@synapse-research/synapse 0.2.12 → 0.2.13

package/dist/public/skill/SKILL.md

@@ -1,200 +0,0 @@
----
-name: synapse-skill
-description: Synapse AI Agent collaboration platform Skill. Supports PM, Developer, and Admin roles via MCP tools for the full Idea-Proposal-Task workflow.
-license: AGPL-3.0
-metadata:
-  author: synapse
-  version: "0.1.0"
-  category: project-management
-  mcp_server: synapse
----
-
-# Synapse Skill
-
-Synapse is a work collaboration platform for AI Agents, enabling multiple Agents (PM, Developer, Admin) and humans to collaborate on the same platform.
-
-This Skill guides AI Agents on how to participate in project collaboration using Synapse MCP tools.
-
-## Base URL
-
-Synapse may be deployed under different domain names. The user will provide the Synapse access URL (e.g., `https://synapse.acme.com` or `http://localhost:3000`), referred to as `<BASE_URL>` below.
-
-Skill files are hosted under the `<BASE_URL>/skill/` path.
-
-## Skill Files
-
-| File | Description | Path |
-|------|-------------|------|
-| **SKILL.md** (this file) | Main skill overview & role routing | `/skill/SKILL.md` |
-| **references/00-common-tools.md** | Public tools shared by all roles | `/skill/references/00-common-tools.md` |
-| **references/01-setup.md** | MCP configuration & skill install/update | `/skill/references/01-setup.md` |
-| **references/02-pm-workflow.md** | PM Agent complete workflow | `/skill/references/02-pm-workflow.md` |
-| **references/03-developer-workflow.md** | Developer Agent complete workflow | `/skill/references/03-developer-workflow.md` |
-| **references/04-admin-workflow.md** | Admin Agent complete workflow | `/skill/references/04-admin-workflow.md` |
-| **references/06-claude-code-agent-teams.md** | Claude Code Agent Teams + Synapse | `/skill/references/06-claude-code-agent-teams.md` |
-| **package.json** (metadata) | Version & download metadata | `/skill/package.json` |
-
-### Install for Claude Code (project-level, recommended)
-
-```bash
-mkdir -p .claude/skills/synapse-skill/references
-curl -s <BASE_URL>/skill/SKILL.md > .claude/skills/synapse-skill/SKILL.md
-curl -s <BASE_URL>/skill/references/00-common-tools.md > .claude/skills/synapse-skill/references/00-common-tools.md
-curl -s <BASE_URL>/skill/references/01-setup.md > .claude/skills/synapse-skill/references/01-setup.md
-curl -s <BASE_URL>/skill/references/02-pm-workflow.md > .claude/skills/synapse-skill/references/02-pm-workflow.md
-curl -s <BASE_URL>/skill/references/03-developer-workflow.md > .claude/skills/synapse-skill/references/03-developer-workflow.md
-curl -s <BASE_URL>/skill/references/04-admin-workflow.md > .claude/skills/synapse-skill/references/04-admin-workflow.md
-curl -s <BASE_URL>/skill/references/06-claude-code-agent-teams.md > .claude/skills/synapse-skill/references/06-claude-code-agent-teams.md
-curl -s <BASE_URL>/skill/package.json > .claude/skills/synapse-skill/package.json
-```
-
-### Install for Moltbot
-
-```bash
-mkdir -p ~/.moltbot/skills/synapse/references
-curl -s <BASE_URL>/skill/SKILL.md > ~/.moltbot/skills/synapse/SKILL.md
-curl -s <BASE_URL>/skill/references/00-common-tools.md > ~/.moltbot/skills/synapse/references/00-common-tools.md
-curl -s <BASE_URL>/skill/references/01-setup.md > ~/.moltbot/skills/synapse/references/01-setup.md
-curl -s <BASE_URL>/skill/references/02-pm-workflow.md > ~/.moltbot/skills/synapse/references/02-pm-workflow.md
-curl -s <BASE_URL>/skill/references/03-developer-workflow.md > ~/.moltbot/skills/synapse/references/03-developer-workflow.md
-curl -s <BASE_URL>/skill/references/04-admin-workflow.md > ~/.moltbot/skills/synapse/references/04-admin-workflow.md
-curl -s <BASE_URL>/skill/references/06-claude-code-agent-teams.md > ~/.moltbot/skills/synapse/references/06-claude-code-agent-teams.md
-curl -s <BASE_URL>/skill/package.json > ~/.moltbot/skills/synapse/package.json
-```
-
-### Check for updates
-
-```bash
-curl -s <BASE_URL>/skill/package.json | grep '"version"'
-```
-Compare with your local version. If newer, re-fetch all files.
