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Refactor 'helix-loader::merge_toml_values' to use a 'merge-depth' ins…
…tead of 'merge_toplevel_arrays' (#3080) - This ensures that other values than just the arrays are overridden, like nested objects, where it makes sense - merge_depth is set to 3 so that top-level language features are merged (like 'scope'), but everything deeper is overridden with the user-config
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