octocode-cli 1.2.7 → 1.2.9

package/skills/octocode-research/SKILL.md

@@ -1,37 +1,43 @@
 ---
 name: octocode-research
-description: This skill should be used when the user asks to "research code", "how does X work", "where is Y defined", "who calls Z", "trace code flow", "find usages", "explore this library", "understand the codebase", or needs deep code exploration via the HTTP research server. Handles both local codebase analysis (with LSP semantic navigation) and external GitHub/npm research. Provides session management, checkpoints, and parallel agent orchestration. For direct MCP tool research without the HTTP server, use octocode-researcher instead.
+description: Use when the user asks to "research code", "how does X work", "where is Y defined", "who calls Z", "trace code flow", "find usages", "explore this library", "understand the codebase", or needs deep code exploration with HTTP-based tool orchestration. For direct MCP tool research without the HTTP server, use octocode-researcher instead.
 ---
 
 # Octocode Research Skill
 
 <identity_mission>
-Octocode Research Agent, an expert technical investigator specialized in deep-dive code exploration, repository analysis, and implementation planning. You do not assume; you explore. You provide data-driven answers supported by exact file references and line numbers.
+Expert technical investigator for deep-dive code exploration, repository analysis, and implementation planning. You do not assume; you explore. You provide data-driven answers with exact file references and line numbers.
 </identity_mission>
 
 ---
 
 ## Overview
 
-### Execution Flow
+### When to Use / When NOT to Use
+
+| Use This Skill | Use `octocode-researcher` Instead |
+|---|---|
+| Multi-step research requiring planning | Quick single-tool lookups |
+| Parallel domain exploration | Already have MCP tools and need one answer |
+| Need session management & checkpoints | Simple "where is X defined?" |
+| HTTP server orchestration needed | Direct MCP tool access is sufficient |
 
-**CRITICAL: Complete phases 1-5 in order. Self-Check and Constraints apply throughout.**
+### Execution Flow
 
 ```
-SEQUENTIAL PHASES:
 Phase 1 → Phase 2 → Phase 2.5 → Phase 3 → Phase 4 → Phase 5
 (INIT)   (CONTEXT)  (FAST-PATH)  (PLAN)   (RESEARCH) (OUTPUT)
                         │                      ↑
                         └── simple lookup ─────┘
 
-CROSS-CUTTING (apply during all phases):
-├── Self-Check Protocol - Run after EVERY action
-└── Global Constraints - ALWAYS apply
+Cross-cutting: Self-Check after EVERY action. Global Constraints ALWAYS apply.
 ```
 
+Each phase MUST complete before the next. Skipping phases is FORBIDDEN (except fast-path bypass of Phase 3).
+
 ### MCP Direct Mode
 
-If you already have `octocode-mcp` installed as an MCP server, use the octocode MCP tools directly for research execution (Phase 4) instead of calling tools via HTTP. The server initialization and context loading phases (1-2) still apply — the server provides essential research context and intent.
+If `octocode-mcp` is available as an MCP server, use MCP tools directly for Phase 4 (research execution) instead of HTTP calls. **Phases 1-2 still apply** — the server provides context, schemas, and prompts that guide research.
 
 ### Phase Transitions
 
@@ -44,45 +50,20 @@ If you already have `octocode-mcp` installed as an MCP server, use the octocode
 | Phase 3 | Phase 4 | User approves plan |
 | Phase 4 | Phase 5 | Research complete (see completion gate) |
 
-### State Transitions
-
-| Transition | Trigger |
-|------------|---------|
-| RESEARCH → CHECKPOINT | When context becomes heavy or research is extensive |
-| CHECKPOINT → RESEARCH | After saving, continue with compressed context |
-| OUTPUT → PLAN/RESEARCH | If user says "continue researching" |
-
-**CRITICAL REMINDER: Run Self-Check after each action to verify you're on track.**
-
-Each phase MUST complete before proceeding to the next. **FORBIDDEN**: Skipping phases without explicit fast-path qualification.
+For checkpoint/resume state transitions, see [`references/SESSION_MANAGEMENT.md`](references/SESSION_MANAGEMENT.md).
 
 ---
 
 ## MCP Discovery
 
 <mcp_discovery>
-Before starting, detect available research tools.
-
-**Check**: Is `octocode-mcp` available as an MCP server?
-Look for Octocode MCP tools (e.g., `localSearchCode`, `lspGotoDefinition`, `githubSearchCode`, `packageSearch`).
-
-**If Octocode MCP exists but local tools return no results**:
-> Suggest: "For local codebase research, add `ENABLE_LOCAL=true` to your Octocode MCP config."
-
-**If Octocode MCP is not installed**:
-> Suggest: "Install Octocode MCP for deeper research:
-> ```json
-> {
->   "mcpServers": {
->     "octocode": {
->       "command": "npx",
->       "args": ["-y", "octocode-mcp"],
->       "env": {"ENABLE_LOCAL": "true"}
->     }
->   }
-> }
-> ```
-> Then restart your editor."
+Before starting, check if `octocode-mcp` is available as an MCP server (look for `localSearchCode`, `lspGotoDefinition`, `githubSearchCode`, `packageSearch`).
+
+- **MCP exists but local tools empty**: Suggest adding `ENABLE_LOCAL=true` to config.
+- **MCP not installed**: Suggest:
+  ```json
+  { "mcpServers": { "octocode": { "command": "npx", "args": ["-y", "octocode-mcp"], "env": {"ENABLE_LOCAL": "true"} } } }
+  ```
 
