Add testcase to reproduce failing behavior

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

@@ -273,6 +273,32 @@ private Map<String, String> computeOutputJars(IProject project) throws CoreExcep
 						for (String token : entry.getTokens()) {
 							outputJars.put(token, key);
 						}
+					} else if (name.startsWith(IBuildEntry.JAR_PREFIX)) {
+						// Actually each source.<jar> should have a corresponding output.<jar> but there
+						// are some cases where this is not true... lets cheat and look at the
+						// classpath instead...
+						String key = name.substring(IBuildEntry.JAR_PREFIX.length());
+						IJavaProject javaProject = JavaCore.create(project);
+						if (javaProject != null) {
+							IClasspathEntry[] rawClasspath = javaProject.getRawClasspath();
+							for (String token : entry.getTokens()) {
+								IPath srcPath = project.getFolder(token).getFullPath();
+								for (IClasspathEntry classpathEntry : rawClasspath) {
+									if (classpathEntry.getEntryKind() == IClasspathEntry.CPE_SOURCE) {
+										IPath path = classpathEntry.getPath();
+										if (srcPath.equals(path)) {
+											IPath outputLocation = classpathEntry.getOutputLocation();
+											if (outputLocation == null) {
+												outputLocation = javaProject.getOutputLocation();
+											}
+											IFolder folder = getProjectFolder(outputLocation);
+											String output = folder.getProjectRelativePath().toString();
+											outputJars.putIfAbsent(output, key);
+										}
+									}
+								}
+							}
+						}
 					}
 				}
 			}

tycho-its/projects/api-tools/missing-bin/.mvn/extensions.xml

@@ -0,0 +1,7 @@
+<extensions>
+  <extension>
+    <groupId>org.eclipse.tycho</groupId>
+    <artifactId>tycho-build</artifactId>
+    <version>${tycho-version}</version>
+  </extension>
+</extensions>

tycho-its/projects/api-tools/missing-bin/.mvn/maven.config

@@ -0,0 +1 @@
+-Dtycho-version=5.0.0-SNAPSHOT

tycho-its/projects/api-tools/missing-bin/org.eclipse.equinox.p2.ui/.classpath

@@ -0,0 +1,7 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-17"/>
+	<classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/>
+	<classpathentry kind="src" path="src"/>
+	<classpathentry kind="output" path="bin"/>
+</classpath>

tycho-its/projects/api-tools/missing-bin/org.eclipse.equinox.p2.ui/.project

@@ -0,0 +1,39 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>org.eclipse.equinox.p2.ui</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.jdt.core.javabuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.pde.ManifestBuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.pde.SchemaBuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.pde.api.tools.apiAnalysisBuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.pde.ds.core.builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.pde.PluginNature</nature>
+		<nature>org.eclipse.jdt.core.javanature</nature>
+		<nature>org.eclipse.pde.api.tools.apiAnalysisNature</nature>
+	</natures>
+</projectDescription>

tycho-its/projects/api-tools/missing-bin/org.eclipse.equinox.p2.ui/.settings/org.eclipse.jdt.ui.prefs

