MCP Servers (Model Context Protocol)

Sciorex includes built-in MCP servers that enable AI agents to interact with your workspace, tickets, and user interface. These servers follow the Model Context Protocol standard.

Overview

MCP servers provide tools that Claude can use during conversations and agent runs. Sciorex includes three built-in servers, plus one internal server for permissions:

Server	Purpose
sciorex-tickets	Manage tickets, epics, subtasks, and track progress
sciorex-interactions	Ask questions, send notifications, request approvals
sciorex-resources	Create, read, update, and delete agents and flows
sciorex-permissions	(Internal) Handle permission prompts when MCP permissions are enabled

Built-in Claude Tools

In addition to MCP servers, Claude has access to these built-in tools:

Tool	Description
Bash	Execute shell commands in your environment
BashOutput	Retrieve output from background bash shells
Read	Read contents of files
Write	Create or overwrite files
Edit	Make targeted edits to specific files
Glob	Find files based on pattern matching
Grep	Search for patterns in file contents
WebFetch	Fetch content from URLs
WebSearch	Perform web searches with domain filtering
Task	Run sub-agents for complex multi-step tasks
TodoWrite	Create and manage structured task lists
AskUserQuestion	Ask the user multiple choice questions
NotebookEdit	Modify Jupyter notebook cells
Skill	Execute skills within the conversation
SlashCommand	Run custom slash commands

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sciorex-tickets Server

The sciorex-tickets MCP server provides comprehensive ticket and epic management capabilities. This server works directly with the Ticketing System.

Ticket Tools

sciorex_create_ticket

Create a new ticket in the current workspace.

Parameters:

Parameter	Type	Required	Description
title	string	✅	Ticket title
description	string	❌	Detailed description in markdown
type	enum	❌	feature, bug, task, research, documentation, refactor
priority	enum	❌	critical, high, medium, low
epicId	string	❌	Parent epic ID (e.g., "E-001")
labels	string[]	❌	Tags/labels for the ticket
subtasks	string[]	❌	List of subtask titles to create

Example:

{
  "title": "Implement user authentication",
  "description": "Add OAuth2 login flow with Google and GitHub providers",
  "type": "feature",
  "priority": "high",
  "epicId": "E-001",
  "subtasks": ["Design login UI", "Implement OAuth flow", "Add session management"]
}

sciorex_get_ticket

Get full details of a ticket by ID.

Parameters:

Parameter	Type	Required	Description
ticketId	string	✅	Ticket ID (e.g., "T-001")

Returns: Complete ticket object including subtasks, history, and relationships.

sciorex_update_ticket

Update one or more fields of a ticket.

Parameters:

Parameter	Type	Required	Description
ticketId	string	✅	Ticket ID to update
title	string	❌	New title
description	string	❌	New description
type	enum	❌	New type
priority	enum	❌	New priority
labels	string[]	❌	New labels
epicId	string | null	❌	New epic ID or null to remove

sciorex_change_status

Change the status of a ticket. Validates that the transition is allowed.

Parameters:

Parameter	Type	Required	Description
ticketId	string	✅	Ticket ID
status	enum	✅	backlog, planned, in_progress, in_review, done, cancelled
comment	string	❌	Optional comment explaining the change

Valid Transitions

Status changes must follow the allowed transitions. See Status Transitions for details.

sciorex_list_tickets

List tickets with optional filters.

Parameters:

Parameter	Type	Required	Description
status	string	❌	Filter by status
type	string	❌	Filter by type
priority	string	❌	Filter by priority
epicId	string	❌	Filter by epic
limit	number	❌	Max tickets to return (default: 50)

---

Epic Tools

sciorex_create_epic

Create a new epic.

Parameters:

Parameter	Type	Required	Description
title	string	✅	Epic title
description	string	❌	Epic description in markdown

sciorex_get_epic

Get an epic by ID with its associated tickets.

Parameters:

Parameter	Type	Required	Description
epicId	string	✅	Epic ID (e.g., "E-001")

Returns: Epic details plus list of tickets assigned to it.

sciorex_list_epics

List all epics with progress statistics.

Parameters: None required.

Returns: All epics with ticket counts and completion percentages.

sciorex_update_epic

Update an epic's details.

Parameters:

Parameter	Type	Required	Description
epicId	string	✅	Epic ID to update
title	string	❌	New title
description	string	❌	New description
status	enum	❌	open, in_progress, completed, cancelled

---

Subtask Tools

sciorex_add_subtask

Add a subtask to a ticket.

