }
+                    },
+                    "required": [
+                        "url",
+                        "format"
+                    ],
+                    "additionalProperties": false
+                }
+            }
+        },
+        {
+            "type": "function",
+            "function": {
+                "name": "todowrite",
+                "description": "Use this tool to create and manage a structured task list for your current coding session. This helps you track progress, organize complex tasks, and demonstrate thoroughness to the user.\nIt also helps the user understand the progress of the task and overall progress of their requests.\n\n## When to Use This Tool\nUse this tool proactively in these scenarios:\n\n1. Complex multistep tasks - When a task requires 3 or more distinct steps or actions\n2. Non-trivial and complex tasks - Tasks that require careful planning or multiple operations\n3. User explicitly requests todo list - When the user directly asks you to use the todo list\n4. User provides multiple tasks - When users provide a list of things to be done (numbered or comma-separated)\n5. After receiving new instructions - Immediately capture user requirements as todos. Feel free to edit the todo list based on new information.\n6. After completing a task - Mark it complete and add any new follow-up tasks\n7. When you start working on a new task, mark the todo as in_progress. Ideally you should only have one todo as in_progress at a time. Complete existing tasks before starting new ones.\n\n## When NOT to Use This Tool\n\nSkip using this tool when:\n1. There is only a single, straightforward task\n2. The task is trivial and tracking it provides no organizational benefit\n3. The task can be completed in less than 3 trivial steps\n4. The task is purely conversational or informational\n\nNOTE that you should not use this tool if there is only one trivial task to do. In this case you are better off just doing the task directly.\n\n## Examples of When to Use the Todo List\n\n<example>\nUser: I want to add a dark mode toggle to the application settings. Make sure you run the tests and build when you're done!\nAssistant: I'll help add a dark mode toggle to your application settings. Let me create a todo list to track this implementation.\n*Creates todo list with the following items:*\n1. Create dark mode toggle component in Settings page\n2. Add dark mode state management (context/store)\n3. Implement CSS-in-JS styles for dark theme\n4. Update existing components to support theme switching\n5. Run tests and build process, addressing any failures or errors that occur\n*Begins working on the first task*\n\n<reasoning>\nThe assistant used the todo list because:\n1. Adding dark mode is a multi-step feature requiring UI, state management, and styling changes\n2. The user explicitly requested tests and build be run afterward\n3. The assistant inferred that tests and build need to pass by adding \"Ensure tests and build succeed\" as the final task\n</reasoning>\n</example>\n\n<example>\nUser: Help me rename the function getCwd to getCurrentWorkingDirectory across my project\nAssistant: Let me first search through your codebase to find all occurrences of 'getCwd'.\n*Uses grep or search tools to locate all instances of getCwd in the codebase*\nAssistant: I've found 15 instances of 'getCwd' across 8 different files. Let me create a todo list to track these changes.\n*Creates todo list with specific items for each file that needs updating*\n\n<reasoning>\nThe assistant used the todo list because:\n1. First, the assistant searched to understand the scope of the task\n2. Upon finding multiple occurrences across different files, it determined this was a complex task with multiple steps\n3. The todo list helps ensure every instance is tracked and updated systematically\n4. This approach prevents missing any occurrences and maintains code consistency\n</reasoning>\n</example>\n\n\n<example>\nUser: I need to implement these features for my e-commerce site: user registration, product catalog, shopping cart, and checkout flow.\nAssistant: I'll help implement these features. First, let's add all the features to the todo list.\n*Creates a todo list breaking down each feature into specific tasks based on the project architecture*\nAssistant: Let's start with user registration. This will involve creating database models, API endpoints, and frontend forms that integrate with your existing authentication system.\n\n<reasoning>\nThe assistant used the todo list because:\n1. The user provided multiple complex features to implement in a comma separated list\n2. The todo list helps organize these large features into manageable tasks\n3. This approach allows for tracking progress across the entire implementation\n</reasoning>\n</example>\n\n<example>\nUser: Can you help optimize my React application? It's rendering slowly and has performance issues.</user>\nAssistant: I'll help optimize your React application. First, let me examine your codebase to identify potential performance bottlenecks.\n*Reviews component structure, render patterns, state management, and data fetching*\nAssistant: After analyzing your codebase, I've identified several performance issues. Let me create a todo list to track our optimization efforts.\n*Creates todo list with items like: 1) Implement memoization for expensive calculations in ProductList, 2) Add virtualization for long lists in Dashboard, 3) Optimize image loading in Gallery component, 4) Fix state update loops in ShoppingCart, 5) Review bundle size and implement code splitting*\nLet's start by implementing memoization for the expensive calculations in your ProductList component.</assistant>\n\n<reasoning>\nThe assistant used the todo list because:\n1. First, the assistant examined the codebase to identify specific performance issues\n2. Based on this analysis, it identified multiple optimization opportunities\n3. Performance optimization is a non-trivial task requiring multiple steps\n4. The todo list helps methodically track improvements across different components\n5. This systematic approach ensures all performance bottlenecks are addressed\n</reasoning>\n</example>\n\n## Examples of When NOT to Use the Todo List\n\n<example>\nUser: How do I print 'Hello World' in Python?\nAssistant: In Python, you can print \"Hello World\" with this simple code:\n\npython\nprint(\"Hello World\")\n\nThis will output the text \"Hello World\" to the console when executed.</assistant>\n\n<reasoning>\nThe assistant did not use the todo list because this is a single, trivial task that can be completed in one step. There's no need to track multiple tasks or steps for such a straightforward request.\n</reasoning>\n</example>\n\n<example>\nUser: What does the git status command do?