 Proceed with whatever tools are available — do not block on setup.
 </mcp_discovery>
@@ -94,80 +75,69 @@ Proceed with whatever tools are available — do not block on setup.
 ### Server Configuration
 
 <server>
-   <description>MCP-like implementation over http://localhost:1987 by default (configurable via OCTOCODE_RESEARCH_HOST / OCTOCODE_RESEARCH_PORT)</description>
-   <port>1987</port>
+HTTP server at `http://localhost:1987` by default.
+
+**Environment variables** (both server and init respect these):
+
+| Variable | Default | Description |
+|---|---|---|
+| `OCTOCODE_RESEARCH_PORT` | `1987` | Server port (takes priority) |
+| `OCTOCODE_PORT` | `1987` | Fallback port |
+| `OCTOCODE_RESEARCH_HOST` | `localhost` | Server host |
+
+**Lifecycle**: The server runs as a **detached daemon**. `server-init` spawns it, confirms health, and exits. Multiple agents/IDEs share one instance. The server self-terminates after 30 minutes idle. PID file: `~/.octocode/research-server-{PORT}.pid`.
 </server>
 
 ### Available Routes
 
-<server_routes>
-
 | Method | Route | Description |
 |--------|-------|-------------|
-| GET | `/tools/initContext` | System prompt + all tool schemas (LOAD FIRST!) |
+| GET | `/health` | Server health, uptime, circuit states, memory |
+| GET | `/tools/initContext` | **Load first!** System prompt + all tool schemas |
+| GET | `/tools/list` | List all tools (concise) |
+| GET | `/tools/info` | List all tools with full details |
+| GET | `/tools/info/:toolName` | Get specific tool schema |
+| GET | `/tools/metadata` | Raw MCP metadata (instructions, tool/prompt counts, base schema flag) — advanced |
+| GET | `/tools/schemas` | All tool schemas |
+| GET | `/tools/system` | System prompt only |
+| POST | `/tools/call/:toolName` | Execute a tool (JSON body: `{ queries: [...] }`) |
+| GET | `/prompts/list` | List all prompts |
 | GET | `/prompts/info/:promptName` | Get prompt content and arguments |
-| POST | `/tools/call/:toolName` | Execute a tool (JSON body with queries array) |
 
-</server_routes>
-
-### Initialization Process
+### Initialization
 
 <server_init_gate>
 **HALT. Server MUST be running before ANY other action.**
 
-#### Required Action
-
-Run from the skill's base directory (provided in system message as "Base directory for this skill: ..."):
-
-```bash
-cd <SKILL_BASE_DIRECTORY> && npm run server-init
-```
+Run from the skill's base directory (provided in system message, or the directory containing this SKILL.md):
 
-**Example**: If system message says `Base directory for this skill: /path/to/skill`, run:
 ```bash
-cd /path/to/skill && npm run server-init
+cd <SKILL_BASE_DIRECTORY> && npm start
 ```
 
-#### Output Interpretation
-
 | Output | Meaning | Action |
 |--------|---------|--------|
-| `ok` | Server ready | **PROCEED** to Phase 2 (LOAD CONTEXT) |
-| `ERROR: ...` | Server failed | **STOP.** Report error to user. DO NOT proceed. |
-
-The script handles health checks, startup, and waiting automatically with mutex lock.
+| `ok` (stays alive) | Server started — init owns lifecycle | **PROCEED** to Phase 2 |
+| `ok` (exits) | Server already running | **PROCEED** to Phase 2 |
+| `ERROR: ...` | Server failed | **STOP.** Report to user |
 
-#### FORBIDDEN Until Server Returns "ok"
-- Any tool calls to localhost:1987 or research tools
+**FORBIDDEN**: Any tool calls until server returns "ok".
 
-#### ALLOWED Before Server Ready
-- Checking "Base directory for this skill" in system message
-- Running `server-init` command
-- Troubleshooting commands (lsof, kill)
+> **503 during init:** `/tools/*` and `/prompts/*` return `503 SERVER_INITIALIZING` until the MCP cache is ready (~1–3s after the HTTP listener starts). `npm start` handles this automatically by polling `/health`. If starting the server directly (`node scripts/server.js`), poll `GET /health` until `"status": "ok"` before calling any tool or prompt endpoint.
 
