MCP Tools Reference

Sciorex exposes 59 tools across 6 built-in MCP (Model Context Protocol) servers, giving AI models deep integration with every part of the platform. Models can manage tickets, search research papers, annotate PDFs, compile LaTeX, handle secrets, and orchestrate workflows — all autonomously.

Overview

Server	Tools	Purpose
sciorex-research	16	Paper discovery, reference management, LaTeX compilation, PDF annotation
sciorex-tickets	23	Ticket CRUD, Kanban management, comments, labels, linking
sciorex-resources	11	File management, agent/flow execution, schema introspection
sciorex-interactions	4	User prompts, notifications, approvals, split panel views
sciorex-secrets	4	Secure credential storage and retrieval
sciorex-permissions	1	Tool execution approval gating

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Built-in Claude Tools

In addition to MCP servers, Sciorex provides these built-in tools to all AI models:

Tool	Description
Read	Read files from the local filesystem
Write	Write files to the local filesystem
Edit	Perform exact string replacements in files
Bash	Execute shell commands with optional timeout
Glob	Fast file pattern matching (e.g., **/*.ts)
Grep	Content search powered by ripgrep
TodoWrite	Structured task list management
SendMessage	Inter-agent messaging for Agent Teams

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sciorex-research Server

The research server provides 16 tools for paper discovery, reference management, LaTeX editing, PDF annotation, and citation management. It integrates with 14 external sources for paper discovery and supports 43 Zotero-compatible item types.

sciorex_search_papers

Search for academic papers across multiple sources.

Parameters:

Parameter	Type	Required	Description
query	string	Yes	Search query string
source	string	No	Source to search. One of: semantic_scholar, arxiv, pubmed, crossref, openalex, dblp, core, unpaywall, base, dimensions, google_scholar, ieee, scopus, web_of_science. Defaults to semantic_scholar.
limit	number	No	Maximum number of results to return (default: 10, max: 100)
offset	number	No	Pagination offset (default: 0)
year_from	number	No	Filter papers published from this year
year_to	number	No	Filter papers published up to this year
sort_by	string	No	Sort order: relevance, date, citations (default: relevance)

Returns: Array of paper objects with title, authors, abstract, DOI, URL, year, citation count, and source metadata.

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sciorex_get_paper_details

Get detailed metadata for a specific paper.

Parameters:

Parameter	Type	Required	Description
paper_id	string	Yes	Paper identifier (DOI, arXiv ID, Semantic Scholar ID, or URL)
source	string	No	Source to query (default: auto-detect from ID format)

Returns: Full paper metadata including title, authors with affiliations, abstract, publication venue, year, DOI, references, citation count, and available full-text URLs.

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sciorex_get_citations

Get papers that cite a given paper.

Parameters:

Parameter	Type	Required	Description
paper_id	string	Yes	Paper identifier (DOI, arXiv ID, or Semantic Scholar ID)
limit	number	No	Maximum results (default: 10, max: 100)
offset	number	No	Pagination offset (default: 0)

Returns: Array of citing papers with metadata.

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sciorex_get_references

Get papers referenced by a given paper.

Parameters:

Parameter	Type	Required	Description
paper_id	string	Yes	Paper identifier (DOI, arXiv ID, or Semantic Scholar ID)
limit	number	No	Maximum results (default: 10, max: 100)
offset	number	No	Pagination offset (default: 0)

Returns: Array of referenced papers with metadata.

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sciorex_add_reference

Add a reference to the local reference library.

Parameters:

Parameter	Type	Required	Description
item_type	string	Yes	Zotero-compatible item type. One of 43 types including: journalArticle, book, bookSection, conferencePaper, thesis, report, patent, webpage, preprint, dataset, software, presentation, letter, manuscript, interview, film, podcast, videoRecording, audioRecording, artwork, map, statute, case, bill, hearing, newspaperArticle, magazineArticle, blogPost, forumPost, encyclopediaArticle, dictionaryEntry, instantMessage, email, attachment, note, annotation, computerProgram, standard, tvBroadcast, radioBroadcast, document, classic, periodical
title	string	Yes	Title of the reference
authors	array	No	Array of author objects: [{ "firstName": "", "lastName": "" }]
year	number	No	Publication year
doi	string	No	Digital Object Identifier
url	string	No	URL of the resource
abstract	string	No	Abstract text
journal	string	No	Journal or venue name
volume	string	No	Volume number
issue	string	No	Issue number
pages	string	No	Page range (e.g., "1-15")
publisher	string	No	Publisher name
tags	array	No	Array of tag strings
collection_id	string	No	ID of collection to add reference to
extra_fields	object	No	Additional Zotero-compatible fields

Returns: Created reference object with generated ID.

