update-domain

Update Domain Knowledge

Incrementally update your SciAgent domain configuration. Use this after the initial /configure-domain setup to add new packages, refine workflows, or extend template content without starting from scratch.

When to Use

• You want to add a new package to your domain configuration.
• Your analysis workflows have changed and need updating.
• You discovered a new tool or library relevant to your research.
• You want to refine value ranges, parameters, or guardrails.
• You have new example data that reveals additional file formats or column patterns.

Procedure

Step 1 — Understand the Change

Ask the user what they want to update. Common scenarios:

• "Add package X" — Discover, document, and integrate a new package into the template files.
• "Update workflows" — Modify or add workflow steps in workflows.md.
• "Change parameters" — Update analysis parameters, value ranges, or precision tables in operations.md.
• "Add a custom skill" — Create a new skill entry in skills.md.
• "Full refresh" — Re-audit all templates and fill any remaining placeholders (suggest /configure-domain instead if most content is missing).

Step 2 — Audit Current State

Scan the relevant template files to understand what's already configured:

1. Search for files matching *.instructions.md, operations.md, workflows.md, tools.md, library_api.md, skills.md.
2. Identify which sections have domain content links vs. unfilled <!replace ... ---> markers (or legacy <!-- REPLACE: ... --> placeholders).
3. Check docs/domain/ for existing domain knowledge files from a previous /configure-domain run.
4. Note any domain-specific content that might conflict with the proposed changes.
5. Brief the user: "Here's your current configuration in the affected files. I'll update X and Y."

Step 3 — Discover (If Adding Packages)

If the user wants to add new packages:

1. Fetch PyPI metadata: https://pypi.org/pypi/{name}/json
2. If available, fetch the GitHub README for capabilities overview.
3. Present the package info and ask for confirmation.
4. If the user doesn't know the exact package name, use broader searches based on their description.

Step 4 — Propose Edits

Before making changes, show the user exactly what will be modified:

• Which files will be edited
• What content will be added or changed
• Whether any existing content will be affected

Ask for confirmation before proceeding.

Step 5 — Apply Updates

Use editFiles to make the confirmed changes. Domain content should live in docs/domain/ files, not inlined into the template files:

• Adding a package: Update docs/domain/library-api.md with API reference, docs/domain/tools.md with tool documentation, and docs/domain/operations.md if the package introduces new analysis parameters or workflows. If the template marker doesn't yet have a link below it, add one.
• Updating workflows: Edit the relevant section in docs/domain/workflows.md (or docs/domain/operations.md for the standard workflows section).
• Changing parameters: Edit the parameters section in docs/domain/operations.md.
• Adding skills: Add a new skill section to docs/domain/skills.md and optionally create a SKILL.md file in .github/skills/.

If docs/domain/ doesn't exist yet (e.g. the user ran an older version of /configure-domain), create the directory and the appropriate domain knowledge file.

Step 6 — Verify

1. Confirm the edit was applied correctly by reading the modified file.
2. Summarize what was changed.
3. Note any follow-up actions (e.g. "You may want to run /docs-ingestor on the new package for a deeper API reference").

Re-Run Safety

• Preserve existing content — Only modify the specific sections relevant to the update. Do not touch unrelated template content.
• Ask before overwriting — If the target section already has different domain content, ask the user whether to replace, merge, or skip.
• Append by default — When adding new items (packages, workflows, skills), append to existing lists rather than replacing them.

What This Skill Does NOT Do

• Does not execute Python code or run analysis
• Does not install packages (suggest pip install commands instead)
• Does not require sciagent[wizard]
• Does not replace the full /configure-domain flow for first-time setup — if most template content is missing, suggest running /configure-domain first

Domain Customization