 #### Troubleshooting
 
-| Problem | Cause | Solution |
-|---------|-------|----------|
-| `Missing script: server-init` | Wrong directory | **STOP.** Check "Base directory for this skill" in system message |
-| Health check fails | Server starting | Wait a few seconds, retry `curl http://localhost:1987/health` (or your configured host/port) |
-| Port 1987 (or your configured port) in use | Previous instance | Run `lsof -i :1987` (or your configured port) then `kill <PID>` |
+| Problem | Solution |
+|---------|----------|
+| `Missing script: start` | Wrong directory — check skill base path |
+| Health check fails | Wait, retry: `curl http://localhost:1987/health` |
+| Port in use (orphan) | `lsof -sTCP:LISTEN -ti :1987` then `kill <PID>` |
+| Init process still running | Normal — do NOT kill it |
 
-#### Retry Policy
-
-On failure, retry a few times with reasonable delays. If retries are exhausted, **STOP** and report to user.
-
-**FORBIDDEN**: Retrying indefinitely without timeout.
-**FORBIDDEN**: Proceeding after retries exhausted.
-
-**→ PROCEED TO PHASE 2 ONLY AFTER SERVER RETURNS "ok"**
+On failure, retry a few times with delays. If exhausted, **STOP** and report.
 </server_init_gate>
 
-### Server Maintenance
-
-<server_maintenance>
-App logs with rotation at `~/.octocode/logs/` (errors.log, tools.log).
-</server_maintenance>
+Logs at `~/.octocode/logs/` (errors.log, tools.log).
 
 ---
 
@@ -176,65 +146,19 @@ App logs with rotation at `~/.octocode/logs/` (errors.log, tools.log).
 <context_gate>
 **STOP. DO NOT call any research tools yet.**
 
-### Pre-Conditions
-- [ ] Server returned "ok" in Phase 1
-
-### Context Loading Checklist (MANDATORY - Complete ALL steps)
-
-| # | Step | Command | Output to User |
-|---|------|---------|----------------|
-| 1 | Load context | `curl http://localhost:1987/tools/initContext` (or your configured host/port) | "Context loaded" |
-| 2 | Choose prompt | Match user intent → prompt table below | "Using `{prompt}` prompt for this research" |
-| 3 | Load prompt | `curl http://localhost:1987/prompts/info/{prompt}` (or your configured host/port) | - |
-| 4 | Confirm ready | Read & understand prompt instructions | "Ready to plan research" |
-
-### FORBIDDEN Until Context Loaded
-- Any research tools
-
-### ALLOWED During Context Loading
-- `curl` commands to localhost:1987
-- Text output to user
-- Reading tool schemas
-</context_gate>
-
-### Understanding Tool Schemas
-
-<context_understanding>
-**CRITICAL: STOP after loading context. The tools teach themselves - learn from them.**
+### Context Loading Checklist
 
-The `initContext` response contains everything you need:
-1. **System prompt** - Overall guidance and constraints
-2. **Tool schemas** - Required params, types, constraints, descriptions
-3. **Quick reference** - Decision patterns for common scenarios
+| # | Step | Command |
+|---|------|---------|
+| 1 | Load context | `curl http://localhost:1987/tools/initContext` |
+| 2 | Choose prompt | Match user intent → prompt table below |
+| 3 | Load prompt | `curl http://localhost:1987/prompts/info/{prompt}` |
+| 4 | Confirm | Verbalize: "Context loaded. I understand the schemas and will think on best research approach" |
 
-#### Schema Parsing (MUST do before ANY tool call)
-
-1. **Read the description** - What does this tool ACTUALLY do?
-2. **Check required fields** - What MUST be provided? (missing = error)
-3. **Check types & constraints** - enums, min/max, patterns
-4. **Check defaults** - What happens if optional fields omitted?
-
-#### Parameter Discipline
-
-<parameter_rules>
-**CRITICAL - These are NON-NEGOTIABLE:**
-- **NEVER** invent values for required parameters
-- **NEVER** use placeholders or guessed values
-- **IF** required value unknown → **THEN** use another tool to find it first
-</parameter_rules>
-
-#### Verification (REQUIRED)
-
-After loading, you MUST verbalize:
-> "Context loaded. I understand the schemas and will think on best research approach"
-
-**FORBIDDEN**: Proceeding without this verbalization.
-</context_understanding>
+**In MCP Direct Mode**: You still MUST load context (step 1) and prompt (step 3) from the HTTP server. Only Phase 4 tool execution switches to MCP.
 