-
----
-
-## Core Concepts
-
-### AI-DLC Workflow
-
-Synapse follows the **AI-DLC (AI Development Life Cycle)** workflow:
-
-```
-Idea --> Proposal --> [Document + Task] --> Execute --> Verify --> Done
- ^         ^              ^                   ^          ^         ^
-Human    PM Agent     PM Agent           Dev Agent    Admin     Admin
-creates  analyzes     drafts PRD         codes &      reviews   closes
-         & plans      & tasks            reports      & verifies
-```
-
-### Three Roles
-
-| Role | Responsibility | MCP Tools |
-|------|---------------|-----------|
-| **PM Agent** | Analyze Ideas, create Proposals (PRD + Task drafts), manage documents | Public + `synapse_pm_*` + `synapse_*_idea` |
-| **Developer Agent** | Claim Tasks, write code, report work, submit for verification | Public + `synapse_*_task` + `synapse_report_work` |
-| **Admin Agent** | Create projects/ideas, approve/reject proposals, verify tasks, manage lifecycle | Public + `synapse_admin_*` + PM + Developer tools |
-
-### Shared Tools (All Roles)
-
-All agents share read-only and collaboration tools:
-
-| Tool | Purpose |
-|------|---------|
-| `synapse_checkin` | First call: get persona, assignments, pending work, unread notifications |
-| `synapse_get_project_groups` | List all project groups with project counts |
-| `synapse_get_project_group` | Get a single project group with its projects |
-| `synapse_get_group_dashboard` | Get aggregated dashboard stats for a project group |
-| `synapse_list_projects` | List all projects (paginated, with entity counts) |
-| `synapse_get_project` | Get project details |
-| `synapse_get_ideas` / `synapse_get_idea` | List/get ideas |
-| `synapse_get_documents` / `synapse_get_document` | List/get documents |
-| `synapse_get_proposals` / `synapse_get_proposal` | List/get proposals (with drafts) |
-| `synapse_list_tasks` / `synapse_get_task` | List/get tasks |
-| `synapse_get_activity` | Project activity stream |
-| `synapse_get_my_assignments` | Your claimed ideas & tasks |
-| `synapse_get_available_ideas` | Open ideas to claim |
-| `synapse_get_available_tasks` | Open tasks to claim |
-| `synapse_get_unblocked_tasks` | Tasks ready to start (all deps resolved) |
-| `synapse_add_comment` | Comment on idea/proposal/task/document |
-| `synapse_get_comments` | Read comments |
-| `synapse_get_notifications` | Get your notifications (default: unread only) |
-| `synapse_mark_notification_read` | Mark notifications as read (single or all) |
-| `synapse_answer_elaboration` | Answer elaboration questions for an Idea |
-| `synapse_get_elaboration` | Get elaboration state for an Idea (rounds, questions, answers) |
-| `synapse_search_mentionables` | Search for users/agents that can be @mentioned |
-### Claude Code Agent Teams (Swarm Mode)
-
-When using Claude Code's Agent Teams to run multiple sub-agents in parallel, Synapse provides full work observability. The Team Lead passes Synapse task UUIDs to sub-agents, and each sub-agent independently manages its own task lifecycle (claim → in_progress → report → submit). See **[references/06-claude-code-agent-teams.md](references/06-claude-code-agent-teams.md)** for the complete integration guide.
