Set the real output location for embedded jars in ApiAnalysis

Currently when one configures embedded extra jars these are not found by
the ApiAnalysis because they are placed in different location than the
main classes.

THis computes all jars and compares there resulting path with the
current output location updating those if needed.

tycho-apitools-plugin/src/main/java/org/eclipse/tycho/apitools/ApiAnalysis.java

@@ -16,12 +16,18 @@
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.Serializable;
+import java.nio.file.FileVisitResult;
 import java.nio.file.Files;
 import java.nio.file.Path;
+import java.nio.file.SimpleFileVisitor;
+import java.nio.file.StandardCopyOption;
+import java.nio.file.attribute.BasicFileAttributes;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
 import java.util.Objects;
 import java.util.Properties;
 import java.util.concurrent.Callable;
@@ -63,6 +69,11 @@
 import org.eclipse.pde.api.tools.internal.provisional.model.IApiBaseline;
 import org.eclipse.pde.api.tools.internal.provisional.model.IApiComponent;
 import org.eclipse.pde.api.tools.internal.provisional.problems.IApiProblem;
+import org.eclipse.pde.core.build.IBuild;
+import org.eclipse.pde.core.build.IBuildEntry;
+import org.eclipse.pde.core.build.IBuildModel;
+import org.eclipse.pde.core.plugin.IPluginModelBase;
+import org.eclipse.pde.core.plugin.PluginRegistry;
 import org.eclipse.pde.core.target.ITargetDefinition;
 import org.eclipse.pde.core.target.ITargetLocation;
 import org.eclipse.pde.core.target.ITargetPlatformService;
@@ -74,6 +85,9 @@
 import org.osgi.framework.Bundle;
 import org.osgi.framework.FrameworkUtil;
 
+/**
+ * Performs the API Analysis inside the embedded OSGi Frameworks
+ */
 public class ApiAnalysis implements Serializable, Callable<ApiAnalysisResult> {
 
 	private Collection<String> baselineBundles;
@@ -86,7 +100,7 @@ public class ApiAnalysis implements Serializable, Callable<ApiAnalysisResult> {
 	private String binaryArtifact;
 	private String outputDir;
 
-	public ApiAnalysis(Collection<Path> baselineBundles, Collection<Path> dependencyBundles, String baselineName,
+	ApiAnalysis(Collection<Path> baselineBundles, Collection<Path> dependencyBundles, String baselineName,
 			Path apiFilterFile, Path apiPreferences, Path projectDir, boolean debug, Path binaryArtifact,
 			Path outputDir) {
 		this.targetBundles = dependencyBundles.stream().map(ApiAnalysis::pathAsString).toList();
@@ -222,32 +236,126 @@ private BundleComponent importProject() throws CoreException, IOException {
 	}
 
 	private void createOutputFolder(IProject project, IPath projectPath) throws IOException, CoreException {
+		Map<String, String> outputJars = computeOutputJars(project);
 		IJavaProject javaProject = JavaCore.create(project);
 		if (javaProject != null) {
-			IPath fullPath = project.getFolder(outputDir).getFullPath();
+			IFolder outputFolder = project.getFolder(outputDir);
 			// FIXME see bug https://github.com/eclipse-pde/eclipse.pde/issues/801
 			// it can happen that project output location != maven compiled classes, usually
 			// eclipse uses output = bin/ while maven uses target/classes if not
 			// specifically configured to be even
-			javaProject.setOutputLocation(fullPath, null);
-			makeOutputFolder(javaProject.getOutputLocation(), projectPath);
+			IPath mainOutputLocation = javaProject.getOutputLocation();
+			IPath mainRealPath = getRealPath(mainOutputLocation, outputJars, outputFolder);
+			makeOutputFolder(mainOutputLocation, mainRealPath);
 			IClasspathEntry[] classpath = javaProject.getRawClasspath();
 			for (IClasspathEntry entry : classpath) {
-				// FIXME see bug https://github.com/eclipse-pde/eclipse.pde/issues/791
-				makeOutputFolder(entry.getOutputLocation(), projectPath);
+				IPath entryOutputLocation = entry.getOutputLocation();
+				if (entryOutputLocation != null) {
+					IPath realEntryPath = getRealPath(entryOutputLocation, outputJars, outputFolder);
+					makeOutputFolder(entryOutputLocation, realEntryPath);
+				}
+			}
+		}
+	}
+
+	private Map<String, String> computeOutputJars(IProject project) throws CoreException {
+		Map<String, String> outputJars = new HashMap<String, String>();
+		IPluginModelBase base = PluginRegistry.findModel(project);
+		if (base != null) {
+			IBuildModel model = PluginRegistry.createBuildModel(base);
+			if (model != null) {
+				IBuild ibuild = model.getBuild();
+				IBuildEntry[] entries = ibuild.getBuildEntries();
+				for (IBuildEntry entry : entries) {
+					String name = entry.getName();
+					if (name.startsWith(IBuildEntry.OUTPUT_PREFIX)) {
+						String key = name.substring(IBuildEntry.OUTPUT_PREFIX.length());
+						for (String token : entry.getTokens()) {
+							outputJars.put(token, key);
+						}
+					}
+				}
+			}
+		}
+		return outputJars;
+	}
+
+	private IPath getRealPath(IPath eclipseOutputLocation, Map<String, String> outputJars, IFolder mavenOutputFolder) {
+		if (eclipseOutputLocation == null) {
+			return null;
+		}
+		IFolder projectFolder = getProjectFolder(eclipseOutputLocation);
+		for (Entry<String, String> entry : outputJars.entrySet()) {
+			IFolder jarFolder = projectFolder.getProject().getFolder(entry.getKey());
+			if (jarFolder.equals(projectFolder)) {
+				String jarOutputPath = entry.getValue();
+				if (".".equals(jarOutputPath)) {
+					return mavenOutputFolder.getFullPath();
+				}
+				return mavenOutputFolder.getParent()
+						.getFolder(new org.eclipse.core.runtime.Path(jarOutputPath + "-classes")).getFullPath();
 			}
 		}
+		return eclipseOutputLocation;
 	}
 
