Instructions
Instructions are markdown documents that agents treat as a system prompt. They apply automatically to every session created in the org or by the user.How they layer
Three layers combine into the system prompt the agent sees:- Org instructions - rules that apply to every session in the organization. Set by admins. Useful for coding standards, security rules, or stack-wide conventions.
- User instructions - personal preferences set by each user. Useful for style preferences (“use 2-space indents”) or recurring context (“our team uses Vue, not React”).
- Template instructions - if the session was created from a template, the template’s default instructions apply too.
What to put in instructions
Good instructions tend to fall into these categories:- Coding standards - “Always use type hints in Python”, “Prefer composition over inheritance”
- Architecture rules - “Routes go in
api/, services inservices/”, “Use Pydantic models for validation” - Security constraints - “Never log API keys”, “Use parameterized queries”
- Stack constraints - “Use FastAPI not Flask”, “Frontend is Next.js with Tailwind”
- Protected files - “Never edit
runtm.yamldirectly” - Project context - “We are a fintech with strict audit requirements”
API endpoints
GET/PUT /api/instructions- personal user instructionsGET/PUT /api/organizations/{id}/instructions- org-wide instructions
Skills
Skills are reusable bundles that teach an agent how to do something. Each skill can include:- Entry markdown (
SKILL.md) - the main instruction document the agent reads - Reference files - code samples, schemas, examples, or configuration templates
- Required tooling - system packages installed in the sandbox at build time (via mise)
- Required integrations - knowledge sources the skill depends on
Creating skills
Skills are created from the dashboard’s Context > Skills tab, imported from a Git repository, or managed via the API:- Write a
SKILL.mdwith YAML frontmatter defining the name, description, and version - Optionally add reference files, tooling requirements, and integration dependencies
- Publish the skill so it is available to sessions
- Attach it to a template or individual sessions
Versioning
Each skill has exactly one live version. Editing it changes every template it is attached to on the next rebuild; lock a skill to prevent edits.Importing from Git
You can keep skill source files in a Git repository and pull them into Runtime:- Use Discover to scan a connected repo for directories that look like skills
- Use Import to pull in a skill from a specific path
- Use Resync to refresh the skill content when the repo changes
MCP servers
Model Context Protocol servers give agents additional tools beyond their built-in capabilities. MCP is a standard for connecting AI models to external data and actions. Each MCP server registration defines:How MCP servers are applied
MCP servers can be scoped to personal or team, and attached to all repos or specific ones. When a session boots:- All matching MCP server registrations are collected (personal + org)
- Each server is merged into the agent’s MCP configuration
- The agent sees the new tools in its tool catalog and can call them during prompts
Examples
MCP servers can also be declared inside skills. When a skill with MCP servers is attached to a session, the servers are configured automatically.
API endpoints
MCP servers are managed under the same system as skills. See the Skills API reference withtype=mcp_v0.
Docs
Reference docs are URLs the agent should treat as authoritative documentation. Each entry is a single URL with a display name and description. When applied to a session, reference docs appear as a managed block in the agent’s system prompt (e.g. inCLAUDE.md), giving the agent a curated list of documentation to consult when working on related tasks.
Use reference docs for:
- Framework documentation (e.g. FastAPI docs, Next.js docs)
- Internal API documentation
- Style guides and design systems
- Runbooks and playbooks
API endpoints
Docs are managed withtype=doc_v0. See the Skills API reference.
Knowledge sources
Knowledge sources are tool providers: the agent reaches a vendor (Notion, Confluence, a docs site, any API) through its CLI, SDK or API during the run, and the content stays in the source system. The credentials live on a connection, scoped to the agent by default. See Tools and connections for providers, connections and how to create one, and the Knowledge API reference for the endpoints.How sessions get context
When a session boots, all five layers are resolved and merged:- Org instructions are loaded
- User instructions are appended
- Template instructions (if applicable) are merged in
- Skills are mounted into the workspace, their tooling verified, and their MCP servers configured
- MCP servers (standalone registrations) are added to the agent’s tool catalog
- Reference docs are rendered into the agent’s system prompt
- Knowledge sources are made available as callable tools
Best practices
- Keep org instructions small and stable. They apply to every session; bloat slows everything down.
- Use skills for specialized workflows. If guidance only applies to a subset of work, make it a skill and attach it to the relevant repos.
- Use knowledge sources for content that changes. Anything that updates frequently (docs, runbooks) belongs in a knowledge source rather than in instructions.
- Personal context is for individuals. Anything the whole team needs should be at the org level.
- Pin skill versions in production. When stability matters, attach skills by version rather than floating to latest.
Related guides
Teach the agent your codebase
AGENTS.md, skills, and org instructions - how the three layers compose.
Best practices
Key hygiene, prompt design, and cost controls.