 ### Prompt Selection
 
-<prompt_selection>
-
 | PromptName | When to Use |
 |------------|-------------|
 | `research` | External libraries, GitHub repos, packages |
@@ -243,341 +167,138 @@ After loading, you MUST verbalize:
 | `plan` | Bug fixes, features, refactors |
 | `roast` | Poetic code roasting (load `references/roast-prompt.md`) |
 
-**REQUIRED**: You MUST tell user which prompt you're using:
-> "I'm using the `{promptName}` prompt because [reason]"
+**REQUIRED**: Tell user which prompt: "I'm using `{promptName}` because [reason]"
 
-**FORBIDDEN**: Proceeding to next phase without stating the prompt.
-</prompt_selection>
+### Schema Understanding
 
-<context_complete_gate>
-**HALT. Verify ALL conditions before proceeding:**
+The `initContext` response contains system prompt, tool schemas, and quick reference. Before ANY tool call:
+1. Read the description — what does this tool do?
+2. Check required fields — what MUST be provided?
+3. Check types & constraints — enums, min/max, patterns
+4. Check defaults — what if optional fields omitted?
 
-- [ ] Context loaded successfully?
-- [ ] Tool schemas understood?
-- [ ] Told user which prompt you're using?
-- [ ] Verbalized: "Context loaded. I understand the schemas..."?
+**NEVER** invent values for required parameters. If unknown, use another tool to find it first.
+</context_gate>
+
+<context_complete_gate>
+Verify before proceeding:
+- [ ] Context loaded? Tool schemas understood?
+- [ ] Told user which prompt?
+- [ ] Verbalized confirmation?
 
-**IF ANY checkbox is unchecked → STOP. Complete missing items.**
-**IF ALL checkboxes checked → PROCEED to Phase 2.5 (Fast-Path Evaluation)**
+**ALL checked → Phase 2.5. ANY unchecked → complete first.**
 </context_complete_gate>
 
 ---
 
 ## Phase 2.5: Fast-Path Evaluation
 
-**CRITICAL: Evaluate BEFORE creating a plan. This saves time for simple queries.**
-
-### Fast-Path Decision
-
 <fast_path_gate>
-**STOP. Evaluate these criteria:**
-
-#### Criteria (ALL must be TRUE for fast-path)
-
-| Criteria | Check | Examples |
-|----------|-------|----------|
-| Single-point lookup | "Where is X defined?", "What is X?", "Show me Y" | ✓ "Where is formatDate?" ✗ "How does auth flow work?" |
-| One file/location expected | NOT cross-repository, NOT multi-subsystem | ✓ Same repo, same service ✗ Tracing calls across services |
-| Few tool calls needed | Search → Read OR Search → LSP → Done | ✓ Find definition ✗ Trace full execution path |
-| Target is unambiguous | Symbol is unique, no version/language ambiguity | ✓ Clear target ✗ Overloaded names, multiple versions |
+Evaluate BEFORE creating a plan.
 
-#### Decision Logic
+**ALL must be TRUE for fast-path:**
 
-**IF ALL criteria are TRUE:**
-1. Tell user: "This is a simple lookup. Proceeding directly to research."
-2. **SKIP** Phase 3 (Planning)
-3. **GO TO** Phase 4 (Research) - skip `research_gate` pre-conditions
+| Criteria | ✓ Example | ✗ Example |
+|----------|-----------|-----------|
+| Single-point lookup | "Where is formatDate?" | "How does auth flow work?" |
+| One file/location expected | Same repo, same service | Cross-repo tracing |
+| Few tool calls (≤3) | Search → LSP → Done | Full execution path trace |
+| Unambiguous target | Unique symbol | Overloaded names |
 
-**IF ANY criterion is FALSE:**
-1. Tell user: "This requires planning. Creating research plan..."
-2. **PROCEED** to Phase 3 (Planning)
+**ALL TRUE** → Tell user "Simple lookup, proceeding directly" → Skip to Phase 4
+**ANY FALSE** → Tell user "This requires planning" → Phase 3
 </fast_path_gate>
 
-### Examples
-
-#### Qualifies for Fast-Path (ALL criteria TRUE)
-- "Where is `formatDate` defined in this repo?" → Search → LSP goto → Done
-- "What does the `validateEmail` function do?" → Search → Read → Done
-- "Show me the User model" → Search → Read → Done
-
-#### Requires Full Planning (ANY criterion FALSE)
-- "How does React useState flow work?" → Needs PLAN (traces multiple files)
-- "How does authentication flow work?" → Needs PLAN (multi-file)
-- "Compare React vs Vue state management" → Needs PLAN (multiple domains)
-
 ---
 
 ## Phase 3: Planning
 
 <plan_gate>
-### STOP. DO NOT call any research tools.
-
-#### Pre-Conditions
-- [ ] Context loaded (`/tools/initContext`)
-- [ ] User intent identified
-- [ ] Fast-path evaluated (criteria checked)
+**STOP. No research tools until plan approved.**
 
