highlight_clade

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

With no annotations, the description carries the full burden. It does disclose a genuinely non-obvious destructive behavior — clear_existing wipes '[&!hilight=...]' comments already embedded in the tree text, not just pending annotations — which is exactly the kind of context an agent needs. It says nothing about how run_name/tree_file/tree_content interact, persistence, or side effects on other annotation state.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Is the description appropriately sized, front-loaded, and free of redundancy?

The core purpose is front-loaded in the first sentence and the Args block is efficiently ordered with the most complex parameter first. Minor verbosity in the clear_existing explanation, but every clause carries useful information.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

An output schema exists, so return values need no explanation. However, for a mutation tool with zero annotations and a stated destructive capability, the absence of any description of run_name/tree_file/tree_content and how the tool resolves its target tree leaves a real gap.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 0%, so the description must compensate. It gives rich detail for `highlights` (entry keys taxa/color/width/offset, plus the integer-offset constraint) and explains clear_existing, but leaves run_name, tree_file, and tree_content entirely undocumented — three of five parameters have no semantics anywhere.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Does the description clearly state what the tool does and how it differs from similar tools?

States a specific verb and resource ('Add FigTree hilight annotations (background bands) to one or more clades'), and naming 'background bands' disambiguates the visual effect. It does not, however, differentiate itself from close siblings like color_clade, clear_annotations, or style_tree, so an agent must still infer which annotation tool applies.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Does the description explain when to use this tool, when not to, or what alternatives exist?

There is conditional guidance embedded in clear_existing ('Clear existing highlights before applying'), which tells the agent when that flag is appropriate. But there is no explicit when-to-use-this-vs-color_clade/style_tree routing, and no prerequisites described, leaving usage largely implied.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.