---

sciorex_search_references

Search the local reference library.

Parameters:

Parameter	Type	Required	Description
query	string	Yes	Search query (searches title, authors, abstract, tags)
item_type	string	No	Filter by item type
collection_id	string	No	Filter by collection
tags	array	No	Filter by tags (AND logic)
year_from	number	No	Filter by year range start
year_to	number	No	Filter by year range end
limit	number	No	Maximum results (default: 20)
offset	number	No	Pagination offset (default: 0)

Returns: Array of matching references from the library.

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sciorex_update_reference

Update an existing reference in the library.

Parameters:

Parameter	Type	Required	Description
reference_id	string	Yes	ID of the reference to update
fields	object	Yes	Object of fields to update (same fields as sciorex_add_reference)

Returns: Updated reference object.

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sciorex_delete_reference

Delete a reference from the library.

Parameters:

Parameter	Type	Required	Description
reference_id	string	Yes	ID of the reference to delete

Returns: Confirmation of deletion.

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sciorex_generate_citation

Generate a formatted citation string for a reference.

Parameters:

Parameter	Type	Required	Description
reference_id	string	Yes	ID of the reference to cite
style	string	No	Citation style. One of 11 styles: apa, mla, chicago, harvard, ieee, vancouver, nature, science, cell, bibtex, biblatex (default: apa)

Returns: Formatted citation string in the requested style.

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sciorex_generate_bibliography

Generate a formatted bibliography from multiple references.

Parameters:

Parameter	Type	Required	Description
reference_ids	array	Yes	Array of reference IDs to include
style	string	No	Citation style (same options as sciorex_generate_citation, default: apa)
sort_by	string	No	Sort order: author, year, title (default: author)

Returns: Formatted bibliography string.

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sciorex_export_references

Export references in various formats.

Parameters:

Parameter	Type	Required	Description
reference_ids	array	Yes	Array of reference IDs to export (or ["*"] for all)
format	string	Yes	Export format. One of 5 formats: bibtex, biblatex, ris, csv, json
collection_id	string	No	Export all references in a collection (alternative to reference_ids)

Returns: Exported data as a string in the requested format.

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sciorex_import_references

Import references from external formats or sources.

Parameters:

Parameter	Type	Required	Description
source	string	Yes	Import source. One of 14 sources: bibtex, biblatex, ris, csv, json, doi, arxiv, pubmed, isbn, url, pdf_metadata, crossref, zotero_api, mendeley_api
data	string	Yes	The import data (file content, DOI string, URL, etc.)
collection_id	string	No	Collection to import references into
duplicate_strategy	string	No	How to handle duplicates: skip, merge, create (default: skip)

Returns: Array of imported reference objects with status per item.

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sciorex_compile_latex

Compile a LaTeX document to PDF.

Parameters:

Parameter	Type	Required	Description
file_path	string	Yes	Absolute path to the main .tex file
engine	string	No	LaTeX engine: pdflatex, xelatex, lualatex (default: pdflatex)
bibliography	boolean	No	Whether to run BibTeX/Biber (default: false)
clean	boolean	No	Remove auxiliary files after compilation (default: false)

Returns: Object with success status, output PDF path, compilation log, and any errors/warnings.

---

sciorex_annotate_pdf

Add annotations to a PDF document.

Parameters:

Parameter	Type	Required	Description
file_path	string	Yes	Absolute path to the PDF file
annotations	array	Yes	Array of annotation objects
annotations[].type	string	Yes	Annotation type: highlight, underline, strikethrough, note, text, rectangle, freeform
annotations[].page	number	Yes	Page number (1-indexed)
annotations[].content	string	No	Text content for notes/text annotations
annotations[].color	string	No	Color in hex format (default: #FFFF00)
annotations[].coordinates	object	No	Position: { x, y, width, height } in PDF points
annotations[].quad_points	array	No	For highlight/underline: array of quad point arrays

Returns: Updated annotation list with generated IDs.

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sciorex_get_pdf_annotations

Retrieve annotations from a PDF document.

Parameters:

Parameter	Type	Required	Description
file_path	string	Yes	Absolute path to the PDF file
page	number	No	Filter annotations by page number
type	string	No	Filter by annotation type

Returns: Array of annotation objects with type, content, page, color, coordinates, and timestamps.

