swap_sides isn't symmetrical for the encoder and the decoder. On the encoder,

it affects which logical side is being written to which physical side. On the
decoder, it modifies the logical side bit in the sector header itself.

arch/ibm/decoder.cc

@@ -148,7 +148,7 @@ public:
 			_sector->status = Sector::DATA_MISSING; /* correct but unintuitive */
 
 		if (_config.swap_sides())
-			_sector->logicalSide = 1 - _sector->logicalSide;
+			_sector->logicalSide ^= 1;
 		if (_config.ignore_side_byte())
 			_sector->logicalSide = _sector->physicalHead;
 	}

arch/ibm/encoder.cc

@@ -115,10 +115,11 @@ public:
 		IbmEncoderProto::TrackdataProto trackdata;
 		getTrackFormat(trackdata, physicalTrack, physicalSide);
 
+		int logicalSide = physicalSide ^ trackdata.swap_sides();
 		for (char sectorChar : trackdata.sector_skew())
         {
 			int sectorId = charToInt(sectorChar);
-			const auto& sector = image.get(physicalTrack, physicalSide, sectorId);
+			const auto& sector = image.get(physicalTrack, logicalSide, sectorId);
 			if (sector)
 				sectors.push_back(sector);
         }
@@ -147,8 +148,6 @@ public:
 				writeBytes(bytes);
 		};
 
-		if (trackdata.swap_sides())
-			physicalSide = 1 - physicalSide;
 		double clockRateUs = 1e3 / trackdata.clock_rate_khz();
 		if (!trackdata.use_fm())
 			clockRateUs /= 2.0;
@@ -184,6 +183,7 @@ public:
 			writeFillerBytes(trackdata.gap1(), gapFill);
 		}
 
+		int logicalSide = physicalSide ^ trackdata.swap_sides();
 		bool first = true;
 		for (char sectorChar : trackdata.sector_skew())
 		{
@@ -192,7 +192,7 @@ public:
 				writeFillerBytes(trackdata.gap3(), gapFill);
 			first = false;
 
-			const auto& sectorData = image.get(physicalTrack, physicalSide, sectorId);
+			const auto& sectorData = image.get(physicalTrack, logicalSide, sectorId);
 			if (!sectorData)
 			{
 				/* If there are any missing sectors, this is an empty track. */

arch/ibm/ibm.proto

@@ -6,7 +6,7 @@ message IbmDecoderProto {
 	optional int32 sector_id_base = 1        [default = 1, (help) = "ID of first sector"];
 	optional bool ignore_side_byte = 2       [default = false, (help) = "ignore side byte in sector header"];
 	optional RangeProto required_sectors = 3 [(help) = "require these sectors to exist for a good read"];
-	optional bool swap_sides = 4             [default = false, (help) = "swap side bytes when reading"];
+	optional bool swap_sides = 4             [default = false, (help) = "put logical side 1 on physical side 0"];
 }
 
 message IbmEncoderProto {

lib/decoders/decoders.cc

@@ -59,12 +59,12 @@ std::unique_ptr<AbstractDecoder> AbstractDecoder::create(const DecoderProto& con
 }
 
 std::unique_ptr<TrackDataFlux> AbstractDecoder::decodeToSectors(
-		std::shared_ptr<const Fluxmap> fluxmap, unsigned cylinder, unsigned head)
+		std::shared_ptr<const Fluxmap> fluxmap, unsigned physicalCylinder, unsigned physicalHead)
 {
 	_trackdata = std::make_unique<TrackDataFlux>();
 	_trackdata->fluxmap = fluxmap;
-	_trackdata->physicalCylinder = cylinder;
-	_trackdata->physicalHead = head;
+	_trackdata->physicalCylinder = physicalCylinder;
+	_trackdata->physicalHead = physicalHead;
 	
     FluxmapReader fmr(*fluxmap);
     _fmr = &fmr;
@@ -74,8 +74,8 @@ std::unique_ptr<TrackDataFlux> AbstractDecoder::decodeToSectors(
     {
 		_sector = std::make_shared<Sector>();
 		_sector->status = Sector::MISSING;
-		_sector->physicalCylinder = cylinder;
-		_sector->physicalHead = head;
+		_sector->physicalCylinder = physicalCylinder;
+		_sector->physicalHead = physicalHead;
 
         Fluxmap::Position recordStart = fmr.tell();
         RecordType r = advanceToNextRecord();

src/formats/atarist360.textpb

@@ -34,7 +34,7 @@ encoder {
 
 decoder {
 	ibm {
-		swap_sides: true
+		swap_sides: false
 	}
 }
 

src/formats/atarist370.textpb

@@ -34,7 +34,7 @@ encoder {
 
 decoder {
 	ibm {
-		swap_sides: true
+		swap_sides: false
 	}
 }
 

src/formats/atarist400.textpb

@@ -34,7 +34,7 @@ encoder {
 
 decoder {
 	ibm {
-		swap_sides: true
+		swap_sides: false
 	}
 }
 

src/formats/atarist410.textpb

@@ -34,7 +34,7 @@ encoder {
 
 decoder {
 	ibm {
-		swap_sides: true
+		swap_sides: false
 	}
 }
 

src/formats/atarist720.textpb

@@ -34,7 +34,7 @@ encoder {
 
 decoder {
 	ibm {
-		swap_sides: true
+		swap_sides: false
 	}
 }
 

src/formats/atarist740.textpb

@@ -34,7 +34,7 @@ encoder {
 
 decoder {
 	ibm {
-		swap_sides: true
+		swap_sides: false
 	}
 }
 

src/formats/atarist800.textpb

@@ -34,7 +34,7 @@ encoder {
 
 decoder {
 	ibm {
-		swap_sides: true
+		swap_sides: false
 	}
 }
 

src/formats/atarist820.textpb

@@ -34,7 +34,7 @@ encoder {
 
 decoder {
 	ibm {
-		swap_sides: true
+		swap_sides: false
 	}
 }
 

src/formats/commodore1581.textpb

@@ -34,12 +34,15 @@ encoder {
 			gap2: 22
 			gap3: 34
 			sector_skew: "0123456789"
+			swap_sides: true
 		}
 	}
 }
 
 decoder {
-	ibm {}
+	ibm {
+		swap_sides: false
+	}
 }
 
 cylinders {