I need to merge two shapefiles and the issue is that one shapefile has WGS 84 coordinate system and the second OSGB 1936.
When I try to do the trick with MMQGIS -> Combine -> Merge layers I get an output shapefile but the two layers do not match at all.
Answer
You need to re-project one of your layer (right click then "save as" then select the coordinate system...) before merging. Choose witch one to re-project depending on your final output (for exemple if you want your merge layer to be on OSGB1936 re-project the shapefile on WGS84 to OSGB1936)
MMQGIS didn't re-project layer, you should do it yourself before merging. in QGIS 3.0 you could use the merge layer tool from the processing panel, this tool do the reprojecting for you and work
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