fix: java stack analysis doesn't ignore deps inherited version

src/main/java/io/github/guacsec/trustifyda/providers/JavaMavenProvider.java

@@ -75,24 +75,32 @@ public Content provideStack() throws IOException {
     // create a temp file for storing the dependency tree in
     var tmpFile = Files.createTempFile("TRUSTIFY_DA_dot_graph_", null);
     // the tree command will build the project and create the dependency tree in the temp file
-    var mvnTreeCmd =
-        buildMvnCommandArgs(
-            "org.apache.maven.plugins:maven-dependency-plugin:3.6.0:tree",
-            "-Dverbose",
-            "-DoutputType=text",
-            String.format("-DoutputFile=%s", tmpFile.toString()),
-            "-f",
-            manifest.toString(),
-            "--batch-mode",
-            "-q");
+    var mvnTreeCmdArgs =
+        new ArrayList<>(
+            List.of(
+                "org.apache.maven.plugins:maven-dependency-plugin:3.6.0:tree",
+                "-Dscope=compile",
+                "-Dverbose",
+                "-DoutputType=text",
+                String.format("-DoutputFile=%s", tmpFile.toString()),
+                "-f",
+                manifest.toString(),
+                "--batch-mode",
+                "-q"));
     // if we have dependencies marked as ignored, exclude them from the tree command
     var ignored =
         getDependencies(manifest).stream()
             .filter(d -> d.ignored)
-            .map(DependencyAggregator::toPurl)
+            .map(DependencyAggregator::toPurlWithoutVersion)
             .map(PackageURL::getCoordinates)
             .collect(Collectors.toList());
+
+    if (!ignored.isEmpty()) {
+      mvnTreeCmdArgs.add("-Dexcludes=" + String.join(",", ignored));
+    }
+
     // execute the tree command
+    var mvnTreeCmd = buildMvnCommandArgs(mvnTreeCmdArgs.toArray(String[]::new));
     Operations.runProcess(manifest.getParent(), mvnTreeCmd.toArray(String[]::new), mvnEnvs);
     if (debugLoggingIsNeeded()) {
       String stackAnalysisDependencyTree = Files.readString(tmpFile);
@@ -110,6 +118,7 @@ public Content provideStack() throws IOException {
 
   private Sbom buildSbomFromTextFormat(Path textFormatFile) throws IOException {
     var sbom = SbomFactory.newInstance(Sbom.BelongingCondition.PURL, "sensitive");
+    sbom.setCoordinateBasedMatching();
     List<String> lines = Files.readAllLines(textFormatFile);
     var root = lines.get(0);
     var rootPurl = parseDep(root);
@@ -408,6 +417,15 @@ public PackageURL toPurl() {
       }
     }
 
+    /** Creates a PackageURL without version for coordinate-based matching. */
+    public PackageURL toPurlWithoutVersion() {
+      try {
+        return new PackageURL(Type.MAVEN.getType(), groupId, artifactId, null, null, null);
+      } catch (MalformedPackageURLException e) {
+        throw new IllegalArgumentException("Unable to parse PackageURL", e);
+      }
+    }
+
     @Override
     public boolean equals(Object o) {
       if (this == o) return true;

src/main/java/io/github/guacsec/trustifyda/sbom/CycloneDXSbom.java

@@ -95,6 +95,31 @@ private BiPredicate<Collection<?>, Component> getBelongingConditionByPurl() {
         collection.contains(componentToPurl(component).getCoordinates());
   }
 
+  /**
+   * Creates a coordinate-based belonging condition that matches by groupId:artifactId only,
+   * ignoring version. Used for handling dependencies with unresolved version properties.
+   */
+  private BiPredicate<Collection<?>, Component> getBelongingConditionByCoordinatesOnly() {
+    return (collection, component) -> {
+      PackageURL componentPurl = componentToPurl(component);
+      String componentCoords = componentPurl.getNamespace() + ":" + componentPurl.getName();
+
+      return collection.stream()
+          .filter(String.class::isInstance)
+          .map(String.class::cast)
+          .anyMatch(
+              ignoredPurlCoords -> {
+                try {
+                  PackageURL ignoredPurl = new PackageURL(ignoredPurlCoords);
+                  String ignoredCoords = ignoredPurl.getNamespace() + ":" + ignoredPurl.getName();
+                  return componentCoords.equals(ignoredCoords);
+                } catch (MalformedPackageURLException e) {
+                  return false;
+                }
+              });
+    };
+  }
+
   public Sbom addRoot(PackageURL rootRef) {
     this.root = rootRef;
     Component rootComponent = newRootComponent(rootRef);
@@ -280,6 +305,11 @@ public void setBelongingCriteriaBinaryAlgorithm(BelongingCondition belongingCond
     }
   }
 
+  @Override
+  public void setCoordinateBasedMatching() {
+    belongingCriteriaBinaryAlgorithm = getBelongingConditionByCoordinatesOnly();
+  }
+
   @Override
   public boolean checkIfPackageInsideDependsOnList(PackageURL component, String name) {
     boolean result = false;

src/main/java/io/github/guacsec/trustifyda/sbom/Sbom.java

@@ -33,6 +33,8 @@ public interface Sbom {
 
   public void setBelongingCriteriaBinaryAlgorithm(BelongingCondition belongingCondition);
 
+  public void setCoordinateBasedMatching();
+
   public boolean checkIfPackageInsideDependsOnList(PackageURL component, String name);
 
   void removeRootComponent();