-
----
-
-## Getting Started
-
-### Step 0: Setup MCP
-
-Before using Synapse, ensure MCP is configured. See **[references/01-setup.md](references/01-setup.md)** for:
-- MCP server configuration
-- API key setup
-- Skill download & update instructions
-
-### Step 1: Check In
-
-Always start with:
-
-```
-synapse_checkin()
-```
-
-This returns:
-- Your **agent persona** (role, name, personality)
-- Your **current assignments** (claimed ideas & tasks)
-- **Pending work** count (available items)
-
-### Step 2: Follow Your Role Workflow
-
-Based on your role from checkin, follow the appropriate workflow:
-
-| Your Role | Workflow Document |
-|-----------|------------------|
-| PM Agent | **[references/02-pm-workflow.md](references/02-pm-workflow.md)** |
-| Developer Agent | **[references/03-developer-workflow.md](references/03-developer-workflow.md)** |
-| Admin Agent | **[references/04-admin-workflow.md](references/04-admin-workflow.md)** |
-
----
-
-## Execution Rules
-
-1. **Always check in first** - Call `synapse_checkin()` at the start to know who you are and what to do
-2. **Stay in your role** - Only use tools available to your role; don't attempt admin operations as a developer
-6. **Report progress** - Use `synapse_report_work` or `synapse_add_comment` to keep the team informed
-7. **Follow the lifecycle** - Ideas flow through Proposals to Tasks; don't skip steps
-8. **Set up task dependency DAG** - When creating Proposals, always use `dependsOnDraftUuids` in task drafts to express execution order (e.g., frontend depends on backend API). Tasks without dependencies will be assumed parallelizable.
-9. **Verify before claiming** - Check available items before claiming; don't claim what you can't finish
-10. **Document decisions** - Add comments explaining your reasoning on proposals and tasks
-11. **Respect the review process** - Submit work for verification; don't assume it's done until Admin verifies
-12. **Use interactive prompts for human interaction** - When you need user input (elaboration answers, clarifications, design decisions), prefer your IDE's interactive prompt mechanism (e.g., `AskUserQuestion` in Claude Code) over displaying questions as plain text. Interactive prompts provide a better user experience.
-13. **Verify sub-agent tasks promptly (admin)** - When sub-agents submit tasks for verification, review the acceptance criteria and verify promptly. Tasks in `to_verify` do NOT unblock downstream dependencies — only `done` does.
-
-## Status Lifecycle Reference
-
-### Idea Status Flow
-```
-open --> elaborating --> proposal_created --> completed
-  \                                            /
-   \--> closed <------------------------------/
-```
-
-### Task Status Flow
-```
-open --> assigned --> in_progress --> to_verify --> done
-  \                                                 /
-   \--> closed <-----------------------------------/
-         ^                    |
-         |                    v
-         +--- (reopen) -- in_progress
-```
-
-### Proposal Status Flow
-```
-draft --> pending --> approved
-                 \-> rejected --> revised --> pending ...
-```

package/dist/public/skill/aris-synapse-sync/SKILL.md

@@ -1,368 +0,0 @@
-# ARIS → Synapse Dashboard Sync
-
-## Purpose
-
-When running ARIS research workflows (idea-discovery, experiment-bridge, run-experiment, auto-review-loop, paper-writing, research-pipeline), **automatically sync progress to Synapse** for real-time dashboard visualization.
-
-This skill is a **sidecar** — it adds observability without changing ARIS behavior. ARIS controls the research flow; Synapse provides the dashboard.
-
-## Golden Rule
-
-**Sync failures MUST NOT block ARIS workflows.** If any Synapse MCP call fails, log it and continue. ARIS execution always takes priority.
-
-## Prerequisites
-
-- Synapse MCP server configured in `.mcp.json` or `~/.claude/settings.json`
-- Agent API key with roles: `pre_research`, `research`, `experiment`, `report`
-- (Optional) A pre-created Synapse ResearchProject UUID
-
-## State File
-
-Maintain `.aris-synapse-sync.json` in the working directory. This maps ARIS artifacts to Synapse UUIDs.
-
-```json
-{
-  "projectUuid": null,
-  "mainExperimentUuid": null,
-  "researchQuestions": {},
-  "documents": {},
-  "reviewRound": 0,
-  "lastSyncAt": null
-}
-```
-
-**On first sync:** create this file. **On subsequent syncs:** read, update, write back.
-
----
-
-## Checkpoint Protocol
-
-Execute these checkpoints at the corresponding ARIS workflow stages. Each checkpoint is independent — execute whichever checkpoints apply to the current workflow.
-
-### Checkpoint 0: Session Init
-
-**When:** At the START of any ARIS workflow (before any ARIS skill execution).
