Customizing Atlas's Behavior

Atlas is designed to be customized. Several files in your vault control how it behaves — from its communication style and personality to which tools it’s allowed to use. All of these files are plain Markdown, so editing them is as simple as opening a file in a text editor.

Behavioral Rules

Path: atlas/rules/rules.md

This file contains the rules that guide how Atlas behaves in conversations. The default rules set sensible baselines — asking before making major changes, being honest about uncertainty, and so on. You can add your own rules to fine-tune the behavior.

Examples of useful custom rules:

- Always ask before creating or modifying a note
- When I ask for a summary, keep it to 3 bullet points or fewer
- Never suggest external tools — only work with what's in my vault
- If I ask about a project, check my Projects folder first before answering
- Use British English spelling

Be specific. Vague rules like “be careful” don’t have much effect. Rules like “always ask for confirmation before deleting anything” work well because they’re concrete.

Tool Guidance

Path: atlas/rules/tools.md

This file gives Atlas guidance on how to use its tools. You can use it to tell Atlas when to prefer certain tools or how to approach specific situations.

For example, you might add:

- When creating notes, always use the daily note for quick captures unless I specify otherwise
- Prefer search_notes over memory_search for finding information in my vault
- When adding tasks, put them in the ## Tasks section of today's daily note

Most users don’t need to edit this file often, but it’s useful if you have a specific workflow you want Atlas to follow consistently.

Disabling Tools

Path: atlas/rules/allowed-tools.md

This file uses an opt-out model — all tools are enabled by default. To disable a tool, comment it out with a # at the start of the line.

# Tools are enabled by default. Comment out any tool you want to disable.

search_notes
create_note
read_note
# delete_file      ← this tool is now disabled
# get_weather      ← disabled if you don't want weather lookups
remember_fact
memory_search
...

When a tool is disabled, Atlas won’t use it at all — it won’t even see the tool in its available tool list.

Personality and Style

Path: atlas/identity/persona.md

The persona file is the most powerful customization option. It defines who Atlas is — not just how it behaves, but its voice, tone, and approach.

To change Atlas’s communication style, edit this file directly. Some ideas:

Make it more concise: “Keep responses short. Use bullet points. Avoid long paragraphs.”
Change the tone: “Be casual and conversational. Use plain language, not formal prose.”
Add expertise: “You are deeply knowledgeable about software architecture and system design.”
Set a focus: “Prioritize helping me with writing and editing above all else.”

Changes to persona.md take effect on your next message.

Custom Instructions in Settings

In Settings > AI, there’s a Custom Instructions field. Anything you put there is included in every conversation as an additional instruction block.

This is the right place for short, always-on instructions that don’t fit naturally in any of the rule files — for example:

“Always end responses with a suggested next action.”
“I’m a software engineer. Assume technical knowledge.”
“My timezone is Pacific Time. Use that for dates and times.”

Custom instructions from Settings are easier to access and change than editing vault files, so use them for things you might want to adjust frequently.

Tips for Effective Customization

Be specific over general — “always ask before creating notes” is more effective than “be careful”
Edit persona.md for style changes — communication style, tone, verbosity, expertise
Edit rules.md for behavioral changes — what Atlas should or shouldn’t do
Edit allowed-tools.md for tool access — disable anything you don’t want Atlas to touch
Use Settings > Custom Instructions for quick, always-on additions — no file editing needed
Test your changes — send a message after editing and see how Atlas responds