DataFlow: Add code to do overlay informed dataflow.

java/ql/lib/semmle/code/java/dataflow/internal/DataFlowImplSpecific.qll

@@ -6,6 +6,7 @@ module;
 
 private import semmle.code.Location
 private import codeql.dataflow.DataFlow
+private import semmle.code.java.Overlay
 
 module Private {
   import DataFlowPrivate
@@ -29,4 +30,6 @@ module JavaDataFlow implements InputSig<Location> {
   predicate mayBenefitFromCallContext = Private::mayBenefitFromCallContext/1;
 
   predicate viableImplInCallContext = Private::viableImplInCallContext/2;
+
+  predicate isEvaluatingInOverlay = isOverlay/0;
 }

shared/dataflow/codeql/dataflow/DataFlow.qll

@@ -349,6 +349,18 @@ signature module InputSig<LocationSig Location> {
 
   /** Holds if `fieldFlowBranchLimit` should be ignored for flow going into/out of `c`. */
   default predicate ignoreFieldFlowBranchLimit(DataFlowCallable c) { none() }
+
+  /**
+   * Holds if the evaluator is currently evaluating with an overlay. The
+   * implementation of this predicate needs to be `overlay[local]`. For a
+   * language with no overlay support, `none()` is a valid implementation.
+   *
+   * When called from a local predicate, this predicate holds if we are in the
+   * overlay-only local evaluation. When called from a global predicate, this
+   * predicate holds if we are evaluating globally with overlay and base both
+   * visible.
+   */
+  default predicate isEvaluatingInOverlay() { none() }
 }
 
 module Configs<LocationSig Location, InputSig<Location> Lang> {
@@ -1101,6 +1113,8 @@ module DataFlowMake<LocationSig Location, InputSig<Location> Lang> {
       predicate isAdditionalFlowStep(Node node1, Node node2, string model) {
         Config::isAdditionalFlowStep(node1, node2) and model = "Config"
       }
+
+      predicate observeOverlayInformedIncrementalMode() { none() }
     }
 
     private module Stage1 = ImplStage1<C>;
@@ -1130,6 +1144,8 @@ module DataFlowMake<LocationSig Location, InputSig<Location> Lang> {
       ) {
         Config::isAdditionalFlowStep(node1, state1, node2, state2) and model = "Config"
       }
+
+      predicate observeOverlayInformedIncrementalMode() { none() }
     }
 
     private module Stage1 = ImplStage1<C>;

shared/dataflow/codeql/dataflow/TaintTracking.qll

@@ -167,6 +167,8 @@ module TaintFlowMake<
       ) {
         Config::isAdditionalFlowStep(node1, node2) and model = "Config"
       }
+
+      predicate observeOverlayInformedIncrementalMode() { none() }
     }
 
     private module C implements DataFlowInternal::FullStateConfigSig {
@@ -201,6 +203,8 @@ module TaintFlowMake<
       ) {
         Config::isAdditionalFlowStep(node1, state1, node2, state2) and model = "Config"
       }
+
+      predicate observeOverlayInformedIncrementalMode() { none() }
     }
 
     private module C implements DataFlowInternal::FullStateConfigSig {
@@ -232,6 +236,8 @@ module TaintFlowMake<
       ) {
         Config::isAdditionalFlowStep(node1, node2) and model = "Config"
       }
+
+      predicate observeOverlayInformedIncrementalMode() { none() }
     }
 
     private module C implements DataFlowInternal::FullStateConfigSig {
@@ -270,6 +276,8 @@ module TaintFlowMake<
       ) {
         Config::isAdditionalFlowStep(node1, state1, node2, state2) and model = "Config"
       }
+
+      predicate observeOverlayInformedIncrementalMode() { none() }
     }
 
     private module C implements DataFlowInternal::FullStateConfigSig {

shared/dataflow/codeql/dataflow/internal/DataFlowImpl.qll

@@ -143,6 +143,14 @@ module MakeImpl<LocationSig Location, InputSig<Location> Lang> {
      */
     predicate observeDiffInformedIncrementalMode();
 
