Harden Java adapter identities and SootUp coverage

docs/flpath-5002-java-adapter.md

@@ -58,9 +58,10 @@ policy, controller, runtime validation, or durable repository-profile wiring.
 ## Manual VPE integration
 
 The VPE `AnalysisContext` JSON handoff is loaded by
-`AnalysisContextLoader`. The manual command preserves source/build/provenance
-fingerprints and emits normalized facts with separate provider and framework
-sets:
+`AnalysisContextLoader`. The manual command preserves the selected profile,
+production/test scope, generated-root declarations, source/build/provenance
+fingerprints, and handoff limitations. It emits normalized facts with separate
+provider and framework sets:
 
 ```sh
 spike/scripts/run-manual-integration.sh

src/main/java/com/projectlightpath/analysis/java/AnalysisContext.java

@@ -57,7 +57,19 @@ public record SourceRoot(
       Scope scope,
       boolean generated,
       boolean included,
-      boolean required) {
+      boolean required,
+      String fingerprint) {
+    /** Compatibility constructor for callers that do not provide a root fingerprint. */
+    public SourceRoot(
+        String declaredPath,
+        Path path,
+        Scope scope,
+        boolean generated,
+        boolean included,
+        boolean required) {
+      this(declaredPath, path, scope, generated, included, required, null);
+    }
+
     /** Validates and normalizes one source root declaration. */
     public SourceRoot {
       if (declaredPath == null || declaredPath.isBlank()) {
@@ -70,12 +82,27 @@ public record SourceRoot(
 
     /** Creates an included application source root. */
     public static SourceRoot source(String declaredPath, Path path, Scope scope, boolean required) {
-      return new SourceRoot(declaredPath, path, scope, false, true, required);
+      return source(declaredPath, path, scope, required, null);
+    }
+
+    public static SourceRoot source(
+        String declaredPath, Path path, Scope scope, boolean required, String fingerprint) {
+      return new SourceRoot(declaredPath, path, scope, false, true, required, fingerprint);
     }
 
     public static SourceRoot generated(
         String declaredPath, Path path, Scope scope, boolean included, boolean required) {
-      return new SourceRoot(declaredPath, path, scope, true, included, required);
+      return generated(declaredPath, path, scope, included, required, null);
+    }
+
+    public static SourceRoot generated(
+        String declaredPath,
+        Path path,
+        Scope scope,
+        boolean included,
+        boolean required,
+        String fingerprint) {
+      return new SourceRoot(declaredPath, path, scope, true, included, required, fingerprint);
     }
   }
 
@@ -616,14 +643,32 @@ public Builder analysisScope(Scope value) {
 
     /** Adds an included application source root. */
     public Builder sourceRoot(String declaredPath, Path path, Scope scope, boolean required) {
-      sourceRoots.add(SourceRoot.source(declaredPath, path, scope, required));
+      return sourceRoot(declaredPath, path, scope, required, null);
+    }
+
+    /** Adds an included application source root with its handoff fingerprint. */
+    public Builder sourceRoot(
+        String declaredPath, Path path, Scope scope, boolean required, String fingerprint) {
+      sourceRoots.add(SourceRoot.source(declaredPath, path, scope, required, fingerprint));
       return this;
     }
 
     /** Adds an included or excluded generated source root. */
     public Builder generatedSourceRoot(
         String declaredPath, Path path, Scope scope, boolean included, boolean required) {
-      generatedSourceRoots.add(SourceRoot.generated(declaredPath, path, scope, included, required));
+      return generatedSourceRoot(declaredPath, path, scope, included, required, null);
+    }
+
+    /** Adds an included or excluded generated source root with its handoff fingerprint. */
+    public Builder generatedSourceRoot(
+        String declaredPath,
+        Path path,
+        Scope scope,
+        boolean included,
+        boolean required,
+        String fingerprint) {
+      generatedSourceRoots.add(
+          SourceRoot.generated(declaredPath, path, scope, included, required, fingerprint));
       return this;
     }
 

src/main/java/com/projectlightpath/analysis/java/AnalysisContextLoader.java

@@ -195,12 +195,13 @@ private static void addRoot(
     AnalysisContext.Scope scope = parseScope(root.scope());
     boolean generated = generatedCollection || root.generated();
     if (generated) {
-      builder.generatedSourceRoot(declaredPath, resolved, scope, root.included(), root.required());
+      builder.generatedSourceRoot(
+          declaredPath, resolved, scope, root.included(), root.required(), root.fingerprint());
     } else {
       if (root.required() && !root.included()) {
         throw new IllegalArgumentException("required source root must be included: " + declaredPath);
       }
-      builder.sourceRoot(declaredPath, resolved, scope, root.required());
+      builder.sourceRoot(declaredPath, resolved, scope, root.required(), root.fingerprint());
     }
   }