@@ -0,0 +1,68 @@
+eclipse.preferences.version=1
+editor_save_participant_org.eclipse.jdt.ui.postsavelistener.cleanup=true
+formatter_profile=org.eclipse.jdt.ui.default.eclipse_profile
+formatter_settings_version=16
+org.eclipse.jdt.ui.ignorelowercasenames=true
+org.eclipse.jdt.ui.importorder=;
+org.eclipse.jdt.ui.ondemandthreshold=3
+org.eclipse.jdt.ui.staticondemandthreshold=3
+org.eclipse.jdt.ui.text.custom_code_templates=<?xml version\="1.0" encoding\="UTF-8" standalone\="no"?><templates/>
+sp_cleanup.add_default_serial_version_id=true
+sp_cleanup.add_generated_serial_version_id=false
+sp_cleanup.add_missing_annotations=true
+sp_cleanup.add_missing_deprecated_annotations=true
+sp_cleanup.add_missing_methods=false
+sp_cleanup.add_missing_nls_tags=false
+sp_cleanup.add_missing_override_annotations=true
+sp_cleanup.add_missing_override_annotations_interface_methods=true
+sp_cleanup.add_serial_version_id=false
+sp_cleanup.always_use_blocks=true
+sp_cleanup.always_use_parentheses_in_expressions=false
+sp_cleanup.always_use_this_for_non_static_field_access=false
+sp_cleanup.always_use_this_for_non_static_method_access=false
+sp_cleanup.convert_functional_interfaces=true
+sp_cleanup.convert_to_enhanced_for_loop=true
+sp_cleanup.correct_indentation=false
+sp_cleanup.format_source_code=true
+sp_cleanup.format_source_code_changes_only=false
+sp_cleanup.insert_inferred_type_arguments=false
+sp_cleanup.make_local_variable_final=false
+sp_cleanup.make_parameters_final=false
+sp_cleanup.make_private_fields_final=true
+sp_cleanup.make_type_abstract_if_missing_method=false
+sp_cleanup.make_variable_declarations_final=false
+sp_cleanup.never_use_blocks=false
+sp_cleanup.never_use_parentheses_in_expressions=true
+sp_cleanup.on_save_use_additional_actions=true
+sp_cleanup.organize_imports=true
+sp_cleanup.qualify_static_field_accesses_with_declaring_class=false
+sp_cleanup.qualify_static_member_accesses_through_instances_with_declaring_class=true
+sp_cleanup.qualify_static_member_accesses_through_subtypes_with_declaring_class=true
+sp_cleanup.qualify_static_member_accesses_with_declaring_class=false
+sp_cleanup.qualify_static_method_accesses_with_declaring_class=false
+sp_cleanup.remove_private_constructors=true
+sp_cleanup.remove_redundant_modifiers=true
+sp_cleanup.remove_redundant_semicolons=true
+sp_cleanup.remove_redundant_type_arguments=true
+sp_cleanup.remove_trailing_whitespaces=true
+sp_cleanup.remove_trailing_whitespaces_all=true
+sp_cleanup.remove_trailing_whitespaces_ignore_empty=false
+sp_cleanup.remove_unnecessary_casts=true
+sp_cleanup.remove_unnecessary_nls_tags=false
+sp_cleanup.remove_unused_imports=true
+sp_cleanup.remove_unused_local_variables=false
+sp_cleanup.remove_unused_private_fields=true
+sp_cleanup.remove_unused_private_members=false
+sp_cleanup.remove_unused_private_methods=true
+sp_cleanup.remove_unused_private_types=true
+sp_cleanup.sort_members=false
+sp_cleanup.sort_members_all=false
+sp_cleanup.use_anonymous_class_creation=false
+sp_cleanup.use_blocks=false
+sp_cleanup.use_blocks_only_for_return_and_throw=false
+sp_cleanup.use_lambda=true
+sp_cleanup.use_parentheses_in_expressions=false
+sp_cleanup.use_this_for_non_static_field_access=false
+sp_cleanup.use_this_for_non_static_field_access_only_if_necessary=true
+sp_cleanup.use_this_for_non_static_method_access=false
+sp_cleanup.use_this_for_non_static_method_access_only_if_necessary=true

tycho-its/projects/api-tools/missing-bin/org.eclipse.equinox.p2.ui/META-INF/MANIFEST.MF

