Settings Reference

All settings are accessible via Settings (Ctrl/Cmd + ,). Changes are saved automatically to your workspace.

Appearance

Customize how Sciorex looks.

Setting	Description	Default	Options
Color Theme	Application color scheme	Dark	Dark, Light, System
Accent Color	Primary highlight color	Purple	Purple, Blue, Green, Orange, Red, Pink, Cyan, Yellow, Custom
Gray Palette	Background and border tones	Cool	Cool, Neutral, Warm
Border Radius	Corner rounding preset	Normal	Tight, Normal, Round, Full
UI Font Size	Base font size for the interface	Medium (14px)	Small (13px), Medium (14px), Large (16px), XL (18px)
Code Font Size	Font size for code blocks and terminal	14px	12, 14, 16, 18
Sidebar Width	Navigation sidebar width	Default (256px)	Narrow (200px), Default (256px), Wide (320px), Extra Wide (400px)
Reduce Motion	Minimize animations	Off	On, Off
Process Explorer Mode	How Process Explorer opens	Modal	Modal (current window), Window (new window)

See Process Explorer for details on monitoring running processes.

Editor

Code editor behavior and appearance.

Setting	Description	Default	Options
Vim Mode	Enable vim keybindings	Off	On, Off
Editor Theme	Code editor color scheme	VS Dark	Sciorex, Sciorex Dark, Sciorex Light, VS Dark, VS, High Contrast Black, High Contrast Light
Insert Spaces	Use spaces instead of tabs	On	On, Off
Tab Size	Spaces per indentation level	2	2, 4, 8
Word Wrap	Wrap long lines	Off	On, Off
Line Numbers	Show line numbers	On	On, Off
Minimap	Show code overview on right	On	On, Off
Single Click to Open	Open files with single click	Off	On, Off

External Editor Integration

Integrate with external code editors for file opening and editing.

Setting	Description	Default	Options
Enable VS Code	Enable VS Code integration	Off	On, Off
Editor Mode	How to use VS Code	Embedded	Embedded (server), External (app)
Editor Path	Path to external editor CLI	Auto-detect	Custom path
Editor Name	Display name for external editor	Auto-detect	Custom name
Auto-Launch	Auto-launch editor when editor view opens	Off	On, Off

AI Providers

Configure AI providers and models.

Provider Settings

Setting	Description	Default	Options
Default Provider	AI provider for new chats	Claude Code	Claude Code, Gemini, Codex, OpenCode, LM Studio, Ollama
Default Model	Model for new chats	Provider-specific	See Models Reference
Default Permission Mode	How tool calls are approved	Auto-approve edits	Normal (ask all), Auto-approve edits, YOLO (approve all)
Default Thinking Level	Extended thinking depth (Claude)	Think Harder	Off, Think, Think Hard, Think Harder, Ultrathink
Default Effort Level	Reasoning depth (Claude Opus 4.6 only)	High	Low, Medium, High, Max
MCP Permission Prompts	Experimental proactive permissions	Off	On, Off
Provider Priority	Fallback order for providers	Claude Code, Gemini, Codex, OpenCode, Ollama, LM Studio	Drag to reorder

Provider Configuration

Each provider has its own configuration tab:

Provider	Configuration
Claude Code	CLI path (auto-detect or custom)
Google Gemini	CLI path (auto-detect or custom)
OpenAI Codex	CLI path, OSS mode toggle
OpenCode	CLI path (auto-detect or custom)
LM Studio	Server URL (default: http://localhost:1234)
Ollama	Server URL (default: http://localhost:11434)

TIP

See the setup instructions in each provider's tab for installation and authentication details.

System Prompt Override

Add custom instructions to every conversation:

Setting	Description
Custom Instructions	Text added to all conversations
Mode	Append (add to default) or Replace (override default)
Templates	Save and load reusable prompt templates

Thinking Token Budgets

Configure maximum tokens for each thinking level:

Level	Default Budget	Range
Think	1,024	1,024 to 128,000
Think Hard	10,000	1,024 to 128,000
Think Harder	16,000	1,024 to 128,000
Ultrathink	32,000	1,024 to 128,000

Chat

Chat interface behavior.

Setting	Description	Default	Options
Default Display Mode	How messages are shown	Focus	Extended (full details), Compact (collapsed tools), Focus (minimal)
Expand Tool Calls	Auto-expand tool details in Extended mode	On	On, Off
Default Diff View	How file edits display	Unified	Split (side by side), Unified (inline)
Send Shortcut	How to send messages	Enter	Enter, Shift+Enter, Ctrl+Enter, Cmd+Enter
Preprocess @ Mentions	Resolve @file mentions before sending	On	On, Off
Preprocess / Commands	Execute slash commands via CLI	On	On, Off
Open Links Externally	Open links in system browser	Off	On, Off
Internal Browser User Agent	Custom user agent for internal browser	Default	Custom string or preset

See Chat Interface for full chat documentation.

Files

File tree behavior.

Setting	Description	Default	Options
Respect .gitignore	Hide gitignored files	On	On, Off
Exclude Patterns	Additional patterns to hide	node_modules, .git, .sciorex, .tickets	Custom patterns

Common patterns you can add: __pycache__, .cache, .DS_Store, vendor, target, .idea, .vscode, *.log, tmp, temp

Tickets

Ticket system configuration.

