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My suggestion is to extract InterruptedException from org.jenkinsci.plugins.gitclient.CliGitAPIImpl.launchCommandIn(ArgumentListBuilder, File, EnvVars, Integer) method call and peform cleanup (removing index.lock file) in org.jenkinsci.plugins.gitclient.CliGitAPIImpl.checkout().new CheckoutCommand() {...}.execute() method.
I suggest to add new Exception - GitInterruptedException, which should indicate, that git operation is interrupted and reuse its information to remove lock file.
What's your opinion?