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sciorex_extract_pdf_text

Extract text content from a PDF document.

Parameters:

Parameter	Type	Required	Description
file_path	string	Yes	Absolute path to the PDF file
pages	string	No	Page range (e.g., "1-5", "3", "1,3,5-7"). Defaults to all pages.
format	string	No	Output format: plain, structured, markdown (default: plain)

Returns: Extracted text content in the requested format. Structured format includes page breaks and paragraph detection.

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sciorex-tickets Server

The tickets server provides 23 tools for full project management, including ticket CRUD, Kanban boards, comments, labels, and resource linking.

sciorex_create_ticket

Create a new ticket.

Parameters:

Parameter	Type	Required	Description
title	string	Yes	Ticket title
description	string	No	Ticket description (supports Markdown)
status	string	No	Status: backlog, todo, in_progress, in_review, done, cancelled (default: todo)
priority	string	No	Priority: none, low, medium, high, urgent (default: none)
assignee	string	No	Assignee username or ID
labels	array	No	Array of label IDs or names
due_date	string	No	Due date in ISO 8601 format
parent_id	string	No	Parent ticket ID for sub-tasks
board_id	string	No	Kanban board ID
estimate	number	No	Story point estimate
sprint_id	string	No	Sprint ID to assign to

Returns: Created ticket object with generated ID.

---

sciorex_get_ticket

Get a ticket by ID.

Parameters:

Parameter	Type	Required	Description
ticket_id	string	Yes	Ticket ID
include_comments	boolean	No	Include comments (default: false)
include_history	boolean	No	Include change history (default: false)
include_links	boolean	No	Include linked resources (default: false)

Returns: Full ticket object with optional related data.

---

sciorex_update_ticket

Update an existing ticket.

Parameters:

Parameter	Type	Required	Description
ticket_id	string	Yes	Ticket ID to update
title	string	No	New title
description	string	No	New description
status	string	No	New status
priority	string	No	New priority
assignee	string	No	New assignee
labels	array	No	Updated label list
due_date	string	No	New due date
estimate	number	No	New story point estimate
sprint_id	string	No	Move to different sprint

Returns: Updated ticket object.

---

sciorex_delete_ticket

Delete a ticket permanently.

Parameters:

Parameter	Type	Required	Description
ticket_id	string	Yes	Ticket ID to delete
delete_subtasks	boolean	No	Also delete sub-tasks (default: false)

Returns: Confirmation of deletion.

---

sciorex_list_tickets

List tickets with filtering and pagination.

Parameters:

Parameter	Type	Required	Description
board_id	string	No	Filter by board
status	string	No	Filter by status
priority	string	No	Filter by priority
assignee	string	No	Filter by assignee
label	string	No	Filter by label
sprint_id	string	No	Filter by sprint
parent_id	string	No	Filter by parent (get sub-tasks)
search	string	No	Full-text search in title and description
sort_by	string	No	Sort: created, updated, priority, due_date, title (default: updated)
sort_order	string	No	asc or desc (default: desc)
limit	number	No	Maximum results (default: 50)
offset	number	No	Pagination offset (default: 0)

Returns: Array of ticket objects with total count.

---

sciorex_search_tickets

Full-text search across all tickets.

Parameters:

Parameter	Type	Required	Description
query	string	Yes	Search query
board_id	string	No	Limit search to a board
include_archived	boolean	No	Include archived tickets (default: false)
limit	number	No	Maximum results (default: 20)

Returns: Array of matching tickets with relevance scores.

---

sciorex_add_comment

Add a comment to a ticket.

Parameters:

Parameter	Type	Required	Description
ticket_id	string	Yes	Ticket ID
content	string	Yes	Comment text (supports Markdown)
author	string	No	Author name (default: current AI model name)

Returns: Created comment object with ID and timestamp.

---

sciorex_list_comments

List comments on a ticket.

Parameters:

Parameter	Type	Required	Description
ticket_id	string	Yes	Ticket ID
sort_order	string	No	asc or desc (default: asc)
limit	number	No	Maximum results (default: 50)
offset	number	No	Pagination offset (default: 0)

Returns: Array of comment objects.

---

sciorex_update_comment

Update an existing comment.

Parameters:

Parameter	Type	Required	Description
comment_id	string	Yes	Comment ID
content	string	Yes	Updated comment text

Returns: Updated comment object.

---

sciorex_delete_comment

Delete a comment from a ticket.

