Prefer the Reactome tool that needs no installation

src/retrievers/userguide/prompt.py

@@ -15,6 +15,9 @@
    - Use a clear display name (page title or section title).
    - If multiple excerpts support the same fact, cite them together (space-separated).
 3. How-to focus: Give clear, actionable steps when the user asks how to perform a task. Name UI elements accurately (buttons, panels, tabs) as they appear in the context.
+   - When several Reactome tools can do the same job, **lead with the one that needs the least setup** — a web tool on reactome.org before a desktop application, a plugin, or an R package. Mention the others afterwards as alternatives.
+   - Concretely: gene set analysis is **ReactomeGSA** (web, at reactome.org/gsa, nothing to install). ReactomeFIViz also performs GSEA, but it is a Cytoscape plugin and requires installing Cytoscape first, so it is the alternative rather than the answer.
+   - Do not pick a tool because its page happens to contain the most step-by-step text. The most detailed instructions are often for the most involved tool, which is rarely what someone asking "can you run this for me" wants.
 4. Tone and style:
    - Write in a clear, friendly, and conversational tone.
    - Use accessible language; avoid unnecessary jargon.

tests/agent/test_safety_scope.py

@@ -56,3 +56,25 @@ def test_capability_is_answered_downstream_not_refused_here() -> None:
     """Whether the assistant can run an analysis is a different question from
     whether it is allowed to be asked."""
     assert "decided later" in safety_check_message
+
+
+def test_the_user_guide_prefers_the_tool_that_needs_no_install() -> None:
+    """Asked "can you run gsea for me", beta answered with ReactomeFIViz --
+    the Cytoscape plugin -- rather than ReactomeGSA, the web tool.
+
+    Not a retrieval failure: the top four passages were the ReactomeGSA page.
+    The FIViz page arrived fifth (the rephrase expands "gsea" to "Gene Set
+    Enrichment Analysis", and that page has a "Perform GSEA Analysis" menu
+    item), and the model led with it because the prompt asks for actionable
+    steps and FIViz has the most step-by-step text.
+
+    The most detailed instructions are usually for the most involved tool,
+    which is rarely what someone asking "can you run this for me" wants.
+    """
+    from retrievers.userguide.prompt import userguide_system_prompt
+
+    assert "least setup" in userguide_system_prompt
+    assert "ReactomeGSA" in userguide_system_prompt
+    assert "Cytoscape" in userguide_system_prompt
+    # The trap that caused it, named so a later edit does not reintroduce it.
+    assert "most step-by-step text" in userguide_system_prompt