@@ -0,0 +1,46 @@
+Manifest-Version: 1.0
+Bundle-ManifestVersion: 2
+Bundle-Name: %bundleName
+Bundle-SymbolicName: org.eclipse.equinox.p2.ui;singleton:=true
+Bundle-Version: 2.9.0.qualifier
+Bundle-Activator: org.eclipse.equinox.internal.p2.ui.ProvUIActivator
+Bundle-Vendor: %providerName
+Bundle-Localization: plugin
+Export-Package: org.eclipse.equinox.internal.p2.ui;
+  x-friends:="org.eclipse.equinox.p2.ui.admin,
+   org.eclipse.pde.ui,
+   org.eclipse.equinox.p2.ui.sdk,
+   org.eclipse.equinox.p2.ui.rcp,
+   org.eclipse.equinox.p2.ui.importexport,
+   org.eclipse.equinox.p2.ui.sdk.scheduler,
+   org.eclipse.equinox.p2.discovery,
+   org.eclipse.equinox.p2.ui.discovery",
+ org.eclipse.equinox.internal.p2.ui.actions;x-friends:="org.eclipse.equinox.p2.ui.admin,org.eclipse.equinox.p2.ui.sdk.scheduler",
+ org.eclipse.equinox.internal.p2.ui.dialogs;
+  x-friends:="org.eclipse.equinox.p2.ui.admin,
+   org.eclipse.equinox.p2.ui.sdk.scheduler,
+   org.eclipse.equinox.p2.ui.sdk,
+   org.eclipse.pde.ui,
+   org.eclipse.equinox.p2.ui.importexport",
+ org.eclipse.equinox.internal.p2.ui.model;
+  x-friends:="org.eclipse.equinox.internal.p2.ui.analysis,
+   org.eclipse.equinox.p2.ui.admin,
+   org.eclipse.equinox.p2.ui.sdk.scheduler,
+   org.eclipse.equinox.p2.ui.sdk,
+   org.eclipse.equinox.p2.ui.importexport",
+ org.eclipse.equinox.p2.ui;version="2.6.0"
+Require-Bundle: org.eclipse.ui;bundle-version="3.107.0",
+ org.eclipse.core.runtime;bundle-version="[3.0.0,4.0.0)"
+Import-Package: org.eclipse.equinox.internal.p2.metadata,
+ org.eclipse.equinox.internal.provisional.p2.repository,
+ org.eclipse.equinox.p2.core;version="[2.7.0,3.0.0)",
+ org.eclipse.equinox.p2.engine;version="[2.0.0,3.0.0)",
+ org.eclipse.equinox.p2.engine.query;version="[2.0.0,3.0.0)",
+ org.eclipse.equinox.p2.metadata;version="[2.0.0,3.0.0)",
+ org.eclipse.equinox.p2.operations;version="[2.0.0,3.0.0)",
+ org.eclipse.equinox.p2.query;version="[2.0.0,3.0.0)",
+ org.eclipse.equinox.p2.repository.artifact;version="[2.0.0,3.0.0)",
+ org.eclipse.equinox.p2.repository.metadata;version="[2.0.0,3.0.0)"
+Bundle-ActivationPolicy: lazy
+Bundle-RequiredExecutionEnvironment: JavaSE-17
+Automatic-Module-Name: org.eclipse.equinox.p2.ui

tycho-its/projects/api-tools/missing-bin/org.eclipse.equinox.p2.ui/build.properties

@@ -0,0 +1,19 @@
+###############################################################################
+# Copyright (c) 2007, 2010 IBM Corporation and others.
+#
+# This program and the accompanying materials
+# are made available under the terms of the Eclipse Public License 2.0
+# which accompanies this distribution, and is available at
+# https://www.eclipse.org/legal/epl-2.0/
+#
+# SPDX-License-Identifier: EPL-2.0
+#
+# Contributors:
+#     IBM Corporation - initial API and implementation
+###############################################################################
+bin.includes = plugin.properties,\
+               .,\
+               META-INF/,\
+               plugin.xml
+source.. = src/
+# this is the missing one we want to test: output.. = bin/

tycho-its/projects/api-tools/missing-bin/org.eclipse.equinox.p2.ui/plugin.properties

