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fix(core): auto-exclude git and .garden dirs for modules in project root
Because we require an `include` or `exclude` to be set on modules if there are multiple modules in the same directory, this would only have come up as an issue if there's a single module in the project root _or_ if users had used `exclude` fields and not `include` fields to specify the module context. Which is likely why this passed by for so long, but certainly this change is the more sane default behavior.
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