Use Season Folder is set in config (also set per Series), default is true.

NzbDrone.Core/Providers/RenameProvider.cs

@@ -45,7 +45,11 @@ namespace NzbDrone.Core.Providers
                 var series = _seriesProvider.GetSeries(episodeFile.SeriesId);
                 var erm = new EpisodeRenameModel();
                 erm.SeriesName = series.Title;
-                erm.Folder = series.Path + Path.DirectorySeparatorChar + GetSeasonFolder(episodeFile.Episodes[0].SeasonNumber);
+                erm.Folder = series.Path;
+
+                if (series.SeasonFolder)
+                    erm.Folder += Path.DirectorySeparatorChar + GetSeasonFolder(episodeFile.Episodes[0].SeasonNumber);
+
                 erm.EpisodeFile = episodeFile;
                 _epsToRename.Add(erm);
                 StartRename();
@@ -62,7 +66,12 @@ namespace NzbDrone.Core.Providers
             {
                 var erm = new EpisodeRenameModel();
                 erm.SeriesName = series.Title;
-                erm.Folder = series.Path + Path.DirectorySeparatorChar + GetSeasonFolder(episodeFile.Episodes[0].SeasonNumber);
+
+                erm.Folder = series.Path;
+
+                if (series.SeasonFolder)
+                    erm.Folder += Path.DirectorySeparatorChar + GetSeasonFolder(episodeFile.Episodes[0].SeasonNumber);
+
                 erm.EpisodeFile = episodeFile;
                 _epsToRename.Add(erm);
                 StartRename();
@@ -79,7 +88,12 @@ namespace NzbDrone.Core.Providers
             {
                 var erm = new EpisodeRenameModel();
                 erm.SeriesName = series.Title;
-                erm.Folder = series.Path + Path.DirectorySeparatorChar + GetSeasonFolder(episodeFile.Episodes[0].SeasonNumber);
+
+                erm.Folder = series.Path;
+
+                if (series.SeasonFolder)
+                    erm.Folder += Path.DirectorySeparatorChar + GetSeasonFolder(episodeFile.Episodes[0].SeasonNumber);
+
                 erm.EpisodeFile = episodeFile;
                 _epsToRename.Add(erm);
                 StartRename();
@@ -96,7 +110,12 @@ namespace NzbDrone.Core.Providers
 
             var erm = new EpisodeRenameModel();
             erm.SeriesName = series.Title;
-            erm.Folder = series.Path + Path.DirectorySeparatorChar + GetSeasonFolder(episodeFile.Episodes[0].SeasonNumber);
+
+            erm.Folder = series.Path;
+
+            if (series.SeasonFolder)
+                erm.Folder += Path.DirectorySeparatorChar + GetSeasonFolder(episodeFile.Episodes[0].SeasonNumber);
+
             erm.EpisodeFile = episodeFile;
             _epsToRename.Add(erm);
             StartRename();

NzbDrone.Core/Providers/SeriesProvider.cs

@@ -111,6 +111,11 @@ namespace NzbDrone.Core.Providers
             repoSeries.CleanTitle = Parser.NormalizeTitle(series.SeriesName);
             repoSeries.Monitored = true; //New shows should be monitored
             repoSeries.QualityProfileId = Convert.ToInt32(_config.GetValue("DefaultQualityProfile", "1", true));
+            repoSeries.SeasonFolder = true;
+
+            if (!Convert.ToBoolean(_config.GetValue("SeasonFolder", true, true)))
+                repoSeries.SeasonFolder = false;
+
             _sonioRepo.Add(repoSeries);
         }
 

NzbDrone.Core/Repository/Series.cs

@@ -32,6 +32,8 @@ namespace NzbDrone.Core.Repository
 
         public int QualityProfileId { get; set; }
 
+        public bool SeasonFolder { get; set; }
+
         [SubSonicToOneRelation(ThisClassContainsJoinKey = true)]
         public virtual QualityProfile QualityProfile { get; private set; }