Parameters:

Parameter	Type	Required	Description
ticketId	string	✅	Ticket ID (e.g., "T-001")
title	string	✅	Subtask title

sciorex_complete_subtask

Mark a subtask as complete (by ID or title match).

Parameters:

Parameter	Type	Required	Description
ticketId	string	✅	Ticket ID
subtaskId	string	❌	Subtask ID (takes precedence)
title	string	❌	Subtask title (used for matching)
completed	boolean	❌	Completion status (default: true)

Flexible Matching

You can complete subtasks by providing either the exact ID or a partial title match. Title matching is case-insensitive.

sciorex_list_subtasks

List all subtasks for a ticket with completion status.

Parameters:

Parameter	Type	Required	Description
ticketId	string	✅	Ticket ID

Returns: Subtasks with summary statistics (total, completed, pending, percentage).

---

Query Tools

sciorex_search_tickets

Search tickets by text in title, description, and ID.

Parameters:

Parameter	Type	Required	Description
query	string	✅	Search text (case-insensitive)
limit	number	❌	Max results (default: 20)

sciorex_get_ready_tickets

Get tickets that are ready to work on (status = "planned" and no blockers).

Parameters:

Parameter	Type	Required	Description
limit	number	❌	Max results (default: 10)
priority	string	❌	Filter by priority
type	string	❌	Filter by type

sciorex_get_blocked_tickets

Get tickets that are currently blocked.

Parameters:

Parameter	Type	Required	Description
limit	number	❌	Max results (default: 10)

---

Progress Tools

sciorex_report_progress

Report progress on a ticket. Creates a history entry.

Parameters:

Parameter	Type	Required	Description
ticketId	string	✅	Ticket ID
message	string	✅	Progress update message
percentage	number	❌	Optional progress percentage (0-100)

sciorex_add_comment

Add a comment to a ticket.

Parameters:

Parameter	Type	Required	Description
ticketId	string	✅	Ticket ID
comment	string	✅	Comment text

sciorex_add_blocker

Add a blocker relationship between tickets.

Parameters:

Parameter	Type	Required	Description
ticketId	string	✅	The ticket being blocked
blockerTicketId	string	✅	The ticket causing the block
reason	string	❌	Reason for the block

sciorex_remove_blocker

Remove a blocker from a ticket.

Parameters:

Parameter	Type	Required	Description
ticketId	string	✅	The ticket being blocked
blockerTicketId	string	✅	The blocker to remove

---

sciorex-interactions Server

The sciorex-interactions MCP server enables AI agents to communicate with users during execution.

sciorex_ask_user

Ask the user a question and wait for their response.

Parameters:

Parameter	Type	Required	Description
question	string	✅	The question to ask
context	string	❌	Additional context
responseType	enum	❌	single (radio), multiple (checkbox), text (textarea)
options	string[]	❌	Predefined options for selection
allowCustomText	boolean	❌	Show textarea for custom input (default: true)
urgency	enum	❌	blocking, important, optional
placeholder	string	❌	Placeholder text for textarea

Example:

{
  "question": "Which authentication provider should I implement first?",
  "responseType": "single",
  "options": ["Google OAuth", "GitHub OAuth", "Email/Password"],
  "allowCustomText": true,
  "urgency": "important"
}

Returns:

• selectedOptions: Array of selected option strings
• customText: User's custom text input
• skipped: Whether user skipped the question

sciorex_notify_user

Send a notification to the user without waiting for response.

Parameters:

Parameter	Type	Required	Description
message	string	✅	Notification message
type	enum	❌	info, warning, error, success
details	string	❌	Additional details

sciorex_request_approval

Request explicit approval before proceeding with an action.

Parameters:

Parameter	Type	Required	Description
action	string	✅	Description of proposed action
reason	string	✅	Why this action is needed
alternatives	string[]	❌	Alternative actions if rejected
impact	enum	❌	low, medium, high

Example:

{
  "action": "Delete the legacy authentication module",
  "reason": "It's no longer used since the new OAuth implementation",
  "alternatives": ["Archive instead of delete", "Keep but mark as deprecated"],
  "impact": "high"
}

Returns:

• approved: Whether user approved
• selectedAlternative: Alternative chosen (if any)
• userComment: User's additional comments

---

sciorex-resources Server

The sciorex-resources MCP server allows AI agents to create, modify, and manage agents and flows programmatically. This enables dynamic workflow creation and agent self-modification.

Agent Tools

sciorex_list_agents

List all available agents in the workspace.

Parameters: None required.

