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We have recently added support to provide collection options either as an command line arguments or options in the collection file. But that is only working on the site interface, and the collection cli still expect the `output-folder` as required option. This commit changes that, so it's not required anymore and it will try to read the option from the file, and if none of those source has this value, then it will use the source as output directory, and to keep this file separated it will use the `source/output` Fixes #283
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