Releasing

[cc0/argeo-build.git] / build / Repackage.java

package org.argeo.build;

import static java.lang.System.Logger.Level.DEBUG;
import static java.lang.System.Logger.Level.ERROR;
import static java.lang.System.Logger.Level.INFO;
import static java.lang.System.Logger.Level.TRACE;
import static java.lang.System.Logger.Level.WARNING;
import static java.nio.file.FileVisitResult.CONTINUE;
import static java.util.jar.Attributes.Name.MANIFEST_VERSION;
import static org.argeo.build.Repackage.ManifestConstants.ARGEO_ORIGIN_EMBED;
import static org.argeo.build.Repackage.ManifestConstants.ARGEO_ORIGIN_M2;
import static org.argeo.build.Repackage.ManifestConstants.ARGEO_ORIGIN_M2_MERGE;
import static org.argeo.build.Repackage.ManifestConstants.ARGEO_ORIGIN_M2_REPO;
import static org.argeo.build.Repackage.ManifestConstants.ARGEO_ORIGIN_MANIFEST_NOT_MODIFIED;
import static org.argeo.build.Repackage.ManifestConstants.ARGEO_ORIGIN_URI;
import static org.argeo.build.Repackage.ManifestConstants.BUNDLE_LICENSE;
import static org.argeo.build.Repackage.ManifestConstants.BUNDLE_SYMBOLICNAME;
import static org.argeo.build.Repackage.ManifestConstants.BUNDLE_VERSION;
import static org.argeo.build.Repackage.ManifestConstants.ECLIPSE_SOURCE_BUNDLE;
import static org.argeo.build.Repackage.ManifestConstants.EXPORT_PACKAGE;
import static org.argeo.build.Repackage.ManifestConstants.IMPORT_PACKAGE;
import static org.argeo.build.Repackage.ManifestConstants.SPDX_LICENSE_IDENTIFIER;

import java.io.BufferedWriter;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.lang.System.Logger;
import java.net.MalformedURLException;
import java.net.URL;
import java.nio.charset.StandardCharsets;
import java.nio.file.DirectoryStream;
import java.nio.file.FileSystem;
import java.nio.file.FileSystems;
import java.nio.file.FileVisitResult;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.PathMatcher;
import java.nio.file.Paths;
import java.nio.file.SimpleFileVisitor;
import java.nio.file.StandardOpenOption;
import java.nio.file.attribute.BasicFileAttributes;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Objects;
import java.util.Properties;
import java.util.Set;
import java.util.TreeMap;
import java.util.TreeSet;
import java.util.concurrent.CompletableFuture;
import java.util.jar.Attributes;
import java.util.jar.JarEntry;
import java.util.jar.JarInputStream;
import java.util.jar.JarOutputStream;
import java.util.jar.Manifest;
import java.util.zip.Deflater;

import aQute.bnd.osgi.Analyzer;
import aQute.bnd.osgi.Jar;

/**
 * Simple tool repackaging existing jar files into OSGi bundles in an A2
 * repository.
 */
public class Repackage {
        final static Logger logger = System.getLogger(Repackage.class.getName());

        /**
         * Environment variable on whether sources should be packaged separately or
         * integrated in the bundles.
         */
        final static String ENV_SOURCE_BUNDLES = "SOURCE_BUNDLES";

        /** Whether repackaging should run in parallel or sequentially. */
        final static boolean parallel = true;

        // cache
        /** Summary of all license seen during the repackaging. */
        final static Map<String, Set<String>> licensesUsed = new TreeMap<>();

        /** Main entry point. */
        public static void main(String[] args) {
                if (args.length < 2) {
                        System.err.println("Usage: <path to a2 output dir> <category1> <category2> ...");
                        System.exit(1);
                }
                Path a2Base = Paths.get(args[0]).toAbsolutePath().normalize();
                Path descriptorsBase = Paths.get(".").toAbsolutePath().normalize();
                Repackage factory = new Repackage(a2Base, descriptorsBase);