Returns: Array of agents with id, name, description, and path.

sciorex_get_agent

Get the full YAML definition of an agent.

Parameters:

Parameter	Type	Required	Description
id	string	✅	Agent ID (kebab-case, e.g., "code-reviewer")

Returns: The complete YAML content of the agent definition.

sciorex_save_agent

Create or update an agent definition.

Parameters:

Parameter	Type	Required	Description
id	string	✅	Agent ID (kebab-case)
content	string	✅	Full YAML content of the agent definition

Example:

{
  "id": "code-reviewer",
  "content": "name: Code Reviewer\ndescription: Reviews code for quality and best practices\nsystemPrompt: |\n  You are a code review expert..."
}

Agent Schema

See Creating Agents for the full agent YAML schema and available options.

sciorex_delete_agent

Delete an agent from the workspace.

Parameters:

Parameter	Type	Required	Description
id	string	✅	Agent ID to delete

---

Flow Tools

sciorex_list_flows

List all available flows in the workspace.

Parameters: None required.

Returns: Array of flows with id, name, description, and path.

sciorex_get_flow

Get the full JSON definition of a flow.

Parameters:

Parameter	Type	Required	Description
id	string	✅	Flow ID

Returns: The complete JSON content of the flow definition.

sciorex_save_flow

Create or update a flow definition.

Parameters:

Parameter	Type	Required	Description
id	string	✅	Flow ID (kebab-case)
content	string	✅	Full JSON content of the flow definition

Flow Schema

See Flow Editor for the flow JSON schema and node types.

sciorex_delete_flow

Delete a flow from the workspace.

Parameters:

Parameter	Type	Required	Description
id	string	✅	Flow ID to delete

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Enabling MCP Tools

In Chat Sessions

When starting a chat, you can enable MCP tools using the tool selector:

1. Click the 🔧 Tools button in the chat input area
2. Toggle on the MCP servers you want to enable
3. Optionally select specific tools from each server

In Agent Definitions

When creating agents, you can configure allowed tools:

# In agent definition
allowedTools:
  - mcp__sciorex-tickets__sciorex_create_ticket
  - mcp__sciorex-tickets__sciorex_change_status
  - mcp__sciorex-tickets__sciorex_complete_subtask
  - mcp__sciorex-interactions__sciorex_ask_user

Tool Name Format

MCP tool names follow this pattern:

mcp__{server-name}__{tool-name}

Examples:

• mcp__sciorex-tickets__sciorex_create_ticket
• mcp__sciorex-tickets__sciorex_get_epic
• mcp__sciorex-interactions__sciorex_notify_user

---

Tool Discovery

Sciorex automatically discovers available tools from MCP servers at startup and caches them.

How It Works

1. Startup: Sciorex spawns each configured MCP server
2. Query: Sends tools/list request to discover available tools
3. Cache: Stores tool definitions for quick access
4. UI: Updates tool selector with available options

Refreshing Tools

If you add or modify MCP servers:

1. Restart the application, or
2. Open Settings and the tools will be re-discovered

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Adding Custom MCP Servers

You can configure additional MCP servers in your Claude Code configuration:

{
  "mcpServers": {
    "my-custom-server": {
      "command": "node",
      "args": ["/path/to/server.js"],
      "env": {
        "API_KEY": "your-api-key"
      }
    }
  }
}

Custom servers will be discovered automatically and their tools will appear in the tool selector.

MCP Ecosystem

There's a growing ecosystem of MCP servers. Check out the MCP Registry for community-contributed servers.

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Use Cases

Ticket Automation

AI agents can work on tickets autonomously:

Agent: "Starting work on ticket T-001"
- Uses sciorex_get_ticket to read requirements
- Uses sciorex_change_status to mark as in_progress
- Implements the feature using Bash, Read, Write, Edit
- Uses sciorex_complete_subtask as it finishes each item
- Uses sciorex_report_progress to log updates
- Uses sciorex_change_status to mark as done

Interactive Development

Agents can ask for clarification:

Agent: "I found multiple approaches to implement this..."
- Uses sciorex_ask_user with options for user to choose
- Waits for user response
- Proceeds with selected approach

Progress Tracking

Keep stakeholders informed:

Agent: "Task 3 of 5 complete"
- Uses sciorex_notify_user to send progress update
- Uses sciorex_report_progress to log in ticket history
- Continues with next task

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Related Documentation

• Ticketing Dashboard - Full ticketing documentation
• Creating Agents - Configure agents with MCP tools
• Extended Thinking - AI reasoning capabilities