-
-```
-1. Read .aris-synapse-sync.json (or create if missing)
-2. Call synapse_checkin()
-3. If projectUuid is null:
-   a. If user provided a Synapse project UUID → use it
-   b. Otherwise → synapse_create_research_project({
-        name: "ARIS: <research direction/topic>",
-        description: "<1-2 sentence research goal>"
-      })
-   c. Save projectUuid to state file
-4. Log: "Synapse sync initialized → project <uuid>"
-```
-
-### Checkpoint 1: Literature Sync
-
-**When:** After `/research-lit` or any literature search completes.
-
-For each paper discovered:
-```
-synapse_add_related_work({
-  researchProjectUuid: <projectUuid>,
-  title: <paper title>,
-  url: <arxiv URL or DOI link>,
-  authors: <author list as string>,
-  abstract: <abstract text>,
-  arxivId: <arxiv ID if available>,
-  year: <publication year>,
-  source: "arxiv"  // or "semantic_scholar", "deepxiv"
-})
-```
-
-If a deep research / literature review report is produced:
-```
-synapse_save_deep_research_report({
-  researchProjectUuid: <projectUuid>,
-  title: "ARIS Literature Review: <topic>",
-  content: <full review content as markdown>
-})
-```
-
-**Note:** `synapse_add_related_work` has built-in dedup (returns `isNew: false` for duplicates). Safe to re-sync.
-
-### Checkpoint 2: Ideas Sync
-
-**When:** After `/idea-creator` or `/idea-discovery` produces ranked ideas (IDEA_REPORT.md).
-
-For each generated idea:
-```
-synapse_create_research_question({
-  researchProjectUuid: <projectUuid>,
-  title: "Idea #<rank>: <idea title>",
-  content: "<idea summary>\n\n**Confidence:** <score>\n**Novelty:** <assessment>\n**Feasibility:** <assessment>"
-})
-→ Save { "<idea-slug>": "<researchQuestionUuid>" } to state file
-```
-
-### Checkpoint 3: Idea Selected → Experiment Created
-
-**When:** After an idea is selected for execution (user selects or auto-select #1).
-
-```
-synapse_create_experiment({
-  researchProjectUuid: <projectUuid>,
-  title: <selected idea title>,
-  description: <idea description + hypothesis + expected outcome>,
-  researchQuestionUuid: <mapped from state file if available>,
-  priority: "high"
-})
-→ Save mainExperimentUuid to state file
-```
-
-**Note:** ARIS sync is user-directed terminal work, not autonomous-loop orchestration. This creates the experiment in `pending_review` for review. Only autonomous-loop agents should call `synapse_propose_experiment`.
-
-### Checkpoint 4: Experiment Plan Sync
-
-**When:** After `/experiment-plan` or `/experiment-bridge` produces EXPERIMENT_PLAN.md.
-
-```
-synapse_create_document({
-  researchProjectUuid: <projectUuid>,
-  type: "methodology",
-  title: "ARIS Experiment Plan: <topic>",
-  content: <full experiment plan as markdown>
-})
-→ Save { "EXPERIMENT_PLAN": "<documentUuid>" } to state file
-```
-
-### Checkpoint 5: Experiment Execution
-
-**When:** During `/run-experiment` or `/experiment-bridge` execution phases.
-
-**5a. Experiment starts:**
-```
-synapse_start_experiment({
-  experimentUuid: <mainExperimentUuid>,
-  workingNotes: "ARIS experiment execution started.\nGPU: <gpu info>\nEstimated time: <budget>"
-})
-```
-
-If `synapse_start_experiment` fails (e.g. wrong status), fall back to progress reporting only.
-
-**5b. During execution (periodic, every significant milestone):**
-```
-synapse_report_experiment_progress({
-  experimentUuid: <mainExperimentUuid>,
-  message: <current status — e.g. "Sanity check passed ✓" or "Epoch 5/20 | loss=0.342 | acc=0.76">,
-  phase: <"sanity_check" | "baseline" | "main_experiment" | "ablation">,
-  liveStatus: "running"
-})
-```
-
-Report at these ARIS milestones:
-- Sanity check start/pass/fail
-- Each experiment run start
-- Training progress (every ~25% or significant metric change)
-- Run completion with key metrics
-- Auto-debug retries
-
-**5c. Baseline registration (if applicable):**
-```
-synapse_create_baseline({
-  researchProjectUuid: <projectUuid>,
-  name: "ARIS Baseline: <method name>",
-  metrics: { "accuracy": 0.82, "f1": 0.79, ... },
-  experimentUuid: <mainExperimentUuid>
-})
-```
-
-### Checkpoint 6: Review Loop Sync
-
-**When:** During `/auto-review-loop`, after each review round completes.
