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Why cant the tools be made on Java so that they run everywhere? They dont need to be pretty just run.

Agreed, .jar is an underrated deployment mechanism.

Or, you know, make the darned thing a web app.

It is a web app. Runs a local webserver & talks to a browser.

OK, a .WAR file then!

HMRC will never launch a web app for this, as they don't want to be a custodian for company payroll data.