When I try to scaffold existing MySQL DB using:

Scaffold-DbContext "server=server;user=user;password=pw;database=db" "Pomelo.EntityFrameworkCore.MySql" -OutputDir EF -f

I get the following error:

System.InvalidOperationException: The annotation 'MySql:IndexPrefixLength' cannot be added because an annotation with the same name already exists**.
   at Microsoft.EntityFrameworkCore.Infrastructure.Annotatable.AddAnnotation(String name, Annotation annotation)
   at Microsoft.EntityFrameworkCore.Infrastructure.Annotatable.AddAnnotation(String name, Object value)
   at Microsoft.EntityFrameworkCore.Infrastructure.Annotatable.Microsoft.EntityFrameworkCore.Metadata.IMutableAnnotatable.AddAnnotation(String name, Object value)
   at Microsoft.EntityFrameworkCore.MutableAnnotatableExtensions.AddAnnotations(IMutableAnnotatable annotatable, IEnumerable`1 annotations)
   at Microsoft.EntityFrameworkCore.Scaffolding.Internal.RelationalScaffoldingModelFactory.VisitIndex(EntityTypeBuilder builder, DatabaseIndex index)
   at Microsoft.EntityFrameworkCore.Scaffolding.Internal.RelationalScaffoldingModelFactory.VisitIndexes(EntityTypeBuilder builder, ICollection`1 indexes)
   at Microsoft.EntityFrameworkCore.Scaffolding.Internal.RelationalScaffoldingModelFactory.VisitTable(ModelBuilder modelBuilder, DatabaseTable table)
   at Microsoft.EntityFrameworkCore.Scaffolding.Internal.RelationalScaffoldingModelFactory.VisitTables(ModelBuilder modelBuilder, ICollection`1 tables)
   at Microsoft.EntityFrameworkCore.Scaffolding.Internal.RelationalScaffoldingModelFactory.VisitDatabaseModel(ModelBuilder modelBuilder, DatabaseModel databaseModel)
   at Microsoft.EntityFrameworkCore.Scaffolding.Internal.RelationalScaffoldingModelFactory.Create(DatabaseModel databaseModel, Boolean useDatabaseNames)
   at Microsoft.EntityFrameworkCore.Scaffolding.Internal.ReverseEngineerScaffolder.ScaffoldModel(String connectionString, DatabaseModelFactoryOptions databaseOptions, ModelReverseEngineerOptions modelOptions, ModelCodeGenerationOptions codeOptions)
   at Microsoft.EntityFrameworkCore.Design.Internal.DatabaseOperations.ScaffoldContext(String provider, String connectionString, String outputDir, String outputContextDir, String dbContextClassName, IEnumerable`1 schemas, IEnumerable`1 tables, Boolean useDataAnnotations, Boolean overwriteFiles, Boolean useDatabaseNames)
   at Microsoft.EntityFrameworkCore.Design.OperationExecutor.ScaffoldContextImpl(String provider, String connectionString, String outputDir, String outputDbContextDir, String dbContextClassName, IEnumerable`1 schemaFilters, IEnumerable`1 tableFilters, Boolean useDataAnnotations, Boolean overwriteFiles, Boolean useDatabaseNames)
   at Microsoft.EntityFrameworkCore.Design.OperationExecutor.ScaffoldContext.<>c__DisplayClass0_0.<.ctor>b__0()
   at Microsoft.EntityFrameworkCore.Design.OperationExecutor.OperationBase.<>c__DisplayClass3_0`1.<Execute>b__0()
   at Microsoft.EntityFrameworkCore.Design.OperationExecutor.OperationBase.Execute(Action action)
The annotation 'MySql:IndexPrefixLength' cannot be added because an annotation with the same name already exists.*

I have succeded with the scaffolding for the same DB in the same project using the Microsoft packages without any problems.

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The issue has been confirmed to be a bug by Pomelo team. This exception will happen if there are more than one index on one column and both of them uses index prefix. A fix will be released soon:

https://github.com/PomeloFoundation/Pomelo.EntityFrameworkCore.MySql/issues/1189