                List<CompletableFuture<Void>> toDos = new ArrayList<>();
                for (int i = 1; i < args.length; i++) {
                        Path p = Paths.get(args[i]);
                        if (parallel)
                                toDos.add(CompletableFuture.runAsync(() -> factory.processCategory(p)));
                        else
                                factory.processCategory(p);
                }
                CompletableFuture.allOf(toDos.toArray(new CompletableFuture[toDos.size()])).join();

                // Summary
                StringBuilder sb = new StringBuilder();
                for (String licenseId : licensesUsed.keySet())
                        for (String name : licensesUsed.get(licenseId))
                                sb.append((licenseId.equals("") ? "Proprietary" : licenseId) + "\t\t" + name + "\n");
                logger.log(INFO, "# License summary:\n" + sb);
        }

        /** Name of the file centralising information for multiple M2 artifacts. */
        final static String COMMON_BND = "common.bnd";
        /** Name of the file centralising information for mergin M2 artifacts. */
        final static String MERGE_BND = "merge.bnd";
        /**
         * Subdirectory of the jar file where origin informations (changes, legal
         * notices etc. are stored)
         */
        final static String A2_ORIGIN = "A2-ORIGIN";

        /** Directory where to download archives */
        Path originBase;
        /** Directory where to download Maven artifacts */
        Path mavenBase;

        /** A2 repository base for binary bundles */
        Path a2Base;
        /** A2 repository base for source bundles */
        Path a2SrcBase;
        /** A2 base for native components */
        Path a2LibBase;
        /** Location of the descriptors driving the packaging */
        Path descriptorsBase;
        /** URIs of archives to download */
        Properties uris = new Properties();
        /** Mirrors for archive download. Key is URI prefix, value list of base URLs */
        Map<String, List<String>> mirrors = new HashMap<String, List<String>>();

        /** Whether sources should be packaged separately */
        final boolean sourceBundles;

        /** Constructor initialises the various variables */
        public Repackage(Path a2Base, Path descriptorsBase) {
                sourceBundles = Boolean.parseBoolean(System.getenv(ENV_SOURCE_BUNDLES));
                if (sourceBundles)
                        logger.log(INFO, "Sources will be packaged separately");

                Objects.requireNonNull(a2Base);
                Objects.requireNonNull(descriptorsBase);
                this.originBase = Paths.get(System.getProperty("user.home"), ".cache", "argeo/build/origin");
                this.mavenBase = Paths.get(System.getProperty("user.home"), ".m2", "repository");

                // TODO define and use a build base
                this.a2Base = a2Base;
                this.a2SrcBase = a2Base.getParent().resolve(a2Base.getFileName() + ".src");
                this.a2LibBase = a2Base.resolve("lib");
                this.descriptorsBase = descriptorsBase;
                if (!Files.exists(this.descriptorsBase))
                        throw new IllegalArgumentException(this.descriptorsBase + " does not exist");

                // URIs mapping
                Path urisPath = this.descriptorsBase.resolve("uris.properties");
                if (Files.exists(urisPath)) {
                        try (InputStream in = Files.newInputStream(urisPath)) {
                                uris.load(in);
                        } catch (IOException e) {
                                throw new IllegalStateException("Cannot load " + urisPath, e);
                        }
                }

                // Eclipse mirrors
                Path eclipseMirrorsPath = this.descriptorsBase.resolve("eclipse.mirrors.txt");
                List<String> eclipseMirrors = new ArrayList<>();
                if (Files.exists(eclipseMirrorsPath)) {
                        try {
                                eclipseMirrors = Files.readAllLines(eclipseMirrorsPath, StandardCharsets.UTF_8);
                        } catch (IOException e) {
                                throw new IllegalStateException("Cannot load " + eclipseMirrorsPath, e);
                        }
                        for (Iterator<String> it = eclipseMirrors.iterator(); it.hasNext();) {
                                String value = it.next();
                                if (value.strip().equals(""))
                                        it.remove();
                        }
                }
                mirrors.put("http://www.eclipse.org/downloads", eclipseMirrors);
        }

