feat(workspace): add Maven multi-module workspace discovery (#443)

Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>

Author: Strum355

src/main/java/io/github/guacsec/trustifyda/impl/ExhortApi.java

@@ -30,6 +30,7 @@
 import io.github.guacsec.trustifyda.image.ImageUtils;
 import io.github.guacsec.trustifyda.license.LicenseCheck;
 import io.github.guacsec.trustifyda.logging.LoggersFactory;
+import io.github.guacsec.trustifyda.providers.JavaMavenProvider;
 import io.github.guacsec.trustifyda.providers.golang.model.GoWorkspace;
 import io.github.guacsec.trustifyda.providers.javascript.workspace.JsWorkspaceDiscovery;
 import io.github.guacsec.trustifyda.providers.rust.model.CargoMetadata;
@@ -843,7 +844,7 @@ int resolveBatchConcurrency() {
   }
 
   private static final Set<String> DEFAULT_WORKSPACE_DISCOVERY_IGNORE =
-      Set.of("**/node_modules/**", "**/.git/**");
+      Set.of("**/node_modules/**", "**/.git/**", "**/target/**");
 
   /** Merges default ignore patterns, env var overrides, and caller-provided patterns. */
   Set<String> resolveIgnorePatterns(Set<String> callerPatterns) {
@@ -865,7 +866,8 @@ Set<String> resolveIgnorePatterns(Set<String> callerPatterns) {
 
   /**
    * Detects the workspace ecosystem and discovers manifest paths. Checks for Cargo workspace first
-   * (Cargo.toml + Cargo.lock), then falls back to JS workspace discovery.
+   * (Cargo.toml + Cargo.lock), then Maven multi-module (pom.xml), then falls back to JS workspace
+   * discovery.
    */
   List<Path> discoverWorkspaceManifests(Path workspaceDir, Set<String> ignorePatterns)
       throws IOException {
@@ -884,6 +886,15 @@ List<Path> discoverWorkspaceManifests(Path workspaceDir, Set<String> ignorePatte
       }
     }
 
+    // Maven multi-module: pom.xml
+    Path pomXml = workspaceDir.resolve("pom.xml");
+    if (Files.isRegularFile(pomXml)) {
+      List<Path> mavenManifests = discoverMavenModules(workspaceDir, ignorePatterns);
+      if (!mavenManifests.isEmpty()) {
+        return mavenManifests;
+      }
+    }
+
     // JS workspace: require package.json + a lock file
     Path packageJson = workspaceDir.resolve("package.json");
     boolean hasJsLock =
@@ -976,6 +987,128 @@ private List<Path> discoverGoWorkspaceModules(Path workspaceDir, Set<String> ign
     }
   }
 
+  /**
+   * Discovers Maven multi-module workspace manifests by invoking {@code mvn help:evaluate} to list
+   * declared modules, then recursively checking each module for nested aggregators.
+   *
+   * <p>Uses {@link JavaMavenProvider#resolveVerifiedMavenBinary} for Maven binary resolution,
+   * including wrapper support. Always includes the root {@code pom.xml}. Uses a visited set to
+   * prevent cycles in the module graph.
+   *
+   * @param workspaceDir the root directory containing the aggregator pom.xml
+   * @param ignorePatterns glob patterns for paths to exclude from results
+   * @return list of discovered pom.xml paths; always includes the root pom.xml even if Maven is
+   *     unavailable
+   */
+  private List<Path> discoverMavenModules(Path workspaceDir, Set<String> ignorePatterns) {
+    Path rootPom = workspaceDir.resolve("pom.xml");
+    String mvnBin = JavaMavenProvider.resolveVerifiedMavenBinary(workspaceDir).orElse(null);
+    if (mvnBin == null) {
+      LOG.warning("Maven binary not available; returning root pom.xml only");
+      return List.of(rootPom);
+    }
+
+    var visited = new java.util.HashSet<Path>();
+    var manifestPaths = new ArrayList<Path>();
+    manifestPaths.add(rootPom);
+
+    collectMavenModules(workspaceDir, mvnBin, visited, manifestPaths);
+
+    return WorkspaceUtils.filterByIgnorePatterns(workspaceDir, manifestPaths, ignorePatterns);
+  }
+
+  /**
+   * Recursively collects Maven module pom.xml paths by invoking {@code mvn help:evaluate} on each
+   * directory and descending into sub-modules.
+   *
+   * @param dir the directory to evaluate for modules
+   * @param mvnBin the resolved Maven binary path
+   * @param visited set of already-visited directories to prevent cycles
+   * @param manifestPaths accumulator list for discovered pom.xml paths
+   */
+  private void collectMavenModules(
+      Path dir, String mvnBin, java.util.HashSet<Path> visited, List<Path> manifestPaths) {
+    Path resolvedDir = dir.toAbsolutePath().normalize();
+    if (!visited.add(resolvedDir)) {
+      return;
+    }
+
+    List<String> modules = listMavenModules(resolvedDir, mvnBin);
+    for (String mod : modules) {
+      Path moduleDir = resolvedDir.resolve(mod);
+      Path modulePom = moduleDir.resolve("pom.xml");
+      if (Files.isRegularFile(modulePom)) {
+        manifestPaths.add(modulePom);
+        collectMavenModules(moduleDir, mvnBin, visited, manifestPaths);
+      }
+    }
+  }
+
+  /**
+   * Invokes {@code mvn help:evaluate -Dexpression=project.modules} on the given directory and
+   * parses the output to extract module names.
+   *
+   * @param dir the directory containing a pom.xml to evaluate
+   * @param mvnBin the resolved Maven binary path
+   * @return list of module names, or empty list on failure
+   */
+  private List<String> listMavenModules(Path dir, String mvnBin) {
+    try {
+      Path pomFile = dir.resolve("pom.xml");
+      Operations.ProcessExecOutput output =
+          Operations.runProcessGetFullOutput(
+              dir,
+              new String[] {
+                mvnBin,
+                "help:evaluate",
+                "-Dexpression=project.modules",
+                "-q",
+                "-DforceStdout",
+                "-f",
+                pomFile.toString(),
+                "--batch-mode"
+              },
+              null);
+      if (output.getExitCode() != 0) {
+        LOG.warning(
+            "mvn help:evaluate failed with exit code " + output.getExitCode() + " in " + dir);
+        return Collections.emptyList();
+      }
+      String raw = output.getOutput().trim();
+      if (raw.isEmpty() || "null".equals(raw)) {
+        return Collections.emptyList();
+      }
+      return parseMavenModuleList(raw);
+    } catch (Exception e) {
+      LOG.warning("Failed to list Maven modules in " + dir + ": " + e.getMessage());
+      return Collections.emptyList();
+    }
+  }
+
+  /**
+   * Parses the output of {@code mvn help:evaluate -Dexpression=project.modules} which returns a
+   * string like {@code [module-a, module-b]}.
+   *
+   * @param raw the raw output string
+   * @return list of module name strings
+   */
+  static List<String> parseMavenModuleList(String raw) {
+    if (raw == null || raw.isEmpty()) {
+      return Collections.emptyList();
+    }
+    // Expected format: [module-a, module-b, ...]
+    java.util.regex.Matcher matcher =
+        java.util.regex.Pattern.compile("^\\[(.+)]$").matcher(raw.trim());
+    if (!matcher.matches()) {
+      return Collections.emptyList();
+    }
+    String inner = matcher.group(1);
+    return java.util.Arrays.stream(inner.split(","))
+        .map(String::trim)
+        .filter(s -> !s.isEmpty())
+        .toList();
+  }
+
   /**
    * Checks whether a package.json has "private": true, meaning it should not be analyzed as a
    * publishable package.