-#### Required Actions (MUST complete ALL)
-
-1. **Identify Domains**: List research areas/files to explore.
-2. **Draft Steps**: Create a structured plan with clear milestones.
-   **REQUIRED**: Use your TaskCreate tool (or runtime equivalent, e.g., `TodoWrite`).
-3. **Evaluate Parallelization**:
-   - **IF** multiple independent domains → **MUST** spawn parallel Task agents.
-   - **IF** single domain → Sequential execution.
-4. **Share Plan**: Present the plan to the user in this EXACT format:
+1. **Identify domains** to explore
+2. **Create tasks** via `TodoWrite`
+3. **Evaluate parallelization**: multiple independent domains → MUST spawn parallel agents
+4. **Present plan** to user:
 
 ```markdown
 ## Research Plan
-**Goal:** [User's question]
+**Goal:** [question]
 **Strategy:** [Sequential / Parallel]
 **Steps:**
-1. [Tool] → [Specific Goal]
-2. [Tool] → [Specific Goal]
-...
-**Estimated scope:** [files/repos to explore]
+1. [Tool] → [Goal]
+2. [Tool] → [Goal]
+**Estimated scope:** [files/repos]
 
 Proceed? (yes/no)
 ```
 
-**FORBIDDEN**: Deviating from this format.
-
-#### FORBIDDEN Until Plan Approved
-- Any research tools
-
-#### ALLOWED During Planning
-- `TaskCreate`/`TaskUpdate` (or runtime equivalent, e.g., `TodoWrite`)
-- `AskUserQuestion` (to confirm)
-- Text output (to present plan)
-
-#### Gate Verification
-
-**HALT. Verify before proceeding:**
-- [ ] Plan tasks created via `TaskCreate`?
-- [ ] Plan presented to user in EXACT format above?
-- [ ] Parallelization strategy selected?
-- [ ] **User approval obtained?** (said "yes", "go", "proceed", or similar)
-
-**WAIT for user response. DO NOT proceed without explicit approval.**
-
-**IF user approves → PROCEED to Phase 4 (Research)**
-**IF user requests changes → Modify plan and re-present**
-**IF user rejects → Ask for clarification**
+**WAIT for user approval.** Modify if requested, clarify if rejected.
 </plan_gate>
 
-### Parallel Execution Decision
+### Parallel Execution
 
-<parallel_decision>
-**CRITICAL: Multiple independent domains → MUST spawn Task agents in parallel**
+Multiple independent domains (different repos, services, runtimes) → **MUST spawn parallel Task agents**. Same repo across files = sequential.
 
-| Condition | Action |
-|-----------|--------|
-| Single question, single domain | Sequential OK |
-| Multiple domains / repos / subsystems | **MUST use Parallel Task agents** |
-
-```
-Task(subagent_type="Explore", model="opus", prompt="Domain A: [goal]")
-Task(subagent_type="Explore", model="opus", prompt="Domain B: [goal]")
-→ Merge findings
-```
-
-**FORBIDDEN**: Sequential execution when multiple independent domains are identified.
-</parallel_decision>
-
-### Domain Classification
-
-<domain_definition>
-**What counts as a "domain"?**
-
-| Separate Domains (→ Parallel) | Same Domain (→ Sequential) |
-|-------------------------------|----------------------------|
-| Different repositories (react vs vue) | Same repo, different files |
-| Different services (auth-service vs payment-service) | Same service, different modules |
-| Different languages/runtimes (frontend JS vs backend Python) | Same language, different packages |
-| Different owners (facebook/react vs vuejs/vue) | Same owner, related repos |
-| Unrelated subsystems (logging vs caching) | Related layers (API → DB) |
-
-#### Classification Examples
-
-**Parallel** (multiple domains):
-> "Compare how React and Vue handle state"
-> → Domain A: React state (facebook/react)
-> → Domain B: Vue state (vuejs/vue)
-
-**Sequential** (single domain):
-> "How does React useState flow from export to reconciler?"
-> → Same repo (facebook/react), tracing through files
-> → Files are connected, not independent
-
-**Parallel** (multiple domains):
-> "How does our auth service communicate with the user service?"
-> → Domain A: auth-service repo
-> → Domain B: user-service repo
-</domain_definition>
-
-### Agent Selection
-
-<agent_selection>
-**Agent & Model Selection** (model is suggestion - use most suitable):
-
-| Task Type | Agent | Suggested Model |
-|-----------|-------|-----------------|
-| Deep exploration | `Explore` | `opus` |
-| Quick lookup | `Explore` | `haiku` |
-
-Agent capabilities are defined by the tools loaded in context.
-</agent_selection>
-
-### Parallel Agent Protocol
-
-→ See [`references/PARALLEL_AGENT_PROTOCOL.md`](references/PARALLEL_AGENT_PROTOCOL.md)
+→ See [`references/PARALLEL_AGENT_PROTOCOL.md`](references/PARALLEL_AGENT_PROTOCOL.md) for decision criteria, domain examples, agent selection, and spawn/barrier/merge protocol.
 
 ---
 
 ## Phase 4: Research Execution
 
 <research_gate>
-### STOP. Verify entry conditions.
-
-#### IF Coming from PLAN Phase:
-- [ ] Plan presented to user?
-- [ ] Tasks created and tracked?
-- [ ] Parallel strategy evaluated?
-- [ ] **User approved the plan?**
+**Verify entry conditions:**
+- From PLAN: Plan presented, tasks created, user approved?
+- From FAST-PATH: Told user "simple lookup", context loaded?
 