        /*
         * MAVEN ORIGIN
         */
        /** Process a whole category/group id. */
        void processCategory(Path categoryRelativePath) {
                try {
                        Path targetCategoryBase = descriptorsBase.resolve(categoryRelativePath);
                        DirectoryStream<Path> bnds = Files.newDirectoryStream(targetCategoryBase,
                                        (p) -> p.getFileName().toString().endsWith(".bnd") && !p.getFileName().toString().equals(COMMON_BND)
                                                        && !p.getFileName().toString().equals(MERGE_BND));
                        for (Path p : bnds) {
                                processSingleM2ArtifactDistributionUnit(p);
                        }

                        DirectoryStream<Path> dus = Files.newDirectoryStream(targetCategoryBase, (p) -> Files.isDirectory(p));
                        for (Path duDir : dus) {
                                if (duDir.getFileName().toString().startsWith("eclipse-")) {
                                        processEclipseArchive(duDir);
                                } else {
                                        processM2BasedDistributionUnit(duDir);
                                }
                        }
                } catch (IOException e) {
                        throw new RuntimeException("Cannot process category " + categoryRelativePath, e);
                }
        }

        /** Process a standalone Maven artifact. */
        void processSingleM2ArtifactDistributionUnit(Path bndFile) {
                try {
                        Path categoryRelativePath = descriptorsBase.relativize(bndFile.getParent());
                        Path targetCategoryBase = a2Base.resolve(categoryRelativePath);

                        Properties fileProps = new Properties();
                        try (InputStream in = Files.newInputStream(bndFile)) {
                                fileProps.load(in);
                        }
                        String repoStr = fileProps.containsKey(ARGEO_ORIGIN_M2_REPO.toString())
                                        ? fileProps.getProperty(ARGEO_ORIGIN_M2_REPO.toString())
                                        : null;

                        if (!fileProps.containsKey(BUNDLE_SYMBOLICNAME.toString())) {
                                // use file name as symbolic name
                                String symbolicName = bndFile.getFileName().toString();
                                symbolicName = symbolicName.substring(0, symbolicName.length() - ".bnd".length());
                                fileProps.put(BUNDLE_SYMBOLICNAME.toString(), symbolicName);
                        }

                        String m2Coordinates = fileProps.getProperty(ARGEO_ORIGIN_M2.toString());
                        if (m2Coordinates == null)
                                throw new IllegalArgumentException("No M2 coordinates available for " + bndFile);
                        M2Artifact artifact = new M2Artifact(m2Coordinates);
                        URL url = M2ConventionsUtils.mavenRepoUrl(repoStr, artifact);
                        Path downloaded = downloadMaven(url, artifact);

                        A2Origin origin = new A2Origin();
                        Path targetBundleDir = processBndJar(downloaded, targetCategoryBase, fileProps, artifact, origin);

                        downloadAndProcessM2Sources(repoStr, artifact, targetBundleDir, false);

                        createJar(targetBundleDir, origin);
                } catch (Exception e) {
                        throw new RuntimeException("Cannot process " + bndFile, e);
                }
        }

        /**
         * Process multiple Maven artifacts coming from a same project and therefore
         * with information in common (typically the version), generating single bundles
         * or merging them if necessary.
         */
        void processM2BasedDistributionUnit(Path duDir) {
                try {
                        Path categoryRelativePath = descriptorsBase.relativize(duDir.getParent());
                        Path targetCategoryBase = a2Base.resolve(categoryRelativePath);

                        Path mergeBnd = duDir.resolve(MERGE_BND);
                        if (Files.exists(mergeBnd)) // merge
                                mergeM2Artifacts(mergeBnd);

                        Path commonBnd = duDir.resolve(COMMON_BND);
                        if (!Files.exists(commonBnd))
                                return;

                        Properties commonProps = new Properties();
                        try (InputStream in = Files.newInputStream(commonBnd)) {
                                commonProps.load(in);
                        }

                        String m2Version = commonProps.getProperty(ARGEO_ORIGIN_M2.toString());
                        if (m2Version == null) {
                                logger.log(WARNING, "Ignoring " + duDir + " as it is not an M2-based distribution unit");
                                return;// ignore, this is probably an Eclipse archive
                        }
                        if (!m2Version.startsWith(":")) {
                                throw new IllegalStateException("Only the M2 version can be specified: " + m2Version);
                        }
                        m2Version = m2Version.substring(1);

