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Query jobs use the user flag of the job to control whether password prompts are shown. This allows synchronization jobs to run in the background and fail without disrupting workflows. All other jobs such as task submissions respect the user flag in the same manner.
Related reviews: https://git.eclipse.org/r/#/c/11624/ https://git.eclipse.org/r/#/c/11475/
Created attachment 229356 [details] mylyn/context/zip
Pushed another change to set the user flag for the task submission job by default and make the same change for the get history, task deletion and update repository configuration jobs: https://git.eclipse.org/r/#/c/11667/.
The change was merged. Thanks for your contirbutions, Tomasz!