octocode-cli 1.2.5 → 1.2.7

package/skills/octocode-research/README.md

@@ -0,0 +1,494 @@
+<div align="center">
+  <img src="https://github.com/bgauryy/octocode-mcp/raw/main/packages/octocode-mcp/assets/logo_white.png" width="400px" alt="Octocode Logo">
+
+  <h1> Octocode Research Skill</h1>
+
+  <p><strong>Turn your agent into a code research powerhouse</strong></p>
+  <p>Zero-config MCP tools • Intent-driven workflows • Smart discovery</p>
+
+  [![Skill](https://img.shields.io/badge/skill-agentskills.io-purple)](https://agentskills.io/what-are-skills)
+  [![License](https://img.shields.io/badge/license-MIT-blue)](https://github.com/bgauryy/octocode-mcp/blob/main/LICENSE)
+  [![Port](https://img.shields.io/badge/port-1987-green)](http://localhost:1987)
+
+</div>
+
+---
+
+## The Problem
+
+agents struggle with code research because:
+- **Too many tools** — Which one do I use? In what order?
+- **No context** — Tools work in isolation, losing research continuity
+- **Manual orchestration** — You have to chain tools yourself
+- **Different APIs** — Local, GitHub, LSP tools all work differently
+
+## The Solution
+
+**Octocode Research** gives your agent:
+
+```
+┌─────────────────────────────────────────────────────────────────────────────┐
+│  🎯 Intent Detection  →  📋 Auto-Select Prompt  →  🔧 Smart Tool Chaining  │
+│                                                                             │
+│     "How does React                  research              GitHub + LSP    │
+│      useState work?"         ──────────────────►          tool chain       │
+│                                                                             │
+│     "Review PR #123"                 reviewPR              Diff analysis   │
+│                              ──────────────────►          + code review    │
+│                                                                             │
+│     "Trace auth flow                 research_local        LSP semantic    │
+│      in our app"             ──────────────────►          analysis         │
+└─────────────────────────────────────────────────────────────────────────────┘
+```
+
+
+
+https://github.com/user-attachments/assets/d1260dbc-e7b6-4bec-909f-232ebee91ce9
+
+
+---
+
+## 🚀 Quick Start
+
+### Installation
+
+```bash
+npx add-skill https://github.com/bgauryy/octocode-mcp/tree/main/skills/octocode-research
+```
+
+> **Important**: Make sure you are authenticated with GitHub!
+> See [Authentication Setup](https://github.com/bgauryy/octocode-mcp/blob/main/packages/octocode-mcp/docs/AUTHENTICATION_SETUP.md) in the main README.
+
+### Option 2: Manual Setup
+
+```bash
+cd skills/octocode-research
+npm install && npm start
+
+> By default the server listens on `localhost:1987`. You can override this with:
+> - `OCTOCODE_RESEARCH_HOST` (default: `localhost`)
+> - `OCTOCODE_RESEARCH_PORT` (default: `1987`)
+
+# Verify it's running (defaults to localhost:1987)
+curl http://localhost:1987/health
+```
+
+---
+
+## ✨ Key Features
+
+### 1. All MCP Tools Work Out of the Box
+
+No configuration. No token setup. Just ask your question.
+
+```
+┌─────────────────────────────────────────────────────────────────────────────┐
+│                         13 TOOLS • ONE INTERFACE                            │
+├─────────────────────────────────────────────────────────────────────────────┤
+│                                                                             │
+│   LOCAL TOOLS              LSP TOOLS              EXTERNAL TOOLS            │
+│   ────────────             ─────────              ──────────────            │
+│   localSearchCode          lspGotoDefinition      githubSearchCode          │
+│   localGetFileContent      lspFindReferences      githubGetFileContent      │
+│   localFindFiles           lspCallHierarchy       githubViewRepoStructure   │
+│   localViewStructure                              githubSearchRepositories  │
+│                                                   githubSearchPullRequests  │
+│                                                   packageSearch             │
+│                                                                             │
+│   ──────────────────────────────────────────────────────────────────────    │
+│   All tools: POST /tools/call/:toolName  { "queries": [...] }               │
+│                                                                             │
+└─────────────────────────────────────────────────────────────────────────────┘
+```
+
+### 2. Smart Tool & Prompt Discovery
+
+Your agent discovers what's available at runtime:
+
+```bash
+# List available tools
+GET /tools/list
+
+# Get tool schema BEFORE calling (required!)