Parameters:

Parameter	Type	Required	Description
comment_id	string	Yes	Comment ID to delete

Returns: Confirmation of deletion.

---

sciorex_create_board

Create a new Kanban board.

Parameters:

Parameter	Type	Required	Description
name	string	Yes	Board name
description	string	No	Board description
columns	array	No	Custom column definitions. Default: ["Backlog", "To Do", "In Progress", "In Review", "Done"]
default_assignee	string	No	Default assignee for new tickets

Returns: Created board object with ID.

---

sciorex_list_boards

List all Kanban boards.

Parameters:

Parameter	Type	Required	Description
include_ticket_counts	boolean	No	Include per-column ticket counts (default: false)

Returns: Array of board objects.

---

sciorex_move_ticket

Move a ticket between columns or boards.

Parameters:

Parameter	Type	Required	Description
ticket_id	string	Yes	Ticket ID to move
status	string	No	New status/column
board_id	string	No	Move to different board
position	number	No	Position within the column (0-indexed)

Returns: Updated ticket object.

---

sciorex_create_label

Create a new label.

Parameters:

Parameter	Type	Required	Description
name	string	Yes	Label name
color	string	No	Label color in hex (e.g., #FF5733)
description	string	No	Label description

Returns: Created label object with ID.

---

sciorex_list_labels

List all available labels.

Parameters:

Parameter	Type	Required	Description
board_id	string	No	Filter labels by board

Returns: Array of label objects.

---

sciorex_add_label_to_ticket

Add a label to a ticket.

Parameters:

Parameter	Type	Required	Description
ticket_id	string	Yes	Ticket ID
label_id	string	Yes	Label ID to add

Returns: Updated ticket labels array.

---

sciorex_remove_label_from_ticket

Remove a label from a ticket.

Parameters:

Parameter	Type	Required	Description
ticket_id	string	Yes	Ticket ID
label_id	string	Yes	Label ID to remove

Returns: Updated ticket labels array.

---

sciorex_create_sprint

Create a new sprint.

Parameters:

Parameter	Type	Required	Description
name	string	Yes	Sprint name
board_id	string	Yes	Board ID the sprint belongs to
start_date	string	No	Start date in ISO 8601 format
end_date	string	No	End date in ISO 8601 format
goal	string	No	Sprint goal description

Returns: Created sprint object with ID.

---

sciorex_list_sprints

List sprints for a board.

Parameters:

Parameter	Type	Required	Description
board_id	string	Yes	Board ID
status	string	No	Filter by status: planning, active, completed
include_ticket_counts	boolean	No	Include ticket count per sprint (default: false)

Returns: Array of sprint objects.

---

sciorex_get_ticket_history

Get the change history of a ticket.

Parameters:

Parameter	Type	Required	Description
ticket_id	string	Yes	Ticket ID
limit	number	No	Maximum entries (default: 50)

Returns: Array of history entries with field, old value, new value, author, and timestamp.

---

sciorex_bulk_update_tickets

Update multiple tickets at once.

Parameters:

Parameter	Type	Required	Description
ticket_ids	array	Yes	Array of ticket IDs to update
fields	object	Yes	Fields to update (same options as sciorex_update_ticket)

Returns: Array of updated ticket objects.

---

sciorex_link_resource

Link an external resource to a ticket.

Parameters:

Parameter	Type	Required	Description
ticket_id	string	Yes	Ticket ID to link to
resource_type	string	Yes	Type of resource: file, reference, url, chat_thread, flow, agent
resource_id	string	Yes	ID or path of the resource to link
label	string	No	Display label for the link
description	string	No	Description of the relationship

Returns: Created link object with ID.

---

sciorex_unlink_resource

Remove a linked resource from a ticket.

Parameters:

Parameter	Type	Required	Description
ticket_id	string	Yes	Ticket ID
link_id	string	Yes	Link ID to remove (from sciorex_link_resource response)

Returns: Confirmation of deletion.

---

sciorex-resources Server

The resources server provides 11 tools for file management, agent and flow execution, and schema introspection.

sciorex_list_files

List files and directories in a given path.

Parameters:

Parameter	Type	Required	Description
path	string	Yes	Directory path to list
recursive	boolean	No	List recursively (default: false)
pattern	string	No	Glob pattern filter (e.g., *.ts)
include_hidden	boolean	No	Include hidden files (default: false)
limit	number	No	Maximum entries (default: 100)

Returns: Array of file/directory entries with name, path, type, size, and modification time.

