Navigate the repository

Start with README.md for the purpose and setup, AGENTS.md for working conventions, and REPO_MAP.md for the main commands and files. Once you understand the task, use a focused search to find the code and tests you need.

rg --files src tests docs
rg -n 'mismatch_threshold' src tests docs/reference

The package has separate files for reading inputs, cleaning data, writing reports, and organizing runs. For example, a search for mismatch_threshold shows where the CLI accepts the value, where cleaning uses it, and which tests check it. Following that path helps you see the effect of a change before editing.

Read the relevant tests alongside the data contract. The tests show what is checked; the contract explains what should happen. If they disagree, discuss the intended behavior with your collaborator and update the appropriate code, test, or explanation.

When you move a main command or file, update REPO_MAP.md so the next person can find it.