+GET /tools/info/localSearchCode
+
+# List available prompts
+GET /prompts/list
+
+# Get prompt content by intent
+GET /prompts/info/research
+```
+
+### 3. Intent-Driven Prompt Selection
+
+The skill auto-selects the right workflow based on your question:
+
+| Your Intent | Auto-Selected Prompt | What Happens |
+|-------------|---------------------|--------------|
+| *"How does React useState work?"* | `research` | GitHub repo exploration, source code analysis |
+| *"Trace the auth flow in our app"* | `research_local` | LSP-powered semantic analysis, call hierarchies |
+| *"Review PR #123"* | `reviewPR` | Diff analysis, code review, change impact |
+| *"Plan adding caching to the API"* | `plan` | Architecture design, implementation steps |
+
+### 4. Production-Ready Resilience
+
+Built-in protection against failures:
+
+```
+┌──────────────────────────────────────────────────────────────────┐
+│                    RESILIENCE PATTERNS                           │
+├──────────────────────────────────────────────────────────────────┤
+│                                                                  │
+│  CIRCUIT BREAKER          RETRY + BACKOFF         THROTTLING     │
+│  ───────────────          ───────────────         ──────────     │
+│                                                                  │
+│  CLOSED ──► OPEN          Attempt 1 ────►         50 req/min     │
+│    │         │            wait 1s                 then gradual   │
+│    │    [timeout]         Attempt 2 ────►         slowdown       │
+│    │         │            wait 3s                                │
+│    ▼         ▼            Attempt 3 ────►                        │
+│  HALF-OPEN ◄─┘            success/fail                           │
+│                                                                  │
+│  Per-service configs:     GitHub: 3 attempts, 30s max            │
+│  GitHub: 60s timeout      LSP: 3 attempts, 5s max                │
+│  LSP: 10s timeout         Local: 2 attempts, 1s max              │
+│                                                                  │
+└──────────────────────────────────────────────────────────────────┘
+```
+
+---
+
+## 🔄 The Research Flow
+
+```
+┌─────────────────────────────────────────────────────────────────────────────┐
+│                          OCTOCODE RESEARCH FLOW                             │
+└─────────────────────────────────────────────────────────────────────────────┘
+
+  USER QUESTION                                                    ANSWER
+       │                                                              ▲
+       ▼                                                              │
+┌──────────────┐    ┌──────────────┐    ┌──────────────┐    ┌──────────────┐
+│              │    │              │    │              │    │              │
+│  1. INIT     │───►│  2. CONTEXT  │───►│  3. PLAN     │───►│  4. RESEARCH │
+│              │    │              │    │              │    │              │
+│  Health      │    │  System      │    │  Create      │    │  Execute     │
+│  check       │    │  prompt      │    │  research    │    │  tool        │
+│  /health     │    │  /tools/     │    │  plan with   │    │  chains      │
+│              │    │  system      │    │  tasks       │    │              │
+│              │    │              │    │              │    │  Follow      │
+│              │    │  Select      │    │              │    │  hints       │
+│              │    │  prompt by   │    │              │    │              │
+│              │    │  intent      │    │              │    │  Iterate     │
+│              │    │  /prompts/   │    │              │    │              │
+│              │    │  info/:name  │    │              │    │              │
+└──────────────┘    └──────────────┘    └──────────────┘    └──────────────┘
+
+```
+
+### Phase 1: INIT
+```bash
+# Check server is ready
+curl http://localhost:1987/health
+# → {"status":"ok","port":1987,"uptime":123,...}
+```
+
+### Phase 2: CONTEXT
+```bash
+# Load system prompt (ALWAYS FIRST)
+curl http://localhost:1987/tools/system
+
+# Select prompt by user intent
+curl http://localhost:1987/prompts/info/research
+```
+
+### Phase 3: PLAN
+- Analyze user's question
+- Create research plan with tasks
+- Determine which tools to use
+
+### Phase 4: RESEARCH
+```bash
+# Execute tools with research context
+curl -X POST http://localhost:1987/tools/call/localSearchCode \
+  -H "Content-Type: application/json" \
+  -d '{
+    "queries": [{
+      "mainResearchGoal": "Understand authentication flow",
+      "researchGoal": "Find auth middleware location",
+      "reasoning": "Need to locate entry point before tracing",
+      "pattern": "authenticate",
+      "path": "/Users/me/project/src"
+    }]
+  }'
+```
+
+---
+
+## 📡 API Reference
+
+### Discovery Endpoints
+
+| Method | Endpoint | Description |
+|--------|----------|-------------|
+| `GET` | `/health` | Server health, memory, circuit states |
+| `GET` | `/tools/list` | List all tools (concise) |
+| `GET` | `/tools/info/:toolName` | **Get tool schema (call BEFORE using!)** |
+| `GET` | `/tools/system` | **System prompt (load FIRST!)** |
+| `GET` | `/prompts/list` | List all prompts |
+| `GET` | `/prompts/info/:promptName` | Get prompt content |
+
+### Execution Endpoint
+
+| Method | Endpoint | Description |
+|--------|----------|-------------|
+| `POST` | `/tools/call/:toolName` | **Execute any tool** |
+
+### Request Format
+
+All tool calls use the same structure:
+
+```json
+{
+  "queries": [{
+    "mainResearchGoal": "Overall research objective",
+    "researchGoal": "This specific query's goal",
+    "reasoning": "Why this approach helps",
+    // ... tool-specific parameters
+  }]
+}
+```
+
+### Response Format
+
+```json
+{
+  "tool": "localSearchCode",
+  "success": true,
+  "data": { /* tool results */ },
+  "hints": [
+    "Use lineHint for LSP tools",
+    "Consider narrowing search with path filter"
+  ],
+  "research": {
+    "mainResearchGoal": "...",
+    "researchGoal": "...",
+    "reasoning": "..."
