Fix missing contacts for deeply penetrating boxes.

When penetration exceeds a box's smallest half-size, the midpoint
between the contact surfaces can land outside both boxes. The outside-
box filter in mjc_BoxBox then removed every contact of the manifold,
returning nothing for a visibly overlapping pair, letting boxes fall
through each other. Fixes #1800.

If the filter would remove all contacts, restore the penetrating ones.
This is strictly additive: configurations where any contact survives
the filter are unchanged.

The removed midpoints are bitwise-identical to the witness midpoints
computed by mj_geomDistance for these configurations, so the positions
follow the engine-wide contact position convention; re-anchoring them
onto a box surface would not.

Fixes #1800

PiperOrigin-RevId: 957867315
Change-Id: Ia9c858661d4badeb2a832d25455e33402936011d

src/engine/engine_collision_box.c

@@ -1389,6 +1389,7 @@ int mjc_BoxBox(const mjModel* m, mjData* d, mjPreContact* con, int g1, int g2, m
   const mjtNum* size2 = m->geom_size + 3 * g2;
 
   // find bad: contacts outside one of the boxes
+  int nbad = 0;
   for (int i=0; i < num; i++) {
     // box sizes with margin
     mjtNum sz1[3] = {size1[0] + margin, size1[1] + margin, size1[2] + margin};
@@ -1404,6 +1405,18 @@ int mjc_BoxBox(const mjModel* m, mjData* d, mjPreContact* con, int g1, int g2, m
     // mark as bad if outside one box and not inside the other box
     if ((out1 == 1 && out2 != -1) || (out2 == 1 && out1 != -1)) {
       dupe[i] = -1;
+      nbad++;
+    }
+  }
+
+  // deep penetration can strand the midpoint-convention position outside both boxes; if
+  // that removed every contact, restore the penetrating ones: an empty manifold for
+  // overlapping boxes lets them pass through each other
+  if (nbad && nbad == num) {
+    for (int i=0; i < num; i++) {
+      if (tmp[i].dist < 0) {
+        dupe[i] = 0;
+      }
     }
   }