                        DirectoryStream<Path> ds = Files.newDirectoryStream(duDir,
                                        (p) -> p.getFileName().toString().endsWith(".bnd") && !p.getFileName().toString().equals(COMMON_BND)
                                                        && !p.getFileName().toString().equals(MERGE_BND));
                        for (Path p : ds) {
                                Properties fileProps = new Properties();
                                try (InputStream in = Files.newInputStream(p)) {
                                        fileProps.load(in);
                                }
                                String m2Coordinates = fileProps.getProperty(ARGEO_ORIGIN_M2.toString());
                                M2Artifact artifact = new M2Artifact(m2Coordinates);
                                artifact.setVersion(m2Version);

                                // prepare manifest entries
                                Properties mergeProps = new Properties();
                                mergeProps.putAll(commonProps);

                                fileEntries: for (Object key : fileProps.keySet()) {
                                        if (ARGEO_ORIGIN_M2.toString().equals(key))
                                                continue fileEntries;
                                        String value = fileProps.getProperty(key.toString());
                                        Object previousValue = mergeProps.put(key.toString(), value);
                                        if (previousValue != null) {
                                                logger.log(WARNING,
                                                                commonBnd + ": " + key + " was " + previousValue + ", overridden with " + value);
                                        }
                                }
                                mergeProps.put(ARGEO_ORIGIN_M2.toString(), artifact.toM2Coordinates());
                                if (!mergeProps.containsKey(BUNDLE_SYMBOLICNAME.toString())) {
                                        // use file name as symbolic name
                                        String symbolicName = p.getFileName().toString();
                                        symbolicName = symbolicName.substring(0, symbolicName.length() - ".bnd".length());
                                        mergeProps.put(BUNDLE_SYMBOLICNAME.toString(), symbolicName);
                                }

                                String repoStr = mergeProps.containsKey(ARGEO_ORIGIN_M2_REPO.toString())
                                                ? mergeProps.getProperty(ARGEO_ORIGIN_M2_REPO.toString())
                                                : null;

                                // download
                                URL url = M2ConventionsUtils.mavenRepoUrl(repoStr, artifact);
                                Path downloaded = downloadMaven(url, artifact);

                                A2Origin origin = new A2Origin();
                                Path targetBundleDir = processBndJar(downloaded, targetCategoryBase, mergeProps, artifact, origin);
                                downloadAndProcessM2Sources(repoStr, artifact, targetBundleDir, false);
                                createJar(targetBundleDir, origin);
                        }
                } catch (IOException e) {
                        throw new RuntimeException("Cannot process " + duDir, e);
                }
        }

        /** Merge multiple Maven artifacts. */
        void mergeM2Artifacts(Path mergeBnd) throws IOException {
                Path duDir = mergeBnd.getParent();
                String category = duDir.getParent().getFileName().toString();
                Path targetCategoryBase = a2Base.resolve(category);

                Properties mergeProps = new Properties();
                try (InputStream in = Files.newInputStream(mergeBnd)) {
                        mergeProps.load(in);
                }

                String m2Version = mergeProps.getProperty(ARGEO_ORIGIN_M2.toString());
                if (m2Version == null) {
                        logger.log(WARNING, "Ignoring " + duDir + " as it is not an M2-based distribution unit");
                        return;// ignore, this is probably an Eclipse archive
                }
                if (!m2Version.startsWith(":")) {
                        throw new IllegalStateException("Only the M2 version can be specified: " + m2Version);
                }
                m2Version = m2Version.substring(1);
                mergeProps.put(BUNDLE_VERSION.toString(), m2Version);

                String artifactsStr = mergeProps.getProperty(ARGEO_ORIGIN_M2_MERGE.toString());
                if (artifactsStr == null)
                        throw new IllegalArgumentException(mergeBnd + ": " + ARGEO_ORIGIN_M2_MERGE + " must be set");

                String repoStr = mergeProps.containsKey(ARGEO_ORIGIN_M2_REPO.toString())
                                ? mergeProps.getProperty(ARGEO_ORIGIN_M2_REPO.toString())
                                : null;