+  }
+}
+```
+
+> **Critical**: Every response includes `hints` — **always read and follow them** for optimal research flow!
+
+---
+
+## 🛠 Available Tools
+
+### LSP Tools (Semantic Analysis)
+
+| Tool | Purpose | Use When |
+|------|---------|----------|
+| `lspGotoDefinition` | Jump to symbol definition | "Where is X defined?" |
+| `lspFindReferences` | Find all usages | "Who uses X?" |
+| `lspCallHierarchy` | Trace call flow | "Who calls X? What does X call?" |
+
+### Local Tools (Filesystem)
+
+| Tool | Purpose | Use When |
+|------|---------|----------|
+| `localSearchCode` | Ripgrep search | "Find pattern X in codebase" |
+| `localGetFileContent` | Read file content | "Show me file X" |
+| `localFindFiles` | Find by pattern/metadata | "Find all *.ts files" |
+| `localViewStructure` | Directory tree | "What's in this folder?" |
+
+### GitHub Tools (External)
+
+| Tool | Purpose | Use When |
+|------|---------|----------|
+| `githubSearchCode` | Search code in repos | "Find X in React repo" |
+| `githubGetFileContent` | Read file from repo | "Show React's useState" |
+| `githubViewRepoStructure` | View repo tree | "What's in facebook/react?" |
+| `githubSearchRepositories` | Search repos | "Find auth libraries" |
+| `githubSearchPullRequests` | Search PRs | "Find PR that added X" |
+
+### Package Tools
+
+| Tool | Purpose | Use When |
+|------|---------|----------|
+| `packageSearch` | Search npm/PyPI | "Find the lodash package" |
+
+---
+
+## 🎯 Example: How React Implements useState
+
+```bash
+# 1. Search for useState in React repo
+curl -X POST http://localhost:1987/tools/call/githubSearchCode \
+  -H "Content-Type: application/json" \
+  -d '{
+    "queries": [{
+      "mainResearchGoal": "Understand React useState implementation",
+      "researchGoal": "Find useState source code location",
+      "reasoning": "Need to locate the hook definition first",
+      "owner": "facebook",
+      "repo": "react",
+      "keywordsToSearch": ["useState", "function"],
+      "match": "file"
+    }]
+  }'
+
+# 2. View repository structure
+curl -X POST http://localhost:1987/tools/call/githubViewRepoStructure \
+  -H "Content-Type: application/json" \
+  -d '{
+    "queries": [{
+      "mainResearchGoal": "Understand React useState implementation",
+      "researchGoal": "Find packages directory structure",
+      "reasoning": "Hooks likely in react-reconciler or react package",
+      "owner": "facebook",
+      "repo": "react",
+      "branch": "main",
+      "path": "packages/react/src",
+      "depth": 2
+    }]
+  }'
+
+# 3. Read the implementation file
+curl -X POST http://localhost:1987/tools/call/githubGetFileContent \
+  -H "Content-Type: application/json" \
+  -d '{
+    "queries": [{
+      "mainResearchGoal": "Understand React useState implementation",
+      "researchGoal": "Read useState hook source code",
+      "reasoning": "Found location, now reading implementation",
+      "owner": "facebook",
+      "repo": "react",
+      "path": "packages/react/src/ReactHooks.js",
+      "matchString": "useState"
+    }]
+  }'
+```
+
+---
+
+## 🏗 Architecture
+
+```
+┌─────────────────────────────────────────────────────────────────────────────┐
+│                          AGENT (Claude, GPT, etc.)                       │
+└─────────────────────────────────────────────────────────────────────────────┘
+                                      │
+                                      ▼
+┌─────────────────────────────────────────────────────────────────────────────┐
+│                      OCTOCODE RESEARCH SERVER (:1987)                       │
+├─────────────────────────────────────────────────────────────────────────────┤
+│                                                                             │
+│  ┌───────────────┐   ┌───────────────┐   ┌───────────────────────────────┐  │
