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Run store diagnostics

run_doctor
Read-only

Diagnose 3Notch stores for integrity issues like missing directories, broken symlinks, or exposed secrets before trusting them. Optionally repair derived state when writable.

Instructions

Run when 3Notch behaves oddly or before trusting a store: checks required directories, .notch/.gitignore coverage of the private, index, and log paths, symlinks, invalid or duplicate records, secrets inside records, audit-log corruption, and Claude Code continuation hook drift. Read-only apart from fixDerivedState, which is refused when the server runs in read-only mode.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
strictNoWhen true, escalate warnings — missing .notch/.gitignore entries and Claude Code hook drift — to errors. Default false.
fixDerivedStateNoWhen true, create missing store directories, add the required .notch/.gitignore entries, and rebuild the derived index. The only mutating option here; refused when the server runs in read-only mode. Default false.
Behavior4/5

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

Annotations already flag the tool as read-only and non-destructive. The description adds important nuance: it is read-only except for fixDerivedState, which is refused when the server is read-only. This supplements the annotation with actionable safety context without contradicting it.

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

Conciseness5/5

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

The description is two sentences, front-loaded with the trigger condition, and enumerates checks efficiently. The second sentence clarifies the only mutating option. No wasted words; every phrase carries information.

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

Completeness3/5

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

The description thoroughly covers triggers and the scope of diagnostics, but there is no output schema and the description does not mention return values, exit codes, or how to interpret results. For a diagnostic tool, this leaves a significant gap in what the agent should expect after invocation.

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

Parameters3/5

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

Both parameters (strict and fixDerivedState) are fully described in the schema with details on behavior and defaults. The description adds no additional parameter-level meaning beyond what's already in the schema, so it doesn't compensate beyond the baseline.

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

Purpose5/5

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

The description clearly states the tool runs store diagnostics and enumerates exact checks: directories, .gitignore coverage, symlinks, records, secrets, audit logs, and hook drift. It also gives a specific trigger ('when 3Notch behaves oddly or before trusting a store'), making its purpose explicit and effectively distinguishing it from likely sibling operations.

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

Usage Guidelines4/5

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

It explicitly says when to use the tool and provides context for the mutating fixDerivedState option, noting it's refused in read-only mode. It doesn't mention alternative tools like check_store or exclusions, but the trigger condition is clear enough for correct selection.

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

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