Don't prune inner layers of through-hole parts.

For historical reasons we've always included ALL inner layers in these
items and changing that has uncovered several latent bugs.  Rather
than find all the rest this late in the game, I went back to storing
all inner layers, even those the board doesn't currently have.

Fixes https://gitlab.com/kicad/code/kicad/issues/12863

pcbnew/dialogs/panel_setup_layers.cpp

@@ -31,6 +31,9 @@
 #include <pcb_edit_frame.h>
 #include <board.h>
 #include <collectors.h>
+#include <footprint.h>
+#include <pad.h>
+#include <pcb_track.h>
 #include <panel_setup_layers.h>
 #include <board_stackup_manager/panel_board_stackup.h>
 
@@ -523,12 +526,31 @@ bool PANEL_SETUP_LAYERS::TransferDataFromWindow()
 
         LSET changedLayers = m_enabledLayers ^ previousEnabled;
 
-        /* Ensure enabled layers are also visible
+        /*
-         * This is mainly to avoid mistakes if some enabled
+         * Ensure enabled layers are also visible.  This is mainly to avoid mistakes if some
-         * layers are not visible when exiting this dialog
+         * enabled layers are not visible when exiting this dialog.
          */
         m_pcb->SetVisibleLayers( m_pcb->GetVisibleLayers() | changedLayers );
 
+        /*
+         * Ensure items with through holes have all inner copper layers.  (For historical reasons
+         * this is NOT trimmed to the currently-enabled inner layers.)
+         */
+        for( FOOTPRINT* fp : m_pcb->Footprints() )
+        {
+            for( PAD* pad : fp->Pads() )
+            {
+                if( pad->HasHole() && pad->IsOnCopperLayer() )
+                    pad->SetLayerSet( pad->GetLayerSet() | LSET::InternalCuMask() );
+            }
+        }
+
+        for( PCB_TRACK* via : m_pcb->Tracks() )
+        {
+            if( via->HasHole() )
+                via->SetLayerSet( via->GetLayerSet() | LSET::InternalCuMask() );
+        }
+
         modified = true;
     }
 

pcbnew/tools/pcb_control.cpp

@@ -731,6 +731,10 @@ void PCB_CONTROL::pruneItemLayers( std::vector<BOARD_ITEM*>& aItems )
 
                 if( allowed.any() )
                 {
+                    // Don't prune internal copper layers on items with holes
+                    if( aItem->HasHole() && aItem->IsOnCopperLayer() )
+                        allowed |= LSET::InternalCuMask();
+
                     aItem->SetLayerSet( allowed );
                 }
                 else