+│  │   PROMPTS     │   │    TOOLS      │   │      SYSTEM CONTEXT           │  │
+│  │               │   │               │   │                               │  │
+│  │  research     │   │  GitHub API   │   │  Decision guides              │  │
+│  │  research_    │   │  Local FS     │   │  Tool chaining rules          │  │
+│  │   local       │   │  LSP Server   │   │  Error recovery               │  │
+│  │  reviewPR     │   │  Package APIs │   │  Best practices               │  │
+│  │  plan         │   │               │   │                               │  │
+│  └───────────────┘   └───────────────┘   └───────────────────────────────┘  │
+│                                                                             │
+│  ┌───────────────────────────────────────────────────────────────────────┐  │
+│  │                     RESILIENCE LAYER                                  │  │
+│  │  Circuit Breaker  •  Retry + Backoff  •  Throttling  •  Error Queue   │  │
+│  └───────────────────────────────────────────────────────────────────────┘  │
+│                                                                             │
+└─────────────────────────────────────────────────────────────────────────────┘
+                                      │
+              ┌───────────────────────┼───────────────────────┐
+              ▼                       ▼                       ▼
+        ┌──────────┐           ┌──────────┐           ┌──────────┐
+        │ Your     │           │ GitHub   │           │ npm/PyPI │
+        │ Codebase │           │ Repos    │           │ Registry │
+        └──────────┘           └──────────┘           └──────────┘
+```
+
+---
+
+## 📊 Bulk Queries
+
+Execute up to 3 queries in parallel:
+
+```bash
+curl -X POST http://localhost:1987/tools/call/localSearchCode \
+  -H "Content-Type: application/json" \
+  -d '{
+    "queries": [
+      {
+        "mainResearchGoal": "Understand state management",
+        "researchGoal": "Find useState usages",
+        "reasoning": "Compare with useReducer",
+        "pattern": "useState",
+        "path": "/project/src"
+      },
+      {
+        "mainResearchGoal": "Understand state management",
+        "researchGoal": "Find useReducer usages",
+        "reasoning": "Compare with useState",
+        "pattern": "useReducer",
+        "path": "/project/src"
+      }
+    ]
+  }'
+```
+
+Response:
+```json
+{
+  "tool": "localSearchCode",
+  "bulk": true,
+  "success": true,
+  "results": [
+    { "id": 1, "status": "hasResults", "data": {...} },
+    { "id": 2, "status": "hasResults", "data": {...} }
+  ],
+  "hints": {
+    "hasResults": ["Use lineHint for LSP follow-up"],
+    "empty": ["Try broader pattern"]
+  },
+  "counts": { "total": 2, "hasResults": 2, "empty": 0, "error": 0 }
+}
+```
+
+---
+
+## 🔒 Privacy & Telemetry
+
+We collect **de-identified** telemetry to improve the tool:
+- Command usage counts
+- Error rates
+- **Never** source code, env vars, or PII
+
+Opt-out anytime:
+```bash
+export LOG=false
+```
+
+Local logs stored at `~/.octocode/logs/` for your debugging — **never uploaded**.
+
+See [Privacy Policy](https://github.com/bgauryy/octocode-mcp/blob/main/PRIVACY.md) and [Terms](https://github.com/bgauryy/octocode-mcp/blob/main/TERMS.md).
+
+---
+
+## 📚 Documentation
+
+| Document | Description |
+|----------|-------------|
+| [SKILL.md](./SKILL.md) | Agent workflow guide |
+| [docs/ARCHITECTURE.md](./docs/ARCHITECTURE.md) | Full architecture details |
+| [docs/API_REFERENCE.md](./docs/API_REFERENCE.md) | Complete API reference |
+| [docs/FLOWS.md](./docs/FLOWS.md) | Request flow diagrams |
+| [../../docs/TROUBLESHOOTING.md](https://github.com/bgauryy/octocode-mcp/blob/main/docs/TROUBLESHOOTING.md) | Common issues and solutions |
+
+---
+
+## License
+
+MIT License © 2026 Octocode
+
+See [LICENSE](https://github.com/bgauryy/octocode-mcp/blob/main/LICENSE) for details.