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ISSUE-97: Time out management and better entity listing handling #101

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See #97

@alliomeria users can still choose to use CRON via the queue manager settings if needed
Hydroponics is more reliable and cron really should only kick off hydroponics not run anything ... but... removing this right now is an UI/UX expectation breaking thing.
Also now finally i am not skipping people's choices on queues anymore. If you decide all to go background, all goes to background
Better/more reliable and hierarchical order.
`@TODO:` sort per branch of the tree
Better checks too and also allows $input_argument != "sequence_number" (for now input_argument = "annotation" but basically anything that is not a number for things that are not consecutive.
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