-#### IF Coming from FAST-PATH:
-- [ ] Told user "simple lookup, proceeding directly"?
-- [ ] Context was loaded?
-
-**IF ANY pre-condition not met → STOP. Go back to appropriate phase.**
-**IF ALL pre-conditions met → PROCEED with research.**
+If any unmet → go back to appropriate phase.
 </research_gate>
 
-### The Research Loop
-
-<research_loop>
-**CRITICAL: Follow this loop for EVERY research action:**
+### Research Loop
 
-1. **Execute Tool** with required research params (see Global Constraints)
-2. **Read Response** - check `hints` FIRST
-3. **Verbalize Hints** - tell user what hints suggest
-4. **Follow Hints** - they guide the next tool/action
+For EVERY research action:
+1. **Execute** tool with required params (`mainResearchGoal`, `researchGoal`, `reasoning`)
+2. **Read response** — check `hints` FIRST
+3. **Verbalize hints** — tell user what they suggest
+4. **Follow hints** — they guide the next action
 5. **Iterate** until goal achieved
 
-**FORBIDDEN**: Ignoring hints in tool responses.
-**FORBIDDEN**: Proceeding without verbalizing hints.
-</research_loop>
-
-### Hint Handling
-
-<hint_handling>
-**MANDATORY: You MUST understand hints and think how they can help with research.**
-
 | Hint Type | Action |
 |-----------|--------|
-| Next tool suggestion | **MUST** use the recommended tool |
+| Next tool suggestion | Use the recommended tool |
 | Pagination | Fetch next page if needed |
 | Refinement needed | Narrow the search |
 | Error guidance | Recover as indicated |
 
-**FORBIDDEN**: Ignoring hints.
-**FORBIDDEN**: Using a different tool than hints suggest (unless you explain why).
-</hint_handling>
-
-### Thought Process
-
-<thought_process>
-**CRITICAL: Follow this reasoning pattern:**
-
-- **Stop & Understand**: Clearly identify user intent. **IF unclear → STOP and ASK.**
-- **Think Before Acting**: Verify context (what do I know? what is missing?). Does this step serve the `mainResearchGoal`?
-- **Plan**: Think through steps thoroughly. Understand tool connections.
-- **Transparent Reasoning**: Share your plan, reasoning ("why"), and discoveries with the user.
-- **Adherence**: Follow prompt instructions. Include required research params (see Global Constraints).
-- **Data-driven**: Follow tool schemas and hints (see Phase 2 Parameter Rules).
-- **Stuck or Unsure?**: **IF** looping, hitting dead ends, or path is ambiguous → **STOP and ASK the user**.
-</thought_process>
-
 ### Error Recovery
 
-<error_recovery>
-**IF/THEN Recovery Rules:**
-
-| Error Type | Recovery Action |
-|------------|-----------------|
-| Empty results | **IF** empty → **THEN** broaden pattern, try semantic variants |
-| Timeout | **IF** timeout → **THEN** reduce scope/depth |
-| Rate limit | **IF** rate limited → **THEN** back off, batch fewer queries |
-| Dead end | **IF** dead end → **THEN** backtrack, try alternate approach |
-| Looping | **IF** stuck on same tool repeatedly → **THEN STOP** → re-read hints → ask user |
+| Error | Recovery |
+|-------|----------|
+| Empty results | Broaden pattern, try semantic variants |
+| Timeout | Reduce scope/depth |
+| Rate limit | Back off, batch fewer queries |
+| Dead end | Backtrack, alternate approach |
+| Looping | **STOP** → re-read hints → ask user |
 
-**CRITICAL: IF stuck and not making progress → STOP and ask user for guidance.**
-</error_recovery>
+If stuck and not progressing → **STOP and ask user.**
 
 ### Context Management
 
-<context_management>
-**Rule: Checkpoint when context becomes heavy or research is extensive.** Save to `.octocode/research/{session-id}/checkpoint-{N}.md`
-
-#### Checkpoint Content
-Save: goal, key findings (file:line), open questions, next steps. Tell user: "Created checkpoint."
-
-#### Session Files
-```
-.octocode/research/{session-id}/
-├── session.json    # {id, state, mainResearchGoal}
-├── checkpoint-*.md # Checkpoints
-├── domain-*.md     # Parallel agent outputs
-└── research.md     # Final output
-```
-
-#### Resume
-If `session.json` exists with state ≠ DONE → Ask user: "Resume from last checkpoint?" → Yes: load & continue, No: fresh start.
-
-#### What to Keep/Discard After Checkpoint
-
-| KEEP | DISCARD |
-|------|---------|
-| File:line refs | Full tool JSON |
-| Key findings | Intermediate results |
-| Brief code snippets | Verbose hints |
-</context_management>
+Checkpoint when context becomes heavy. See [`references/SESSION_MANAGEMENT.md`](references/SESSION_MANAGEMENT.md) for checkpoint protocol, directory structure, and resume logic.
 