                String bundleSymbolicName = mergeProps.getProperty(BUNDLE_SYMBOLICNAME.toString());
                if (bundleSymbolicName == null)
                        throw new IllegalArgumentException("Bundle-SymbolicName must be set in " + mergeBnd);
                CategoryNameVersion nameVersion = new M2Artifact(category + ":" + bundleSymbolicName + ":" + m2Version);

                A2Origin origin = new A2Origin();
                Path bundleDir = targetCategoryBase.resolve(bundleSymbolicName + "." + nameVersion.getBranch());

                String[] artifacts = artifactsStr.split(",");
                artifacts: for (String str : artifacts) {
                        String m2Coordinates = str.trim();
                        if ("".equals(m2Coordinates))
                                continue artifacts;
                        M2Artifact artifact = new M2Artifact(m2Coordinates.trim());
                        if (artifact.getVersion() == null)
                                artifact.setVersion(m2Version);
                        URL url = M2ConventionsUtils.mavenRepoUrl(repoStr, artifact);
                        Path downloaded = downloadMaven(url, artifact);
                        JarEntry entry;
                        try (JarInputStream jarIn = new JarInputStream(Files.newInputStream(downloaded), false)) {
                                entries: while ((entry = jarIn.getNextJarEntry()) != null) {
                                        if (entry.isDirectory())
                                                continue entries;
                                        if (entry.getName().endsWith(".RSA") || entry.getName().endsWith(".SF")) {
                                                origin.deleted.add("cryptographic signatures from " + artifact);
                                                continue entries;
                                        }
                                        if (entry.getName().endsWith("module-info.class")) { // skip Java 9 module info
                                                origin.deleted.add("Java module information (module-info.class) from " + artifact);
                                                continue entries;
                                        }
                                        if (entry.getName().startsWith("META-INF/versions/")) { // skip multi-version
                                                origin.deleted.add("additional Java versions (META-INF/versions) from " + artifact);
                                                continue entries;
                                        }
                                        if (entry.getName().startsWith("META-INF/maven/")) {
                                                origin.deleted.add("Maven information (META-INF/maven) from " + artifact);
                                                continue entries;
                                        }
                                        if (entry.getName().startsWith(".cache/")) { // Apache SSHD
                                                origin.deleted.add("cache directory (.cache) from " + artifact);
                                                continue entries;
                                        }
                                        if (entry.getName().equals("META-INF/DEPENDENCIES")) {
                                                origin.deleted.add("Dependencies (META-INF/DEPENDENCIES) from " + artifact);
                                                continue entries;
                                        }
                                        if (entry.getName().equals("META-INF/MANIFEST.MF")) {
                                                Path originalManifest = bundleDir.resolve(A2_ORIGIN).resolve(artifact.getGroupId())
                                                                .resolve(artifact.getArtifactId()).resolve("MANIFEST.MF");
                                                Files.createDirectories(originalManifest.getParent());
                                                try (OutputStream out = Files.newOutputStream(originalManifest)) {
                                                        Files.copy(jarIn, originalManifest);
                                                }
                                                origin.added.add(
                                                                "original MANIFEST (" + bundleDir.relativize(originalManifest) + ") from " + artifact);
                                                continue entries;
                                        }

                                        if (entry.getName().endsWith("NOTICE") || entry.getName().endsWith("NOTICE.txt")
                                                        || entry.getName().endsWith("LICENSE") || entry.getName().endsWith("LICENSE.md")
                                                        || entry.getName().endsWith("LICENSE-notice.md") || entry.getName().endsWith("COPYING")
                                                        || entry.getName().endsWith("COPYING.LESSER")) {
                                                Path artifactOriginDir = bundleDir.resolve(A2_ORIGIN).resolve(artifact.getGroupId())
                                                                .resolve(artifact.getArtifactId());
                                                Path target = artifactOriginDir.resolve(entry.getName());
                                                Files.createDirectories(target.getParent());
                                                Files.copy(jarIn, target);
                                                origin.moved.add(entry.getName() + " in " + artifact + " to " + bundleDir.relativize(target));
                                                continue entries;
                                        }
                                        Path target = bundleDir.resolve(entry.getName());
                                        Files.createDirectories(target.getParent());
                                        if (!Files.exists(target)) {
                                                Files.copy(jarIn, target);
                                        } else {
                                                if (entry.getName().startsWith("META-INF/services/")) {
                                                        try (OutputStream out = Files.newOutputStream(target, StandardOpenOption.APPEND)) {
                                                                out.write("\n".getBytes());
                                                                jarIn.transferTo(out);
                                                                logger.log(DEBUG, artifact.getArtifactId() + " - Appended " + entry.getName());
                                                        }
                                                        origin.modified.add(entry.getName() + ", merging from " + artifact);
                                                } else if (entry.getName().startsWith("org/apache/batik/")) {
                                                        logger.log(TRACE, "Skip " + entry.getName());
                                                        continue entries;
                                                } else {
                                                        throw new IllegalStateException("File " + target + " from " + artifact + " already exists");
                                                }
                                        }
                                        logger.log(TRACE, () -> "Copied " + target);
                                }
                        }
                        origin.added.add("binary content of " + artifact);

