tolerate and count patterns with no gtfs

these should be the ones created by other modification in the scenario.
also factor out long reference chain as final List variable.

Author: abyrd

Diff for: src/main/java/com/conveyal/r5/analyst/scenario/SelectLink.java

@@ -50,14 +50,17 @@ public class SelectLink extends Modification {
 
     private int nPatternsWithoutShapes = 0;
 
+    private int nPatternsWithoutGtfs = 0;
+
     @Override
     public boolean resolve(TransportNetwork network) {
         // Convert the incoming description of the selected link area to a Geometry for computing intersections.
         boxPolygon = polygonForEnvelope(envelopeForCircle(lon, lat, radiusMeters));
         // Iterate over all TripPatterns in the TransitLayer and ensure that we can associate a feed with each one.
         // These feeds must have been previously supplied with the injectGtfs() method. The feed IDs recorded in the
         // TripPatterns are not bundle-scoped. Check that a feed with a correctly de-scoped ID was supplied for every
-        // TripPattern in this TransitLayer.
+        // TripPattern in this TransitLayer. Note that this only applies to patterns in the base network - other
+        // modifications in the scenario such as add-trips can create new patterns that don't reference any GTFS.
         for (TripPattern tripPattern : network.transitLayer.tripPatterns) {
             String feedId = feedIdForTripPattern(tripPattern);
             if (isNullOrEmpty(feedId)) {
@@ -80,15 +83,23 @@ public boolean apply(TransportNetwork network) {
 
         // During raptor search, paths are recorded in terms of pattern and stop index numbers rather than
         // TripPattern and Stop instance references, so iterate over the numbers.
-        for (int patternIndex = 0; patternIndex < network.transitLayer.tripPatterns.size(); patternIndex++) {
-            TripPattern tripPattern = network.transitLayer.tripPatterns.get(patternIndex);
+        final List<TripPattern> patterns = network.transitLayer.tripPatterns;
+        for (int patternIndex = 0; patternIndex < patterns.size(); patternIndex++) {
+            TripPattern tripPattern = patterns.get(patternIndex);
             // Make a sacrificial protective copy to avoid interfering with other requests using this network.
             // We're going to add shape data to this TripPattern then throw it away immediately afterward.
             // Be careful not to use a reference to this clone as a key in any Maps, it will not match TransitLayer.
             tripPattern = tripPattern.clone();
             String feedId = feedIdForTripPattern(tripPattern);
             GTFSFeed feed = feedForUnscopedId.get(feedId);
-            TransitLayer.addShapeToTripPattern(feed, tripPattern);
+            if (feed == null) {
+                // We could not find any feed ID on this pattern, or the apparent feed ID does not match any known feed.
+                // Since feeds for all patterns were all verified in apply(), this means the pattern must have been
+                // added by another modification in the scenario.
+                nPatternsWithoutGtfs += 1;
+            } else {
+                TransitLayer.addShapeToTripPattern(feed, tripPattern);
+            }
             if (tripPattern.shape == null) {
                 nPatternsWithoutShapes += 1;
             }
@@ -105,9 +116,14 @@ public boolean apply(TransportNetwork network) {
                 hopsInTripPattern.put(patternIndex, intersectedHops.toArray());
             }
         }
+        if (nPatternsWithoutGtfs > 0) {
+            addInfo("Of %d patterns, %d did not reference any GTFS (apparently generated by scenario).".formatted(
+                patterns.size(), nPatternsWithoutGtfs
+            ));
+        }
         if (nPatternsWithoutShapes > 0) {
-            addInfo( "Out of %d patterns, %d had no shapes and used straight lines.".formatted(
-                    network.transitLayer.tripPatterns.size(), nPatternsWithoutShapes
+            addInfo("Of %d patterns, %d had no shapes and used straight lines.".formatted(
+                patterns.size(), nPatternsWithoutShapes
             ));
         }
         // After finding all links (TripPattern hops) in the SelectedLink area, release the GTFSFeeds which don't really