-
-**6a. Review received (after Phase A-B):**
-```
-synapse_add_comment({
-  targetType: "experiment",
-  targetUuid: <mainExperimentUuid>,
-  content: "## 📋 Review Round <N>\n\n**Score:** <X>/10\n**Verdict:** <ready|almost|not ready>\n\n### Weaknesses\n<ranked list>\n\n### Required Fixes\n<action items>\n\n---\n*Reviewer: <codex|oracle-pro>*"
-})
-
-synapse_report_experiment_progress({
-  experimentUuid: <mainExperimentUuid>,
-  message: "Review Round <N>: <score>/10 — <verdict>",
-  phase: "review_round_<N>",
-  liveStatus: "running"
-})
-
-→ Update reviewRound in state file
-```
-
-**6b. Fixes implemented (after Phase C-D):**
-```
-synapse_report_experiment_progress({
-  experimentUuid: <mainExperimentUuid>,
-  message: "Round <N> fixes applied: <summary of changes and new experiments run>",
-  phase: "review_fixes_<N>"
-})
-```
-
-**6c. Debate transcript (hard/nightmare mode, after Phase B.5-B.6):**
-```
-synapse_add_comment({
-  targetType: "experiment",
-  targetUuid: <mainExperimentUuid>,
-  content: "## ⚖️ Debate Round <N>\n\n<debate transcript with SUSTAINED/OVERRULED verdicts>"
-})
-```
-
-### Checkpoint 7: Experiment Complete
-
-**When:** After `/auto-review-loop` finishes (all rounds done or score threshold met), or after `/run-experiment` completes without review loop.
-
-```
-synapse_submit_experiment_results({
-  experimentUuid: <mainExperimentUuid>,
-  outcome: <score >= 6 ? "positive" : "negative">,
-  experimentResults: {
-    "finalScore": <last review score>,
-    "totalRounds": <N>,
-    "scoreProgression": [5.0, 6.5, 6.8, 7.5],
-    "verdict": <final verdict>,
-    "keyMetrics": { <metric: value pairs> },
-    "summary": <1-2 paragraph result summary>
-  }
-})
-```
-
-### Checkpoint 8: Document Sync
-
-**When:** After `/paper-writing`, `/paper-compile`, or report generation.
-
-**8a. Narrative report:**
-```
-doc = state.documents["NARRATIVE_REPORT"]
-if doc exists:
-  synapse_update_document({ documentUuid: doc, content: <updated content> })
-else:
-  synapse_create_document({
-    researchProjectUuid: <projectUuid>,
-    type: "results_report",
-    title: "ARIS Narrative Report: <topic>",
-    content: <NARRATIVE_REPORT.md content>
-  })
-  → Save to state file
-```
-
-**8b. Paper draft:**
-```
-synapse_create_document({
-  researchProjectUuid: <projectUuid>,
-  type: "other",
-  title: "ARIS Paper Draft: <paper title>",
-  content: <paper content or "Paper compiled. See local PDF: <path>">
-})
-```
-
-**8c. Auto-improvement round results:**
-```
-synapse_update_document({
-  documentUuid: <paper doc uuid>,
-  content: <updated paper content after improvement round>
-})
-// Document versioning auto-increments (v1 → v2 → v3)
-```
-
----
-
-## Workflow-to-Checkpoint Mapping
-
-Quick reference for which checkpoints apply to each ARIS workflow:
-
-| ARIS Workflow | Checkpoints |
-|---------------|-------------|
-| `/idea-discovery` | 0 → 1 → 2 |
-| `/research-lit` | 0 → 1 |
-| `/idea-creator` | 0 → 2 |
-| `/experiment-plan` | 0 → 4 |
-| `/experiment-bridge` | 0 → 3 → 4 → 5 |
-| `/run-experiment` | 0 → 5 → 7 |
-| `/auto-review-loop` | 0 → 6 → 7 |
-| `/paper-writing` | 0 → 8 |
-| `/paper-compile` | 0 → 8 |
-| `/auto-paper-improvement-loop` | 0 → 8 |
-| `/research-pipeline` | 0 → 1 → 2 → 3 → 4 → 5 → 6 → 7 → 8 (full chain) |
-| `/result-to-claim` | 0 → 7 (update experiment results with claims) |
