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

Annotations already declare readOnlyHint=true, destructiveHint=false and openWorldHint=false, so safety and scope are covered structurally. The description adds the semantic trait that the alignment is ordered and step-by-step over procedures, which is genuinely useful context. It does not say what happens when no common procedure exists or how partial matches are reported, though the presence of an output schema reduces the burden.

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?

A single front-loaded sentence with the verb and scope first and the motivating question second. Nothing is redundant and nothing is padded.

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?

Annotations and a full output schema are present, and the schema documents all parameters, so much is already covered. Still, for a five-parameter tool with nested `_subject` and `_files` objects, the description never clarifies the two-sided setup (this side via `document`, other side via `against`) or which side defaults. That leaves a moderate gap for a fairly complex call.

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 coverage is 100% and the `key` parameter already carries a rich explanation of the abstract-vs-processId distinction, so the schema does the heavy lifting. The description contributes only the notion of a procedure being compared, without clarifying how `document` and `against` relate to the two sides or how `key` changes the result. Baseline 3 is appropriate.

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: aligning two constructs' build procedures step by step, in order. The parenthetical question ("was this built the same way as that?") pins down the intent as construction-history comparison rather than sequence comparison, which separates it from compare_molecules or align_sequences. It does not explicitly name a sibling it is not, so it stops short of a 5.

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?

Usage is implied through the question "was this built the same way as that?" — an agent can infer this is the tool for checking whether two constructs followed the same assembly path. However, no when-not conditions or alternatives are given: get_construction_history and verify_construct are obvious cousins that are never referenced, leaving the agent to infer which one to reach for.

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