Understanding MCP Tools

MCP (Model Context Protocol) is how agents interact with external systems. It's the bridge between "the AI wants to do something" and "the thing actually gets done."

What is MCP?

MCP servers provide tools that agents can use. Think of them as plugins:

• sciorex-research lets agents compile LaTeX, read PDFs, annotate documents, and manage your reference library
• sciorex-tickets gives agents the ability to create and manage tickets
• sciorex-interactions lets agents ask you questions
• sciorex-resources lets agents create and modify other agents and flows
• sciorex-secrets lets agents securely access credentials without seeing the actual values
• sciorex-permissions lets agents check and request tool permissions at runtime
• A GitHub MCP could let agents create pull requests
• A Slack MCP could let agents send messages

Built-in MCP Servers

Sciorex includes 59 tools across 6 built-in MCP servers:

Server	Tools	Purpose
sciorex-research	16	LaTeX compilation, PDF reading/annotation, reference library management
sciorex-tickets	23	Ticket CRUD, subtasks, epics, queries, progress, resource linking
sciorex-resources	11	Agent and flow management, schema access, execution
sciorex-interactions	4	User prompts, notifications, approvals, split panel control
sciorex-secrets	4	Encrypted vault access with request/release workflow
sciorex-permissions	1	Runtime approval prompts for sensitive operations

sciorex-research

Tools for working with LaTeX, PDFs, and your reference library:

Tool	What it does
pdf_read	Extract text from PDFs by page range
pdf_annotate	Add highlights, underlines, and comments to PDFs
pdf_get_annotations	Retrieve all annotations from a PDF
latex_compile	Compile LaTeX documents (pdflatex/xelatex/lualatex)
latex_get_errors	Retrieve compilation errors and warnings
latex_insert_citation	Insert \cite{} commands into LaTeX documents
latex_insert_template	Scaffold figures, tables, algorithms
library_add_item	Add papers, books, datasets to your library
library_list_items	Search and filter library items
library_update_item	Update metadata, reading status, rating
library_manage	Create and update collections and tags
library_add_note	Attach notes to library items
library_get_item	Get full item details
library_delete_item	Remove items from library
library_list_collections	Browse all collections
library_list_tags	Browse all tags

sciorex-tickets

Tools for working with your ticket system:

Tool	What it does
sciorex_create_ticket	Create a new ticket
sciorex_get_ticket	Get ticket details
sciorex_update_ticket	Modify a ticket
sciorex_change_status	Move ticket through workflow
sciorex_add_subtask	Add a subtask
sciorex_complete_subtask	Mark subtask done
sciorex_list_tickets	Find tickets with filters
sciorex_search_tickets	Search by text

sciorex-interactions

Tools for communicating with you:

Tool	What it does
sciorex_ask_user	Ask a question and wait for your answer
sciorex_notify_user	Send a notification
sciorex_request_approval	Request approval before proceeding
sciorex_set_view_mode	Switch between split panel modes (editor, PDF, markdown, etc.)

sciorex-resources

Tools for managing agents and flows programmatically:

Tool	What it does
sciorex_list_agents	List all available agents
sciorex_get_agent	Get an agent's YAML definition
sciorex_save_agent	Create or update an agent
sciorex_delete_agent	Delete an agent
sciorex_list_flows	List all available flows
sciorex_get_flow	Get a flow's JSON definition
sciorex_save_flow	Create or update a flow
sciorex_delete_flow	Delete a flow
sciorex_execute_agent	Launch agent execution in background
sciorex_execute_flow	Trigger flow execution with parameters
sciorex_get_schema	Get schema documentation

sciorex-secrets

Tools for securely managing credentials:

Tool	What it does
sciorex_list_secrets	Browse stored secrets (values never shown to AI)
sciorex_get_secret	Retrieve a secret by key (triggers user approval)
sciorex_set_secret	Store new secrets with user confirmation
sciorex_delete_secret	Remove a secret from the vault

Security

The secrets server never exposes actual secret values to AI models. When a secret is granted, the AI receives only an environment variable name. The actual value is injected securely at execution time.

sciorex-permissions

Tool for managing runtime permissions:

Tool	What it does
approval_prompt	Request user approval before executing a sensitive tool call

TIP

The permissions server provides a single tool that lets agents proactively request approval before running operations that may need explicit user consent. This is especially useful in auto-approve mode where you still want guardrails on specific actions.

How Agents Use Tools

When an agent needs to do something, it calls a tool:

Agent: "I need to create a ticket for this bug."
        calls sciorex_create_ticket with title and description
        ticket T-007 is created
        agent continues with the ticket ID

You control which tools each agent can access in the agent configuration.

Enabling Tools in Chat

When chatting directly (not using a specific agent), you can toggle tools:

1. Click the Tools button in the chat input
2. Enable or disable specific tools
3. Tools you enable become available for that session

Permission Modes

You decide how much autonomy agents have:

Mode	Behavior
Ask for all	Every tool call requires your approval
Auto-approve edits	File operations are automatic, commands need approval
YOLO Mode	Everything runs automatically (use with caution)

Server Health Monitoring

Sciorex monitors the status of all MCP servers. Each server reports its status (running or error), tool count, and any error messages. Check server health in Settings > MCP Servers.

Adding Custom MCP Servers

You can add custom MCP servers in Settings > MCP Servers. Each server requires:

Field	Description
Name	Display name for the server
Command	Path to server executable (e.g., node, npx, python)
Args	Command-line arguments
Env	Optional environment variables
Enabled	Toggle the server on or off

Once configured, the tools appear in Sciorex automatically and are exposed to all connected CLIs.

Sciorex also supports Playwright sync and Chrome DevTools sync for MCP servers that provide browser automation — these can automatically synchronize with the built-in preview panel.

Common MCP Servers

The MCP ecosystem is growing. Some popular options:

Server	Capabilities
GitHub	Issues, PRs, repositories
Slack	Messages, channels
PostgreSQL	Database queries
Playwright	Browser automation
Filesystem	Extended file operations

Check the MCP registry for community servers.

Best Practices

Start with built-in tools. The 59 built-in tools cover research, tickets, interactions, resources, and secrets.

Limit tool access. Only give agents the tools they actually need.

Require approval for destructive actions. Creating is safer than deleting.

Test custom MCPs carefully. Make sure they handle errors gracefully.

Next Steps

• Full MCP reference
• Configuring agent tools
• MCP in flows