+    /**
+     * Holds if sources and sinks should be filtered to only include those that
+     * are in the overlay database. This only has an effect when running
+     * in overlay-informed incremental mode. This should be used in conjunction
+     * with the `OverlayImpl` implementation to merge the base results back in.
+     */
+    predicate observeOverlayInformedIncrementalMode();
+
     Location getASelectedSourceLocation(Node source);
 
     Location getASelectedSinkLocation(Node sink);

shared/dataflow/codeql/dataflow/internal/DataFlowImplStage1.qll

@@ -4,7 +4,7 @@
  * Provides an implementation of a fast initial pruning of global
  * (interprocedural) data flow reachability (Stage 1).
  */
-overlay[local?]
+overlay[local?] // when this is removed, put `overlay[local?]` on `isOverlayNode`.
 module;
 
 private import codeql.util.Unit
@@ -129,23 +129,75 @@ module MakeImplStage1<LocationSig Location, InputSig<Location> Lang> {
 
       private module AlertFiltering = AlertFilteringImpl<Location>;
 
+      /**
+       * Holds if the given node is visible in overlay-only local evaluation.
+       *
+       * This predicate needs to be `overlay[local?]`, either directly or
+       * through annotations from an outer scope. If `Node` is global for the
+       * language under analysis, then every node is considered an overlay
+       * node, which means there will effectively be no overlay-based
+       * filtering of sources and sinks.
+       */
+      private predicate isOverlayNode(Node node) {
+        isEvaluatingInOverlay() and
+        // Any local node is an overlay node if we are evaluating in overlay mode
+        exists(node)
+      }
+
+      /**
+       * The filtering if we aren't meant to be diff-informed.
+       *
+       * Shared between sources and sinks.
+       */
+      pragma[inline]
+      private predicate nonDiffInformedFilter(Node node) {
+        // If we are in base-only global evaluation, do not filter out any sources.
+        not isEvaluatingInOverlay()
+        or
+        // If the configuration doesn't merge overlays, do not filter out any sources.
+        not Config::observeOverlayInformedIncrementalMode()
+        or
+        // If we are in global evaluation with an overlay present, restrict
+        // sources to those visible in the overlay.
+        isOverlayNode(node)
+      }
+
+      overlay[global]
       pragma[nomagic]
       private predicate isFilteredSource(Node source) {
         Config::isSource(source, _) and
+        // Data flow is always incremental in one of two ways.
+        // 1. If the configuration is diff-informed, we filter to only include nodes in the diff,
+        //    which gives the smallest set of nodes.
+        //    If diff information is not available, we do not filter at all.
+        // 2. If not, in global evaluation with overlay, we filter to only
+        //    include nodes from files in the overlay; flow from
+        //    other nodes will be added back later.
+        // We start by seeing if we should be in case 1.
         if Config::observeDiffInformedIncrementalMode()
-        then AlertFiltering::filterByLocation(Config::getASelectedSourceLocation(source))
-        else any()
+        then
+          // Case 1: We are meant to be diff-informed.
+          // We still only filter if we have diff information.
+          AlertFiltering::diffInformationAvailable()
+          implies
+          AlertFiltering::locationIsInDiff(Config::getASelectedSourceLocation(source))
+        else nonDiffInformedFilter(source)
       }
 
+      overlay[global]
       pragma[nomagic]
       private predicate isFilteredSink(Node sink) {
         (
           Config::isSink(sink, _) or
           Config::isSink(sink)
         ) and
+        // See the comments in `isFilteredSource` for the reasoning behind the following.
         if Config::observeDiffInformedIncrementalMode()
-        then AlertFiltering::filterByLocation(Config::getASelectedSinkLocation(sink))
-        else any()
+        then
+          AlertFiltering::diffInformationAvailable()
+          implies
+          AlertFiltering::locationIsInDiff(Config::getASelectedSinkLocation(sink))
+        else nonDiffInformedFilter(sink)
       }
 
       private predicate hasFilteredSource() { isFilteredSource(_) }