-	private void makeOutputFolder(IPath outputLocation, IPath projectPath) throws CoreException, IOException {
-		if (outputLocation != null) {
+	private IFolder makeOutputFolder(IPath eclipseOutputLocation, IPath mavenOutputLocation)
+			throws CoreException, IOException {
+		if (eclipseOutputLocation != null) {
 			IWorkspace workspace = ResourcesPlugin.getWorkspace();
-			IFolder folder = workspace.getRoot().getFolder(outputLocation);
+			IFolder folder = workspace.getRoot().getFolder(eclipseOutputLocation);
 			if (!folder.exists()) {
 				folder.create(true, true, new NullProgressMonitor());
 			}
+			if (mavenOutputLocation != null && !eclipseOutputLocation.equals(mavenOutputLocation)) {
+				copy(getFile(mavenOutputLocation), getFile(eclipseOutputLocation));
+			}
+			folder.refreshLocal(IResource.DEPTH_INFINITE, new NullProgressMonitor());
+			return folder;
 		}
+		return null;
+	}
 
+	private File getFile(IPath path) {
+		if (path == null) {
+			return null;
+		}
+		IWorkspace workspace = ResourcesPlugin.getWorkspace();
+		IPath location = workspace.getRoot().getFolder(path).getLocation();
+		if (location == null) {
+			return null;
+		}
+		return location.toFile();
+	}
+
+	private void copy(File from, File to) throws IOException {
+		if (from == null || to == null || !from.isDirectory() || !to.isDirectory()) {
+			return;
+		}
+		final Path targetPath = to.toPath();
+		Files.walkFileTree(from.toPath(), new SimpleFileVisitor<Path>() {
+			@Override
+			public FileVisitResult preVisitDirectory(final Path dir, final BasicFileAttributes attrs)
+					throws IOException {
+				Files.createDirectories(targetPath.resolve(from.toPath().relativize(dir)));
+				return FileVisitResult.CONTINUE;
+			}
+
+			@Override
+			public FileVisitResult visitFile(final Path file, final BasicFileAttributes attrs) throws IOException {
+				Files.copy(file, targetPath.resolve(from.toPath().relativize(file)),
+						StandardCopyOption.REPLACE_EXISTING, StandardCopyOption.COPY_ATTRIBUTES);
+				return FileVisitResult.CONTINUE;
+			}
+		});
+	}
+
+	private IFolder getProjectFolder(IPath path) {
+		if (path != null) {
+			IWorkspace workspace = ResourcesPlugin.getWorkspace();
+			return workspace.getRoot().getFolder(path);
+		}
+		return null;
 	}
 
 	private void deleteAllProjects() throws CoreException {

tycho-its/src/test/java/org/eclipse/tycho/test/apitools/ApiToolsTest.java

@@ -33,7 +33,7 @@
 public class ApiToolsTest extends AbstractTychoIntegrationTest {
 	@Test
 	public void testGenerate() throws Exception {
-		Verifier verifier = getVerifier("api-tools", true, true);
+		Verifier verifier = getVerifier("api-tools/api-break", true, true);
 		verifier.executeGoals(List.of("clean", "package"));
 		verifier.verifyErrorFreeLog();
 		File descriptionFile = new File(verifier.getBasedir(), "bundle1/target/.api_description");
@@ -44,8 +44,8 @@ public void testGenerate() throws Exception {
 	}
 
 	@Test
-	public void testVerify() throws Exception {
-		Verifier verifier = getVerifier("api-tools", true, true);
+	public void testApiBreak() throws Exception {
+		Verifier verifier = getVerifier("api-tools/api-break", true, true);
 		File repo = ResourceUtil.resolveTestResource("repositories/api-tools");
 		verifier.addCliOption("-DbaselineRepo=" + repo.toURI());