Setting	Description	Default	Options
Ticket Prefix	Prefix for ticket IDs	T	Up to 5 characters
Epic Prefix	Prefix for epic IDs	E	Up to 5 characters
Auto-increment Start	Starting number for IDs	1	Any number
Default Flow	Flow to run on tickets	None	Any flow ID

WARNING

Changing prefixes does not rename existing tickets. Only new tickets use the new prefix.

Worktrees

Git worktree support for parallel sessions.

Setting	Description	Default	Options
Enable Worktrees	Turn worktree support on/off	On	On, Off
Git Path	Path to Git executable	Auto-detect	Custom path
Directory Prefix	Prefix for worktree folders	wt-	Custom string

Worktrees are stored in .sciorex/worktrees/. See Understanding Worktrees for details.

Research Suite

Settings for the integrated research tools.

LaTeX

Setting	Description	Default	Options
Default Engine	LaTeX compilation engine	pdflatex	pdflatex, xelatex, lualatex
Auto-Compile	Compile on save	Off	On, Off
SyncTeX	Enable source-PDF synchronization	On	On, Off
Template Directory	Path to custom templates	.sciorex/templates	Custom path

PDF Viewer

Setting	Description	Default	Options
Default Tool	Annotation tool on open	Select	Select, Highlight, Note, Underline, Strikethrough
Highlight Color	Default highlight color	Yellow	Yellow, Green, Blue, Pink, Purple
Export Format	Default annotation export format	JSON	JSON, Markdown, CSV

Reference Library

Setting	Description	Default	Options
Default Citation Style	Citation format	APA 7th	APA 7th, MLA 9th, Chicago 17th, IEEE, Harvard, Vancouver, Nature, Science, Cell, ACM, ACS
Auto-Import	Import references from opened PDFs	On	On, Off
Duplicate Detection	Warn about duplicate entries	On	On, Off

Paper Discovery

Setting	Description	Default	Options
Default Sources	APIs to search	All enabled	Semantic Scholar, OpenAlex, CrossRef, arXiv, PubMed, DBLP
Max Results	Results per search	20	10, 20, 50, 100

Council Mode

Setting	Description	Default	Options
Default Rounds	Number of debate rounds	5	1-10
Summary Model	Model for synthesizing conclusions	Same as default	Any available model
Show Thinking	Show model reasoning in debates	On	On, Off

Secrets Vault

Setting	Description	Default	Options
Auto-Lock	Lock vault after inactivity	15 minutes	5, 15, 30 minutes, 1 hour, Never
Vault Location	Where encrypted secrets are stored	.sciorex/vault	Custom path

MCP Servers

Configure Model Context Protocol servers.

Built-in servers (always available):

• sciorex-tickets - Ticket and epic management
• sciorex-interactions - User prompts and notifications
• sciorex-resources - Agent and flow management
• sciorex-research - LaTeX, PDF, references, and discovery tools
• sciorex-secrets - Encrypted secrets vault
• sciorex-permissions - Permission management

Custom servers: Add your own MCP servers with:

• Server name
• Command (e.g., node, npx, python)
• Arguments

Notifications

Control when and how you're notified.

Setting	Description	Default
Sound Notifications	Play sound on events	On
Desktop Notifications	Show system notifications	On
Permission Requests	Notify when AI needs approval	On
Interaction Requests	Notify when AI asks questions	On
Chat Complete	Notify when response finishes	On

| Notify When App Active | Show notifications even when Sciorex is focused | On | On, Off |

TIP

By default, notifications trigger even when the application window is focused. Turn off Notify When App Active if you only want notifications when the app is in the background.

Updates

Setting	Description	Default
Auto Update	Check and download updates automatically	On

Advanced

Setting	Description
Prompt Template	Edit the workspace prompt template (.sciorex/prompt-template.md)

Keyboard Shortcuts

Quick reference for keyboard shortcuts:

Navigation

Shortcut	Action
Ctrl+1	Dashboard
Ctrl+2	Tickets
Ctrl+3	Flow Editor
Ctrl+4	Agents
Ctrl+5	Chat
Ctrl+6	Agent Runs
Ctrl+7	Flow Runs
Ctrl+8	Activity Feed
Ctrl+B	Toggle sidebar
Ctrl+,	Settings

Editor

Shortcut	Action
Ctrl+S	Save file
Ctrl+F	Find
Ctrl+H	Find and replace
Ctrl+G	Go to line
Ctrl+/	Toggle comment
Ctrl+D	Select next occurrence

Chat

Shortcut	Action
Tab	Cycle thinking levels
Shift+Tab	Cycle permission modes
Ctrl+F	Find in Chat
Escape	Close modals

Application

Shortcut	Action
Ctrl+N	New ticket
Ctrl+T	New chat
F11	Toggle fullscreen
Ctrl+Plus	Zoom in
Ctrl+Minus	Zoom out
Ctrl+0	Reset zoom

Configuration Files

Settings are stored in your workspace:

.sciorex/
├── config.json          # All settings
├── prompt-template.md   # Custom prompt template
└── worktrees/           # Worktree registry

You can edit these files directly, but using the Settings UI is recommended.