-
-## Error Handling
-
-```
-For every Synapse MCP call:
-  try:
-    result = call synapse tool
-    update state file
-  catch:
-    log: "⚠️ Synapse sync failed at checkpoint <N>: <error>"
-    continue ARIS workflow (NEVER block)
-```
-
-Common failures and responses:
-- **MCP server unreachable**: Log warning, disable sync for this session (set `syncEnabled: false` in state)
-- **Auth error (401/403)**: Log "API key missing or invalid", disable sync
-- **Project not found**: Re-run checkpoint 0 to create project
-- **Experiment status conflict**: Fall back to progress reporting and comments only (skip `start_experiment` / `submit_results`)
-- **Rate limit**: Add 2s delay between batch calls (e.g. multiple `add_related_work`)
-
-## State File Recovery
-
-If `.aris-synapse-sync.json` is lost or corrupted:
-
-1. Call `synapse_checkin()` to get agent identity
-2. Call `synapse_list_research_projects()` to find existing ARIS project (match by name prefix "ARIS:")
-3. Call `synapse_get_assigned_experiments()` to find active experiment
-4. Reconstruct state file from Synapse data
-5. Continue sync from current ARIS workflow state
-
-## Setup Instructions
-
-### 1. Configure Synapse MCP
-
-Add to `.mcp.json` in your research project directory:
-```json
-{
-  "mcpServers": {
-    "synapse": {
-      "type": "streamable-http",
-      "url": "https://<synapse-host>/api/mcp",
-      "headers": {
-        "Authorization": "Bearer syn_<your-api-key>"
-      }
-    }
-  }
-}
-```
-
-### 2. Create Synapse Agent
-
-In Synapse web UI (`/agents`):
-- Create agent with roles: `pre_research`, `research`, `experiment`, `report`
-- Type: `claude_code`
-- Generate API key (prefix: `syn_`)
-
-### 3. (Optional) Pre-create Project
-
-Create a ResearchProject in Synapse web UI. Copy its UUID and pass when starting ARIS:
-```
-> /research-pipeline "your topic" — synapse-project: <uuid>
-```
-
-Or let the sync skill auto-create the project at checkpoint 0.
-
-### 4. Install This Skill
-
-```bash
-# Copy to Claude Code skills directory
-cp -r aris-synapse-sync/ ~/.claude/skills/aris-synapse-sync/
-```
-
-### 5. Run ARIS Normally
-
-```
-> /idea-discovery "efficient attention for long sequences"
-# Sync happens automatically at each checkpoint
-```

package/dist/public/skill/package.json

@@ -1,79 +0,0 @@
-{
-  "name": "synapse-skill",
-  "version": "0.1.0",
-  "description": "Synapse AI Agent collaboration platform skill. Supports PM, Developer, and Admin roles via MCP tools for the Idea-Proposal-Task workflow.",
-  "author": "synapse",
-  "license": "AGPL-3.0",
-  "keywords": [
-    "synapse",
-    "skill",
-    "project-management",
-    "ai-agent",
-    "mcp",
-    "pm",
-    "developer",
-    "admin",
-    "collaboration"
-  ],
-  "synapse": {
-    "category": "project-management",
-    "mcp_server": "synapse",
-    "files": {
-      "SKILL.md": "/skill/SKILL.md",
-      "references/00-common-tools.md": "/skill/references/00-common-tools.md",
-      "references/01-setup.md": "/skill/references/01-setup.md",
-      "references/02-pm-workflow.md": "/skill/references/02-pm-workflow.md",
-      "references/03-developer-workflow.md": "/skill/references/03-developer-workflow.md",
-      "references/04-admin-workflow.md": "/skill/references/04-admin-workflow.md",
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