clear_annotations

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

No annotations are provided, so the description carries the burden and does well: it discloses the timing of removal (before the tree is loaded/exported) and a non-obvious edge case (Nexus root markers [&R]/[&U] are preserved so rooting is unchanged). It doesn't cover permissions or what the result looks like, but the side-effect disclosure is genuinely beyond structured data.

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 action and scope are front-loaded in the first sentence, followed by a compact Args block that pairs each documented parameter with its meaning and default. Slightly prose-heavy in the second sentence but no wasted sentences.

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 not be described, and the description covers scope, side effects, and the annotative semantics of its flags. The only real gap is the unexplained input-source parameters, which prevents this from being fully self-contained.

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 documents three of six parameters well, including defaults and the subtle strip_annotations behavior, but run_name, tree_file, and tree_content are left completely unexplained, leaving half the surface undocumented in either place.

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 ('Clear') plus a well-defined resource ('highlight and collapse annotations, including embedded ones'), and explicitly carves out what is NOT handled (colors/fonts, routing to color_clade / set_clade_font). An agent can distinguish this from highlight_clade, collapse_clade, and color_clade without opening any schema.

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?

Clear context on when the tool applies: it removes both pending annotations and embedded '[&!hilight=...]'/'[&!collapse=...]' comments before the tree is loaded/exported, and it names sibling alternatives for the excluded color/font concerns. It stops short of explicitly stating when to prefer this over siblings like highlight_clade or collapse_clade as a cleanup step, so not a full 5.

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