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We have a repository of manual tests and about half of them have been automated using Selenium. If the test case has already been automated and then the manual test case is updated is there a flag displayed that the automated test case needs to be updated also?
No I'm afraid not.
For Selenium you're only probably storing a link to the Selenium file, so Spira would not know the Selenium file has been changed or not changed.
If you store the Selenium files in Spira or Git (linked to Spira) you could in theory have a custom report than compares the last updated date of the two.