                        // process sources
                        downloadAndProcessM2Sources(repoStr, artifact, bundleDir, true);
                }

                // additional service files
                Path servicesDir = duDir.resolve("services");
                if (Files.exists(servicesDir)) {
                        for (Path p : Files.newDirectoryStream(servicesDir)) {
                                Path target = bundleDir.resolve("META-INF/services/").resolve(p.getFileName());
                                try (InputStream in = Files.newInputStream(p);
                                                OutputStream out = Files.newOutputStream(target, StandardOpenOption.APPEND);) {
                                        out.write("\n".getBytes());
                                        in.transferTo(out);
                                        logger.log(DEBUG, "Appended " + p);
                                }
                                origin.added.add(bundleDir.relativize(target).toString());
                        }
                }

                Map<String, String> entries = new TreeMap<>();
                try (Analyzer bndAnalyzer = new Analyzer()) {
                        bndAnalyzer.setProperties(mergeProps);
                        Jar jar = new Jar(bundleDir.toFile());
                        bndAnalyzer.setJar(jar);
                        Manifest manifest = bndAnalyzer.calcManifest();

                        keys: for (Object key : manifest.getMainAttributes().keySet()) {
                                Object value = manifest.getMainAttributes().get(key);

                                switch (key.toString()) {
                                case "Tool":
                                case "Bnd-LastModified":
                                case "Created-By":
                                        continue keys;
                                }
                                if ("Require-Capability".equals(key.toString())
                                                && value.toString().equals("osgi.ee;filter:=\"(&(osgi.ee=JavaSE)(version=1.1))\""))
                                        continue keys;// hack for very old classes
                                entries.put(key.toString(), value.toString());
                        }
                } catch (Exception e) {
                        throw new RuntimeException("Cannot process " + mergeBnd, e);
                }

                Manifest manifest = new Manifest();
                Path manifestPath = bundleDir.resolve("META-INF/MANIFEST.MF");
                Files.createDirectories(manifestPath.getParent());
                for (String key : entries.keySet()) {
                        String value = entries.get(key);
                        manifest.getMainAttributes().putValue(key, value);
                }

                try (OutputStream out = Files.newOutputStream(manifestPath)) {
                        manifest.write(out);
                }
                createJar(bundleDir, origin);
        }

        /** Generate MANIFEST using BND. */
        Path processBndJar(Path downloaded, Path targetCategoryBase, Properties fileProps, M2Artifact artifact,
                        A2Origin origin) {

                try {
                        Map<String, String> additionalEntries = new TreeMap<>();
                        boolean doNotModify = Boolean.parseBoolean(
                                        fileProps.getOrDefault(ARGEO_ORIGIN_MANIFEST_NOT_MODIFIED.toString(), "false").toString());

                        // Note: we always force the symbolic name
                        if (doNotModify) {
                                fileEntries: for (Object key : fileProps.keySet()) {
                                        if (ARGEO_ORIGIN_M2.toString().equals(key))
                                                continue fileEntries;
                                        String value = fileProps.getProperty(key.toString());
                                        additionalEntries.put(key.toString(), value);
                                }
                        } else {
                                if (artifact != null) {
                                        if (!fileProps.containsKey(BUNDLE_SYMBOLICNAME.toString())) {
                                                fileProps.put(BUNDLE_SYMBOLICNAME.toString(), artifact.getName());
                                        }
                                        if (!fileProps.containsKey(BUNDLE_VERSION.toString())) {
                                                fileProps.put(BUNDLE_VERSION.toString(), artifact.getVersion());
                                        }
                                }

