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My question is about what happens after tree harvest at 2 temporal scales:

- right after harvest: Forestry harvest work is messy, workers leave a lot of branches everywhere on the ground, machinery makes deep tracks in the soil, the tree stumps might remain in the plot. How to clean the plot and make it suitable for agriculture ? What to do with the stumps?

- on the longer term, where to replant ? (on the same tree lines? at the same location of the old trees?) When to replant? (before harvest, right after harvest, after some time?)

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Good question.   There is no need to replant most broadleaves, which will sprout from the stumps.  You will probably need single" these after 2-5 years. The species which sprout best include willow and poplar (of course) but also Alder (Alnus glutinosa), Ash (Fraxinus excelsior), Beech (Fagus sylvatica), Birch (Betula pendula), Hazel (Corylus avellana), Hornbeam (Carpinus betulus), Lime (Tilia europaea). Oak (Quercus robur), Sycamore (Acer pseudoplatanus).  Species which don't coppice well include Apple (Malus domestica), Cherry (Prunus avium), Field maple (Acer campestre), Horse chestnut (Aesculus hippocastanum), Pear (Pyrus communis), Service tree (Sorbus domestica),  and most conifers most conifers ...   Many of these will sprout from root cuttings however.  You can leave the use a tractor mounted stump grinder to tidy most agroforestry plantations, but it may not be worth the effort.
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Whilst the description of the land after harvesting a pure forestry plot that you give is accurate, the land will not be so covered in branches or tracks for a silvo-arable/pastoral system because the density of timber trees will be much lower in these scenarios and will also depend on whether the trees were planted in sequence. When the timber trees complete their rotation and reach their harvest point the farmer will need to decide if they want to continue having an agroforestry system in place in the same plot or move to a different plot and whether leaving the stumps on the ground will interfere with any future activities or not so much (for instance having stumps in a forestry grazing system does not represent any issues). Once the farmer has made their business decision, an expert in the subject can advice in the best course of action.
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