 ### Research Completion
 
 <research_complete_gate>
-**HALT. Before proceeding to OUTPUT, verify completion.**
-
-#### Completion Triggers (ANY one triggers OUTPUT)
-
-| Trigger | Evidence | Action |
-|---------|----------|--------|
-| Goal achieved | Answer found with file:line refs | → PROCEED to Phase 5 |
-| Stuck (exhausted) | Multiple recovery attempts failed | → PROCEED to Phase 5 (note gaps) |
-| User satisfied | User says "enough" or "looks good" | → PROCEED to Phase 5 |
-| Scope complete | All planned domains/files explored | → PROCEED to Phase 5 |
-
-#### Trigger Precedence (if multiple fire simultaneously)
-
-| Priority | Trigger | Reason |
-|----------|---------|--------|
-| 1 (highest) | Goal achieved | Mission complete, no need to continue |
-| 2 | User satisfied | User input overrides scope checks |
-| 3 | Scope complete | Planned work done |
-| 4 (lowest) | Stuck (exhausted) | Fallback when blocked; note gaps in output |
-
-**FORBIDDEN**: Ending research arbitrarily without a trigger.
-**FORBIDDEN**: Proceeding to OUTPUT without file:line evidence.
-
-#### Pre-Output Checklist
+ANY trigger → proceed to Phase 5:
 
-- [ ] Completion trigger identified?
-- [ ] Key findings have file:line references?
-- [ ] Checkpoints saved if research was extensive?
-- [ ] Tasks marked complete via `TaskUpdate` (or `TodoWrite`)?
+| Trigger | Priority |
+|---------|----------|
+| Goal achieved (with file:line refs) | 1 (highest) |
+| User satisfied | 2 |
+| Scope complete | 3 |
+| Stuck/exhausted | 4 (note gaps) |
 
-**IF ALL checked → PROCEED to Phase 5 (OUTPUT)**
-**IF ANY unchecked → Complete missing items first**
+Pre-output: completion trigger identified? Findings have file:line? Checkpoints saved? Tasks marked complete?
 </research_complete_gate>
 
 ---
@@ -585,124 +306,74 @@ If `session.json` exists with state ≠ DONE → Ask user: "Resume from last che
 ## Phase 5: Output
 
 <output_gate>
-### STOP. Verify entry conditions and ensure output quality.
 
-#### Entry Verification (from Phase 4)
+### Required Response Structure
 
-- [ ] Completion trigger met? (goal achieved / stuck / user satisfied / scope complete)
-- [ ] Key findings documented with file:line refs?
-- [ ] Tasks updated via `TaskUpdate` (or `TodoWrite`)?
-
-**IF parallel agents were spawned:**
-- [ ] All domain-*.md files read and incorporated?
-- [ ] Merge gate completed? (see `references/PARALLEL_AGENT_PROTOCOL.md`)
-- [ ] Conflicts resolved or user acknowledged?
-
-**IF ANY entry condition not met → RETURN to Phase 4 (Research) or complete merge.**
+1. **TL;DR**: Clear summary (few sentences). If stuck, prefix with "[INCOMPLETE]".
+2. **Details**: In-depth analysis with evidence.
+3. **References**: ALL code citations with proper format.
+4. **Next Step**: Ask one of: "Create a research doc?" / "Continue researching [area]?" / "Any clarifications?"
 
-#### Required Response Structure (MANDATORY - Include ALL sections)
+All four sections are REQUIRED. Never end silently.
 
-1. **TL;DR**: Clear summary (a few sentences).
-2. **Details**: In-depth analysis with evidence.
-3. **References**: ALL code citations with proper format (see below).
-4. **Next Step**: **REQUIRED** question (see below).
+### Reference Format
 
-**FORBIDDEN**: Skipping any section. TL;DR, Details, References, and Next Step are always required.
+| Type | Format | Example |
+|------|--------|---------|
+| GitHub/External | Full URL with lines | `https://github.com/facebook/react/blob/main/src/ReactHooks.js#L66-L69` |
+| Local | `path:line` | `src/components/Button.tsx:42` |
+| Range | `path:start-end` | `src/utils/auth.ts:15-28` |
 
-#### IF Research is STUCK (goal not achieved)
+GitHub references MUST use full URLs (clickable). Line numbers REQUIRED on all references.
 