---

sciorex_read_file

Read the contents of a file.

Parameters:

Parameter	Type	Required	Description
path	string	Yes	Absolute file path
encoding	string	No	File encoding (default: utf-8)
line_start	number	No	Start reading from this line (1-indexed)
line_end	number	No	Stop reading at this line

Returns: File content as a string with metadata (size, line count, encoding).

---

sciorex_write_file

Write content to a file.

Parameters:

Parameter	Type	Required	Description
path	string	Yes	Absolute file path
content	string	Yes	Content to write
encoding	string	No	File encoding (default: utf-8)
create_dirs	boolean	No	Create parent directories if they don't exist (default: true)
overwrite	boolean	No	Overwrite existing file (default: true)

Returns: Confirmation with file path and bytes written.

---

sciorex_delete_file

Delete a file or directory.

Parameters:

Parameter	Type	Required	Description
path	string	Yes	Absolute path to delete
recursive	boolean	No	Required for non-empty directories (default: false)

Returns: Confirmation of deletion.

---

sciorex_copy_file

Copy a file or directory.

Parameters:

Parameter	Type	Required	Description
source	string	Yes	Source path
destination	string	Yes	Destination path
overwrite	boolean	No	Overwrite existing (default: false)

Returns: Confirmation with destination path.

---

sciorex_move_file

Move or rename a file or directory.

Parameters:

Parameter	Type	Required	Description
source	string	Yes	Source path
destination	string	Yes	Destination path
overwrite	boolean	No	Overwrite existing (default: false)

Returns: Confirmation with new path.

---

sciorex_search_files

Search for files by name pattern or content.

Parameters:

Parameter	Type	Required	Description
path	string	Yes	Root directory to search from
query	string	Yes	Search query (file name pattern or content string)
search_type	string	No	name or content (default: name)
pattern	string	No	Glob pattern to filter files
max_depth	number	No	Maximum directory depth
limit	number	No	Maximum results (default: 50)

Returns: Array of matching file paths with context.

---

sciorex_get_file_info

Get metadata about a file or directory.

Parameters:

Parameter	Type	Required	Description
path	string	Yes	Absolute path

Returns: Object with name, path, type, size, created, modified, permissions, and MIME type.

---

sciorex_execute_agent

Execute an AI agent configuration.

Parameters:

Parameter	Type	Required	Description
agent_id	string	Yes	ID of the saved agent configuration to execute
input	string	Yes	Input prompt or message to send to the agent
context	object	No	Additional context variables to pass to the agent
timeout	number	No	Execution timeout in milliseconds (default: 300000)
stream	boolean	No	Whether to stream the response (default: false)

Returns: Agent execution result including output text, token usage, and execution metadata.

---

sciorex_execute_flow

Execute a visual flow (workflow).

Parameters:

Parameter	Type	Required	Description
flow_id	string	Yes	ID of the flow to execute
inputs	object	No	Input variables for the flow trigger node
timeout	number	No	Execution timeout in milliseconds (default: 600000)
dry_run	boolean	No	Validate flow without executing (default: false)

Returns: Flow execution result including node-by-node output, final result, execution time, and any errors.

---

sciorex_get_schema

Get the schema definition for a resource type.

Parameters:

Parameter	Type	Required	Description
resource_type	string	Yes	Resource type to get schema for: ticket, board, sprint, label, comment, reference, collection, annotation, agent, flow, persona
format	string	No	Schema format: json_schema, typescript, table (default: json_schema)

Returns: Schema definition in the requested format, including all fields, types, required flags, and validation rules.

---

sciorex-interactions Server

The interactions server provides 4 tools for communicating with the user through the Sciorex UI.

sciorex_ask_user

Ask the user a question and wait for their response. Supports structured input with radio buttons, checkboxes, or free text.

Parameters:

Parameter	Type	Required	Description
question	string	Yes	The question to ask the user
responseType	string	No	Input type: single (radio buttons), multiple (checkboxes), text (textarea). Default: text
options	array	No	Predefined options for single or multiple response types
allowCustomText	boolean	No	Show a textarea for custom input in addition to options (default: true)
placeholder	string	No	Placeholder text for the textarea
context	string	No	Additional context to help the user understand the question
urgency	string	No	How critical: blocking, important, optional (default: important)

Returns: User's response text and/or selected options.

---

sciorex_notify_user

Send a notification to the user without waiting for a response. Useful for status updates, warnings, or informational messages.

