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How to fix overlaps and gaps
When checking vector layers, the QC tool might detect a large number of millimeter shifts between adjacent polygons or vertices that the ArcGIS "Find Overlaps" might miss. The QC tool will report gaps and overlaps (with area smaller than tolerance) as exceptions because we need information about potential issues in the data.
To ensure faster QC tool check execution and accurate identification of neighbours (e.g complex changes or marginal polygons) we strongly recommend removing the microscopic overlaps / gaps before checking the delivery by QC tool.
There is a quick, automated way to fix the gaps/overlaps in minutes using QGIS:
Search for the tool "Snap geometries to layer".
Input layer: Select your CLC layer (for each problematic layer with gaps and overlaps).
Reference layer: Select the same CLC layer (same problematic layer).
Tolerance: Set to 0.002 (2mm, assuming your data is in meters).
Run.

Replace old layers by newly updated layers and include them to the zip delivery.