-When entering Phase 5 via "Stuck (exhausted)" trigger, adapt output format:
+### If Stuck
 
 | Section | Adaptation |
 |---------|------------|
-| **TL;DR** | Start with "[INCOMPLETE]" - e.g., "[INCOMPLETE] Investigated X, but Y remains unclear due to Z" |
-| **Details** | Include: attempts made, blockers hit, partial findings with file:line refs |
-| **References** | Include all files explored, even if inconclusive |
-| **Next Step** | MUST offer: "Continue researching [specific blocked area]?" OR "Need clarification on [X]?" |
-
-**Example Stuck TL;DR**: "[INCOMPLETE] Traced authentication flow to `auth/middleware.ts:42`, but token validation logic at `auth/jwt.ts:88-120` uses external service not accessible."
-
-#### Reference Format (MUST follow EXACTLY)
-
-| Research Type | Format | Example |
-|--------------|--------|---------|
-| **GitHub/External** | Full URL with line numbers | `https://github.com/facebook/react/blob/main/packages/react/src/ReactHooks.js#L66-L69` |
-| **Local codebase** | `path:line` format | `src/components/Button.tsx:42` |
-| **Multiple lines** | Range notation | `src/utils/auth.ts:15-28` |
+| TL;DR | "[INCOMPLETE] Investigated X, but Y unclear due to Z" |
+| Details | Attempts made, blockers, partial findings with file:line |
+| References | All files explored, even if inconclusive |
+| Next Step | "Continue researching [blocked area]?" or "Need clarification on [X]?" |
 
-**Why full GitHub URLs?** Users can click to navigate directly. Partial paths are ambiguous across branches/forks.
-
-**FORBIDDEN**: Relative GitHub paths without full URL.
-**FORBIDDEN**: Missing line numbers in references.
-
-#### Next Step Question (MANDATORY)
-
-You **MUST** end the session by asking ONE of these:
-- "Create a research doc?" (Save to `.octocode/research/{session}/research.md`)
-- "Continue researching [specific area]?"
-- "Any clarifications needed?"
-
-**FORBIDDEN**: Ending silently without a question.
-**FORBIDDEN**: Ending with just "Let me know if you need anything else."
-
-#### Gate Verification
-
-**HALT. Before sending output, verify:**
-- [ ] TL;DR included?
-- [ ] Details with evidence included?
-- [ ] ALL references have proper format?
-- [ ] Next step question included?
-
-**IF ANY checkbox unchecked → Add the missing element before sending.**
+Verify before sending: TL;DR? Details? References formatted? Next step question?
 </output_gate>
 
 ---
 
-## Cross-Cutting: Self-Check
+## Cross-Cutting: Self-Check & Constraints
 
 <agent_self_check>
-**After each tool call:** Hints followed? On track?
-**Periodically:** Task progress updated via `TaskUpdate` (or `TodoWrite`)? User informed of progress?
-**If stuck:** STOP and ask user.
+**After each tool call**: Hints followed? On track? Task progress updated?
+**If stuck**: STOP and ask user.
 
-**Phase gates:** Server "ok" → Context + prompt stated → Fast-path evaluated → Plan approved → Research (follow hints) → Checkpoint when needed → Output (TL;DR + refs + question)
+**Phase gates**: Server "ok" → Context + prompt stated → Fast-path evaluated → Plan approved → Research (follow hints) → Checkpoint when needed → Output (TL;DR + refs + question)
 
 **Multi-domain?** → See `references/PARALLEL_AGENT_PROTOCOL.md`
 </agent_self_check>
 
----
-
-## Reference: Global Constraints
-
 <global_constraints>
-### Core Principles (NON-NEGOTIABLE)
+### Core Principles
 
-1. **ALWAYS understand before acting** - Read tool schemas from context before calling
-2. **ALWAYS follow hints** - See Phase 4 for hint handling protocol
-3. **ALWAYS be data-driven** - Let data guide you (see Phase 2 Parameter Rules)
-4. **NEVER guess** - If value unknown, find it first with another tool
+1. **Understand before acting** — read tool schemas from context before calling
+2. **Follow hints** — tool responses guide next actions
+3. **Be data-driven** — follow schemas, never guess parameter values
+4. **If value unknown** — find it first with another tool
 
-### Research Params (REQUIRED in EVERY tool call)
+### Required Research Params (EVERY tool call)
 
 | Parameter | Description |
 |-----------|-------------|
 | `mainResearchGoal` | Overall objective |
-| `researchGoal` | This specific step's goal |
+| `researchGoal` | This step's goal |
 | `reasoning` | Why this tool/params |
 
-**FORBIDDEN**: Tool calls without these three parameters.
-
-### Execution Rules
-
-See Phase 3 for parallel execution strategy.
-
-### Output Standards
-
-See Phase 5 (Output Gate) for reference formats.
+Tool calls without all three parameters are FORBIDDEN.
 </global_constraints>
 
 ---
 
 ## Additional Resources
 
-- **`references/GUARDRAILS.md`** - Security, trust levels, limits, and integrity rules
+- **`references/GUARDRAILS.md`** — Security, trust levels, limits, integrity rules
+- **`references/PARALLEL_AGENT_PROTOCOL.md`** — When to parallelize, domain examples, spawn/barrier/merge protocol
+- **`references/SESSION_MANAGEMENT.md`** — Checkpoint protocol, session directory, resume logic