Parameters:

Parameter	Type	Required	Description
message	string	Yes	The notification message
type	string	No	Notification type: info, warning, error, success (default: info)
details	string	No	Additional details about the notification

Returns: Confirmation that the notification was sent.

---

sciorex_request_approval

Request explicit approval from the user before proceeding with an action. Blocks until the user approves or rejects.

Parameters:

Parameter	Type	Required	Description
action	string	Yes	Description of what you want to do
reason	string	Yes	Why this action is needed
impact	string	No	Impact level: low, medium, high (default: medium)
alternatives	array	No	Alternative actions if this is rejected

Returns: Boolean approval status and optional user feedback.

---

sciorex_set_view_mode

Open a split panel next to the chat to display content. Supports 11 viewer types for different file formats and use cases.

Parameters:

Parameter	Type	Required	Description
viewMode	string	Yes	The split panel to open. One of 11 modes: normal (close panel), agentic (multi-file diff review), editor (Monaco code editor), preview (live browser preview), pdf (PDF viewer with annotations), markdown (rendered Markdown), html (sandboxed HTML preview), image (image viewer), bibtex (BibTeX citation viewer), molecule (3D molecular structure viewer for PDB/SDF/MOL/XYZ), excalidraw (whiteboard/drawing editor)
url	string	No	For preview mode: an http(s) URL. For file-based panels: a file:///absolute/path URL. If omitted, opens a file picker.
sessionId	string	No	Optional session ID to target a specific chat session

Returns: Confirmation that the view mode was set.

View Mode Details

Mode	Description	URL Format
normal	Closes the split panel, returns to standard chat	N/A
agentic	Multi-file diff review panel for code changes	N/A
editor	Monaco code editor with syntax highlighting	file:///path/to/file
preview	Live browser preview (hot-reloading)	http(s)://url
pdf	PDF viewer with annotations, search, thumbnails	file:///path/to/file.pdf
markdown	Rendered Markdown preview	file:///path/to/file.md
html	Sandboxed HTML preview	file:///path/to/file.html
image	Image viewer (PNG, JPG, SVG, etc.)	file:///path/to/image
bibtex	BibTeX citation viewer and editor	file:///path/to/refs.bib
molecule	3D molecular structure viewer	file:///path/to/structure.pdb
excalidraw	Whiteboard and drawing editor	file:///path/to/drawing.excalidraw

---

sciorex-secrets Server

The secrets server provides 4 tools for secure credential storage and retrieval. All secrets are encrypted at rest and never exposed in logs or chat history.

sciorex_set_secret

Store a secret value securely.

Parameters:

Parameter	Type	Required	Description
key	string	Yes	Secret key name (e.g., OPENAI_API_KEY, GITHUB_TOKEN)
value	string	Yes	Secret value to store (encrypted at rest)
description	string	No	Human-readable description of what this secret is for
category	string	No	Category for organization: api_key, token, password, certificate, other (default: other)

Returns: Confirmation with key name (value is never returned).

---

sciorex_get_secret

Retrieve a secret value.

Parameters:

Parameter	Type	Required	Description
key	string	Yes	Secret key name to retrieve

Returns: The decrypted secret value. Note: This tool requires explicit user approval via sciorex-permissions before execution.

---

sciorex_list_secrets

List all stored secret keys (values are never shown).

Parameters:

Parameter	Type	Required	Description
category	string	No	Filter by category

Returns: Array of secret entries with key name, description, category, and last-modified timestamp. Values are never included.

---

sciorex_delete_secret

Delete a stored secret.

Parameters:

Parameter	Type	Required	Description
key	string	Yes	Secret key name to delete

Returns: Confirmation of deletion.

---

sciorex-permissions Server

The permissions server provides a single gating tool that other tools may be routed through for user approval.

approval_prompt

Request user approval before executing a tool. This is used internally by the system to gate sensitive operations (e.g., reading secrets, executing destructive commands).

Parameters:

Parameter	Type	Required	Description
tool_name	string	Yes	The name of the tool being requested (e.g., Edit, Bash, Write)
tool_input	object	Yes	The input parameters for the tool
reason	string	No	Brief explanation of why this tool is needed

Returns: Object with approved boolean. If approved, the original tool is executed. If denied, the tool call is blocked.

---

Tool Count Summary

Server	Tools
sciorex-research	16
sciorex-tickets	23
sciorex-resources	11
sciorex-interactions	4
sciorex-secrets	4
sciorex-permissions	1
Total	59