Exception is thrown if trying to run mysql in med trust. Migrations arranged to execute schema migrations first and then data migrations. If a schema migration fails it will attempt to run the downgrade scripts of the migrations if running mysql since schema changes aren't supported in transactions. Updated all sql syntax providers to try to return only the column indexes, not key indexes. Updates the db version checker to include errors for all missing columns, indexes and constraints in the db and vice versa in the schema.

src/Umbraco.Core/Persistence/SqlSyntax/MySqlSyntaxProvider.cs

@@ -134,10 +134,11 @@ namespace Umbraco.Core.Persistence.SqlSyntax
                 db.OpenSharedConnection();
 
                 var indexes =
-                db.Fetch<dynamic>(@"SELECT DISTINCT
-    TABLE_NAME, INDEX_NAME, COLUMN_NAME, CASE NON_UNIQUE WHEN 1 THEN 0 ELSE 1 END AS `UNIQUE`
-FROM INFORMATION_SCHEMA.STATISTICS
+                db.Fetch<dynamic>(@"SELECT DISTINCT
+    TABLE_NAME, INDEX_NAME, COLUMN_NAME, CASE NON_UNIQUE WHEN 1 THEN 0 ELSE 1 END AS `UNIQUE`
+FROM INFORMATION_SCHEMA.STATISTICS
 WHERE TABLE_SCHEMA = @TableSchema
+AND INDEX_NAME <> COLUMN_NAME AND INDEX_NAME <> 'PRIMARY'
 ORDER BY TABLE_NAME, INDEX_NAME",
                     new { TableSchema = db.Connection.Database });
                 list =

src/Umbraco.Core/Persistence/SqlSyntax/SqlCeSyntaxProvider.cs

@@ -230,7 +230,9 @@ namespace Umbraco.Core.Persistence.SqlSyntax
         {
             var items =
                 db.Fetch<dynamic>(
-                    "SELECT TABLE_NAME, INDEX_NAME, COLUMN_NAME, [UNIQUE] FROM INFORMATION_SCHEMA.INDEXES ORDER BY TABLE_NAME, INDEX_NAME");
+                    @"SELECT TABLE_NAME, INDEX_NAME, COLUMN_NAME, [UNIQUE] FROM INFORMATION_SCHEMA.INDEXES 
+WHERE INDEX_NAME NOT LIKE 'PK_%'
+ORDER BY TABLE_NAME, INDEX_NAME");
             return
                 items.Select(
                     item => new Tuple<string, string, string, bool>(item.TABLE_NAME, item.INDEX_NAME, item.COLUMN_NAME, item.UNIQUE));

src/Umbraco.Core/Persistence/SqlSyntax/SqlServerSyntaxProvider.cs

@@ -160,6 +160,7 @@ CASE WHEN I.is_unique_constraint = 1 OR  I.is_unique = 1 THEN 1 ELSE 0 END AS [U
 from sys.tables as T inner join sys.indexes as I on T.[object_id] = I.[object_id] 
    inner join sys.index_columns as IC on IC.[object_id] = I.[object_id] and IC.[index_id] = I.[index_id] 
    inner join sys.all_columns as AC on IC.[object_id] = AC.[object_id] and IC.[column_id] = AC.[column_id] 
+WHERE I.name NOT LIKE 'PK_%'
 order by T.name, I.name");
             return items.Select(item => new Tuple<string, string, string, bool>(item.TABLE_NAME, item.INDEX_NAME, item.COLUMN_NAME, 
                 item.UNIQUE == 1)).ToList();