Make sure the last modified timestamp is set correctly

Linux stores modification time with nano-seconds precision, but we
currently set the timestamp of the cached file only in milliseconds.
This can lead to the situation that the source is considered a few
nanoseconds older than the cache file and therefore the cache is
regenerated every time.

tycho-core/src/main/java/org/eclipse/m2e/pde/target/shared/MavenBundleWrapper.java

@@ -141,10 +141,7 @@ public boolean visitEnter(DependencyNode n) {
             Map<DependencyNode, WrappedBundle> visited = new HashMap<>();
             WrappedBundle wrappedNode = getWrappedNode(node, instructionsLookup, visited);
             for (WrappedBundle wrap : visited.values()) {
-                Jar jar = wrap.getJar();
-                if (jar != null) {
-                    jar.close();
-                }
+                wrap.getJar().ifPresent(jar -> jar.close());
             }
             return wrappedNode;
         }
@@ -200,6 +197,7 @@ private static WrappedBundle getWrappedNode(DependencyNode node,
             if (cached == null) {
                 List<ProcessingMessage> messages = new ArrayList<>();
                 wrapArtifactFile.getParentFile().mkdirs();
+                boolean hasErrors = false;
                 try (Analyzer analyzer = new Analyzer(analyzerJar);) {
                     analyzer.setProperty("mvnGroupId", artifact.getGroupId());
                     analyzer.setProperty("mvnArtifactId", artifact.getArtifactId());
@@ -213,7 +211,7 @@ private static WrappedBundle getWrappedNode(DependencyNode node,
                         analyzer.setProperty(property, trimValue);
                     }
                     for (WrappedBundle dep : depends) {
-                        Jar depJar = dep.getJar();
+                        Jar depJar = dep.getJar().orElse(null);
                         if (depJar == null) {
                             messages.add(new ProcessingMessage(artifact, Type.WARN,
                                     "Dependency " + dep.getNode().getDependency() + " was ignored!"));
@@ -230,14 +228,21 @@ private static WrappedBundle getWrappedNode(DependencyNode node,
                             continue;
                         }
                         messages.add(new ProcessingMessage(artifact, Type.ERROR, err));
+                        hasErrors = true;
                     }
                     for (String warn : analyzer.getWarnings()) {
                         messages.add(new ProcessingMessage(artifact, Type.WARN, warn));
                     }
                 }
-                wrapArtifactFile.setLastModified(originalFile.lastModified());
-                visited.put(node, wrappedNode = new WrappedBundle(node, depends, key, wrapArtifactFile.toPath(),
-                        new Jar(wrapArtifactFile), messages));
+                if (hasErrors) {
+                    Files.deleteIfExists(wrapArtifactFile.toPath());
+                    visited.put(node, wrappedNode = new WrappedBundle(node, depends, key, null, null, messages));
+                } else {
+                    Files.setLastModifiedTime(wrapArtifactFile.toPath(),
+                            Files.getLastModifiedTime(originalFile.toPath()));
+                    visited.put(node, wrappedNode = new WrappedBundle(node, depends, key, wrapArtifactFile.toPath(),
+                            new Jar(wrapArtifactFile), messages));
+                }
             } else {
                 visited.put(node, wrappedNode = new WrappedBundle(node, depends, key, wrapArtifactFile.toPath(),
                         new Jar(wrapArtifactFile), List.of()));
@@ -301,7 +306,7 @@ public static boolean isOutdated(Path cacheFile, Path sourceFile) throws IOExcep
         if (Files.exists(cacheFile)) {
             FileTime sourceTimeStamp = Files.getLastModifiedTime(sourceFile);
             FileTime cacheTimeStamp = Files.getLastModifiedTime(cacheFile);
-            return sourceTimeStamp.compareTo(cacheTimeStamp) > 0;
+            return sourceTimeStamp.toMillis() > cacheTimeStamp.toMillis();
         }
         return true;
     }

tycho-core/src/main/java/org/eclipse/m2e/pde/target/shared/WrappedBundle.java

@@ -15,6 +15,7 @@
 import java.nio.file.Path;
 import java.util.List;
 import java.util.Objects;
+import java.util.Optional;
 import java.util.stream.Stream;
 
 import org.eclipse.aether.graph.DependencyNode;
@@ -26,34 +27,38 @@ public final class WrappedBundle {
     private final DependencyNode node;
     private final List<WrappedBundle> depends;
     private final String instructionsKey;
-    private final Path file;
-    private final Jar jar;
+    private final Optional<Path> file;
+    private final Optional<Jar> jar;
     private final List<ProcessingMessage> messages;
 
     WrappedBundle(DependencyNode node, List<WrappedBundle> depends, String key, Path file, Jar jar,
             List<ProcessingMessage> messages) {
         this.node = node;
         this.depends = depends;
         this.instructionsKey = key;
-        this.file = file;
-        this.jar = jar;
+        this.file = Optional.ofNullable(file);
+        this.jar = Optional.ofNullable(jar);
         this.messages = messages;
     }
 
     String getInstructionsKey() {
         return instructionsKey;
     }
 
-    Jar getJar() {
+    Optional<Jar> getJar() {
         return jar;
     }
 
     DependencyNode getNode() {
         return node;
     }
 
-    /** @return the location of the wrapped bundle's files */
-    public Path getFile() {
+    /**
+     * 
+     * @return an optional describing the wrapped bundle, or an empty optional if the bundle was not
+     *         wrapped because of errors in the generation phase.
+     */
+    public Optional<Path> getFile() {
         return file;
     }
 

tycho-core/src/main/java/org/eclipse/tycho/core/resolver/MavenTargetDefinitionContent.java

@@ -226,7 +226,7 @@ public MavenTargetDefinitionContent(MavenGAVLocation location, MavenDependencies
                                     throw new RuntimeException(directErrors.stream().map(ProcessingMessage::message)
                                             .collect(Collectors.joining(System.lineSeparator())));
                                 }
-                                File file = wrappedBundle.getFile().toFile();
+                                File file = wrappedBundle.getFile().get().toFile();
                                 BundleDescription description = BundlesAction.createBundleDescription(file);
                                 WrappedArtifact wrappedArtifact = new WrappedArtifact(file, mavenArtifact,
                                         mavenArtifact.getClassifier(), description.getSymbolicName(),