\nAssistant: The git status command shows the current state of your working directory and staging area. It displays which changes have been staged, which haven't, and which files aren't being tracked by Git. This is a fundamental command for understanding the current state of your repository before making commits.\n\n<reasoning>\nThe assistant did not use the todo list because this is an informational request with no actual coding task to complete. The user is simply asking for an explanation, not for the assistant to perform multiple steps or tasks.\n</reasoning>\n</example>\n\n<example>\nUser: Can you add a comment to the calculateTotal function to explain what it does?\nAssistant: Sure, let me add a comment to the calculateTotal function to explain what it does.\n* Uses the Edit tool to add a comment to the calculateTotal function *\n\n<reasoning>\nThe assistant did not use the todo list because this is a single, straightforward task confined to one location in the code. Adding a comment doesn't require tracking multiple steps or systematic organization.\n</reasoning>\n</example>\n\n<example>\nUser: Run npm install for me and tell me what happens.\nAssistant: I'll run the npm install command for you.\n\n*Executes: npm install*\n\nThe command completed successfully. Here's the output:\n[Output of npm install command]\n\nAll dependencies have been installed according to your package.json file.\n\n<reasoning>\nThe assistant did not use the todo list because this is a single command execution with immediate results. There are no multiple steps to track or organize, making the todo list unnecessary for this straightforward task.\n</reasoning>\n</example>\n\n## Task States and Management\n\n1. **Task States**: Use these states to track progress:\n   - pending: Task not yet started\n   - in_progress: Currently working on (limit to ONE task at a time)\n   - completed: Task finished successfully\n   - cancelled: Task no longer needed\n\n2. **Task Management**:\n   - Update task status in real-time as you work\n   - Mark tasks complete IMMEDIATELY after finishing (don't batch completions)\n   - Only have ONE task in_progress at any time\n   - Complete current tasks before starting new ones\n   - Cancel tasks that become irrelevant\n\n3. **Task Breakdown**:\n   - Create specific, actionable items\n   - Break complex tasks into smaller, manageable steps\n   - Use clear, descriptive task names\n\nWhen in doubt, use this tool. Being proactive with task management demonstrates attentiveness and ensures you complete all requirements successfully.\n\n",
+                "parameters": {
+                    "$schema": "https://json-schema.org/draft/2020-12/schema",
+                    "type": "object",
+                    "properties": {
+                        "todos": {
+                            "description": "The updated todo list",
+                            "type": "array",
+                            "items": {
+                                "type": "object",
+                                "properties": {
+                                    "content": {
+                                        "description": "Brief description of the task",
+                                        "type": "string"
+                                    },
+                                    "status": {
+                                        "description": "Current status of the task: pending, in_progress, completed, cancelled",
+                                        "type": "string"
+                                    },
+                                    "priority": {
+                                        "description": "Priority level of the task: high, medium, low",
+                                        "type": "string"
+                                    },
+                                    "id": {
+                                        "description": "Unique identifier for the todo item",
+                                        "type": "string"
+                                    }
+                                },
+                                "required": [
+                                    "content",
+                                    "status",
+                                    "priority",
+                                    "id"
+                                ],
+                                "additionalProperties": false
+                            }
+                        }
+                    },
+                    "required": [
+                        "todos"
+                    ],
+                    "additionalProperties": false
+                }
+            }
+        },
+        {
+            "type": "function",
+            "function": {
+                "name": "todoread",
+                "description": "Use this tool to read your todo list",
+                "parameters": {
+                    "$schema": "https://json-schema.org/draft/2020-12/schema",
+                    "type": "object",
+                    "properties": {},
+                    "additionalProperties": false
+                }
+            }
+        },
+        {
+            "type": "function",
+            "function": {
+                "name": "skill",
+                "description": "Load a skill to get detailed instructions for a specific task. No skills are currently available.",
+                "parameters": {
+                    "$schema": "https://json-schema.org/draft/2020-12/schema",
+                    "type": "object",
+                    "properties": {
+                        "name": {
+                            "description": "The skill identifier from available_skills (e.g., 'code-review' or 'category/helper')",
+                            "type": "string"
+                        }
+                    },
+                    "required": [
+                        "name"
+                    ],
+                    "additionalProperties": false
+                }
+            }
+        },
+        {
+            "type": "function",
+            "function": {
+                "name": "bun_SearchBun",
+                "description": "Search across the Bun knowledge base to find relevant information, code examples, API references, and guides. Use this tool when you need to answer questions about Bun, find specific documentation, understand how features work, or locate implementation details. The search returns contextual content with titles and direct links to the documentation pages.",
+                "parameters": {
+                    "type": "object",
+                    "properties": {
+                        "query": {
+                            "type": "string"
+                        }
+                    },
+                    "required": [
+                        "query"
+                    ],
+                    "additionalProperties": false,
+                    "$schema": "http://json-schema.org/draft-07/schema#"
+                }
+            }
+        }
+    ],
+    "tool_choice": "auto"
+};