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Use .jina/instruction.md for durable preferences across planning, investigation, and grading. For example:
.jina/instruction.md

Generate your instruction with a coding agent

Copy this prompt into your coding agent at the repository root. It inspects the project, interviews you about your preferences, and proposes .jina/instruction.md for your approval.
Prompt for your coding agent

Set the default investigation depth

Use .jina/config.json to set the maximum investigation rounds:
.jina/config.json
Allowed values are 1–5. Depth follows this order: an explicit /depth command → base-commit configuration → default 2. Use the Prompt Guide for run-specific guidance. Prose in instruction.md does not set depth, and run/skip directives do not bypass Simulations stages.

Know when preferences take effect

Jina reads both files from the PR’s base commit. Changes take effect after they are merged and become the base of a later review. See Grading for scoring preferences.