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

@@ -39,7 +39,7 @@
 import java.util.List;
 import java.util.Map;
 import java.util.Objects;
-import java.util.logging.Level;
+import java.util.Optional;
 import java.util.logging.Logger;
 import java.util.stream.Collectors;
 import javax.xml.stream.XMLInputFactory;
@@ -431,35 +431,45 @@ private List<String> buildMvnCommandArgs(String... baseArgs) {
   }
 
   private String selectMvnRuntime(final Path manifestPath) {
-    boolean preferWrapper = Operations.getWrapperPreference(MVN);
-    if (preferWrapper && manifestPath != null) {
-      String wrapperName = Operations.isWindows() ? "mvnw.cmd" : "mvnw";
-      String mvnw = traverseForMvnw(wrapperName, manifestPath.toString());
-      if (mvnw != null) {
-        try {
-          // verify maven wrapper is accessible
-          Operations.runProcess(manifestPath.getParent(), mvnw, ARG_VERSION);
-          if (debugLoggingIsNeeded()) {
-            log.info(String.format("using maven wrapper from : %s", mvnw));
-          }
-          return mvnw;
-        } catch (Exception e) {
-          log.log(
-              Level.WARNING,
-              "Failed to check for mvnw due to: {0} Fall back to use mvn",
-              e.getMessage());
+    Path dir = (manifestPath != null) ? manifestPath.getParent() : null;
+    if (dir != null) {
+      Optional<String> resolved = resolveVerifiedMavenBinary(dir);
+      if (resolved.isPresent()) {
+        if (debugLoggingIsNeeded()) {
+          log.info(String.format("using maven binary: %s", resolved.get()));
         }
+        return resolved.get();
       }
     }
-    // If maven wrapper is not requested or not accessible, fall back to use mvn
     String mvn = Operations.getExecutable(MVN, ARG_VERSION);
     if (debugLoggingIsNeeded()) {
       log.info(String.format("using mvn executable from : %s", mvn));
     }
     return mvn;
   }
 
-  private String traverseForMvnw(String wrapperName, String startingManifest) {
+  public static Optional<String> resolveVerifiedMavenBinary(Path workspaceDir) {
+    if (Operations.getWrapperPreference(MVN)) {
+      String wrapperName = Operations.isWindows() ? "mvnw.cmd" : "mvnw";
+      String mvnw = traverseForMvnw(wrapperName, workspaceDir.resolve("pom.xml").toString());
+      if (mvnw != null) {
+        try {
+          Operations.runProcess(workspaceDir, mvnw, ARG_VERSION);
+          return Optional.of(mvnw);
+        } catch (Exception e) {
+          // wrapper found but not functional — fall through to system mvn
+        }
+      }
+    }
+    try {
+      String mvn = Operations.getExecutable(MVN, ARG_VERSION);
+      return Optional.of(mvn);
+    } catch (RuntimeException e) {
+      return Optional.empty();
+    }
+  }
+
+  private static String traverseForMvnw(String wrapperName, String startingManifest) {
     return traverseForMvnw(wrapperName, startingManifest, null);
   }