@@ -0,0 +1,22 @@
+###############################################################################
+#  Copyright (c) 2007, 2010 IBM Corporation and others.
+#
+#  This program and the accompanying materials
+#  are made available under the terms of the Eclipse Public License 2.0
+#  which accompanies this distribution, and is available at
+#  https://www.eclipse.org/legal/epl-2.0/
+#
+#  SPDX-License-Identifier: EPL-2.0
+# 
+#  Contributors:
+#     IBM Corporation - initial API and implementation
+###############################################################################
+#
+# Provisioning UI plugin resources
+#
+providerName = Eclipse.org - Equinox
+bundleName=Equinox Provisioning UI Support
+IU.general=General Information
+IU.license=License Agreement
+IU.copyright=Copyright
+

tycho-its/projects/api-tools/missing-bin/org.eclipse.equinox.p2.ui/plugin.xml

@@ -0,0 +1,57 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<?eclipse version="3.2"?>
+<plugin>
+   <extension
+         point="org.eclipse.core.runtime.adapters">
+      <factory
+            adaptableType="org.eclipse.equinox.internal.p2.ui.model.ProvElement"
+            class="org.eclipse.equinox.internal.p2.ui.ProvUIAdapterFactory">
+         <adapter type="org.eclipse.equinox.p2.metadata.IInstallableUnit"/>
+         <adapter type="org.eclipse.equinox.p2.engine.IProfile"/>
+         <adapter type="org.eclipse.equinox.p2.repository.IRepository"/>
+         <adapter type="org.eclipse.equinox.p2.repository.metadata.IMetadataRepository"/>
+         <adapter type="org.eclipse.equinox.p2.repository.artifact.IArtifactRepository"/>
+      </factory>
+      <factory
+            adaptableType="org.eclipse.ui.internal.about.AboutPluginsPage"
+            class="org.eclipse.equinox.internal.p2.ui.KeySigningInfoFactory">
+         <adapter
+               type="org.eclipse.ui.internal.about.AboutBundleData$ExtendedSigningInfo">
+         </adapter>
+      </factory>
+   </extension>
+
+     <extension
+         point="org.eclipse.ui.propertyPages">
+      <page
+            name="%IU.copyright"
+            class="org.eclipse.equinox.internal.p2.ui.dialogs.IUCopyrightPropertyPage"
+            id="org.eclipse.equinox.p2.ui.IUCopyrightPropertyPage">
+            <enabledWhen>
+            <adapt
+                  type="org.eclipse.equinox.p2.metadata.IInstallableUnit">
+             </adapt>
+          </enabledWhen>
+      </page>
+           <page
+            name="%IU.general"
+            class="org.eclipse.equinox.internal.p2.ui.dialogs.IUGeneralInfoPropertyPage"
+            id="org.eclipse.equinox.p2.ui.IUGeneralInfoPropertyPage">
+            <enabledWhen>
+            <adapt
+                  type="org.eclipse.equinox.p2.metadata.IInstallableUnit">
+             </adapt>
+          </enabledWhen>
+      </page>
+      <page
+            name="%IU.license"
+            class="org.eclipse.equinox.internal.p2.ui.dialogs.IULicensePropertyPage"
+            id="org.eclipse.equinox.p2.ui.IULicensePropertyPage">
+            <enabledWhen>
+            <adapt
+                  type="org.eclipse.equinox.p2.metadata.IInstallableUnit">
+             </adapt>
+          </enabledWhen>
+      </page>    
+      </extension>
+ </plugin>

tycho-its/projects/api-tools/missing-bin/org.eclipse.equinox.p2.ui/src/org/eclipse/equinox/internal/p2/ui/ProvisioningOperationRunner.java

@@ -0,0 +1,26 @@
+/*******************************************************************************
+ *  Copyright (c) 2007, 2018 IBM Corporation and others.
+ *
+ *  This program and the accompanying materials
+ *  are made available under the terms of the Eclipse Public License 2.0
+ *  which accompanies this distribution, and is available at
+ *  https://www.eclipse.org/legal/epl-2.0/
+ *
+ *  SPDX-License-Identifier: EPL-2.0
+ *
+ *  Contributors:
+ *     IBM Corporation - initial API and implementation
+ *     Red Hat Inc. - Bug 460967
+ *******************************************************************************/
+package org.eclipse.equinox.internal.p2.ui;
+
+/**
+ * Utility methods for running provisioning operations. Operations can either be
+ * run synchronously or in a job. When scheduled as a job, the operation
+ * determines whether the job is run in the background or in the UI.
+ *
+ * @since 3.4
+ */
+public class ProvisioningOperationRunner {
+
+}