Answer: Based on your description I am not fully certain what is affecting your plantings. There are some soil-carried wilt diseases, but the wilting could also simply be due to poor drainage since it is in a damper low area. Some plants will be more susceptible than others to different problems. And, it could be that the disease (if it is a disease) is being transferred on your tools. Or, perhaps there is something in the manure or bedding that is causing the problem. (There are some herbicides that could be residue in the straw, for example.) So it is really important to figure that out before you try to treat for it.
Clear plastic or solarizing is sometimes used to treat certain weeds and possibly to control fungal problems such as verticillium wilt, however it also damages the soil life so it is not something to do if you can avoid it. I would strongly suggest you work with your local county extension to identify the specific problem and then based on knowing that, determine how to proceed. I'm sorry you are having trouble with your garden.
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