fix(core): Remove useless entries from Stage.context (spinnaker#3359)

Fixes spinnaker/spinnaker#5257

The `Stage` constructor was keeping `refId`, `startTimeExpiry` and `requisiteStageRefIds` from the context map argument in its internal context map. This caused issues when a parent stage's context was used to create a child stage, as these entries aren't expected to be inherited. This wasn't a problem for a long time because these values were accidentally removed by the side effect of `StartStageHandler#shouldSkip`. `shouldSkip()` uses `objectMapper.convertValue()` on a stage context expecting to have a cloned map returned. A long standing design/documentation issue with Jackson made `convertValue()` return the input parameter as is instead of converting/cloning it. This made every `Stage` passing through `StartStageHandler.handle()` having their context map indirectly 'corrected' and persisted.
An upcoming upgrade to Spring Boot 2.2 comes with Jackson 2.10 where `objectMapper.convertValue()` has a new behaviour and would make `shouldSkip()` fail to silently 'correct' the stages context map.
FasterXML/jackson-databind#2220

`BakeStageSpec` was validating `context['refId']` on the generated contexts but the contexts aren't Stages yet; once a context is made into a Stage and added to the graph (`graph.add`) it will have its `refId` generated based on the parent refId; which isn't under test in that spec.

Co-authored-by: mergify[bot] <37929162+mergify[bot]@users.noreply.github.com>

orca-bakery/src/test/groovy/com/netflix/spinnaker/orca/bakery/pipeline/BakeStageSpec.groovy

@@ -218,7 +218,7 @@ class BakeStageSpec extends Specification {
   private
   static List<Map> expectedContexts(String cloudProvider, String amiSuffix, String... regions) {
     return regions.collect {
-      [cloudProviderType: cloudProvider, amiSuffix: amiSuffix, type: BakeStage.PIPELINE_CONFIG_TYPE, "region": it, name: "Bake in ${it}", refId: "1"]
+      [cloudProviderType: cloudProvider, amiSuffix: amiSuffix, type: BakeStage.PIPELINE_CONFIG_TYPE, "region": it, name: "Bake in ${it}"]
     }
   }
 }

orca-core/src/main/java/com/netflix/spinnaker/orca/pipeline/model/Stage.java

@@ -104,7 +104,6 @@ public Stage(Execution execution, String type, String name, Map<String, Object>
     this.execution = execution;
     this.type = type;
     this.name = name;
-    this.context.putAll(context);
 
     this.refId = (String) context.remove("refId");
     this.startTimeExpiry =
@@ -114,6 +113,8 @@ public Stage(Execution execution, String type, String name, Map<String, Object>
     this.requisiteStageRefIds =
         Optional.ofNullable((Collection<String>) context.remove("requisiteStageRefIds"))
             .orElse(emptySet());
+
+    this.context.putAll(context);
   }
 
   public Stage(Execution execution, String type, Map<String, Object> context) {