                                if (!fileProps.containsKey(EXPORT_PACKAGE.toString())) {
                                        fileProps.put(EXPORT_PACKAGE.toString(),
                                                        "*;version=\"" + fileProps.getProperty(BUNDLE_VERSION.toString()) + "\"");
                                }

                                try (Analyzer bndAnalyzer = new Analyzer()) {
                                        bndAnalyzer.setProperties(fileProps);
                                        Jar jar = new Jar(downloaded.toFile());
                                        bndAnalyzer.setJar(jar);
                                        Manifest manifest = bndAnalyzer.calcManifest();

                                        keys: for (Object key : manifest.getMainAttributes().keySet()) {
                                                Object value = manifest.getMainAttributes().get(key);

                                                switch (key.toString()) {
                                                case "Tool":
                                                case "Bnd-LastModified":
                                                case "Created-By":
                                                        continue keys;
                                                }
                                                if ("Require-Capability".equals(key.toString())
                                                                && value.toString().equals("osgi.ee;filter:=\"(&(osgi.ee=JavaSE)(version=1.1))\""))
                                                        continue keys;// !! hack for very old classes
                                                additionalEntries.put(key.toString(), value.toString());
                                        }
                                }
                        }
                        Path targetBundleDir = processBundleJar(downloaded, targetCategoryBase, additionalEntries, origin);
                        logger.log(DEBUG, () -> "Processed " + downloaded);
                        return targetBundleDir;
                } catch (Exception e) {
                        throw new RuntimeException("Cannot BND process " + downloaded, e);
                }

        }

        /** Download and integrates sources for a single Maven artifact. */
        void downloadAndProcessM2Sources(String repoStr, M2Artifact artifact, Path targetBundleDir, boolean merging)
                        throws IOException {
                try {
                        M2Artifact sourcesArtifact = new M2Artifact(artifact.toM2Coordinates(), "sources");
                        URL sourcesUrl = M2ConventionsUtils.mavenRepoUrl(repoStr, sourcesArtifact);
                        Path sourcesDownloaded = downloadMaven(sourcesUrl, artifact, true);
                        processM2SourceJar(sourcesDownloaded, targetBundleDir, merging ? artifact : null);
                        logger.log(TRACE, () -> "Processed source " + sourcesDownloaded);
                } catch (Exception e) {
                        logger.log(ERROR, () -> "Cannot download source for  " + artifact);
                }

        }

        /** Integrate sources from a downloaded jar file. */
        void processM2SourceJar(Path file, Path bundleDir, M2Artifact mergingFrom) throws IOException {
                A2Origin origin = new A2Origin();
                Path sourceDir = sourceBundles ? bundleDir.getParent().resolve(bundleDir.toString() + ".src")
                                : bundleDir.resolve("OSGI-OPT/src");
                try (JarInputStream jarIn = new JarInputStream(Files.newInputStream(file), false)) {

                        String mergingMsg = "";
                        if (mergingFrom != null)
                                mergingMsg = " of " + mergingFrom;

                        Files.createDirectories(sourceDir);
                        JarEntry entry;
                        entries: while ((entry = jarIn.getNextJarEntry()) != null) {
                                if (entry.isDirectory())
                                        continue entries;
                                if (entry.getName().startsWith("META-INF")) {// skip META-INF entries
                                        origin.deleted.add("META-INF directory from the sources" + mergingMsg);
                                        continue entries;
                                }
                                if (entry.getName().startsWith("module-info.java")) {// skip Java module information
                                        origin.deleted.add("Java module information from the sources (module-info.java)" + mergingMsg);
                                        continue entries;
                                }
                                if (entry.getName().startsWith("/")) { // absolute paths
                                        // TODO does it really happen?
                                        logger.log(WARNING, entry.getName() + " has an absolute path");
                                        origin.deleted.add(entry.getName() + " from the sources" + mergingMsg);
                                        continue entries;
                                }
                                Path target = sourceDir.resolve(entry.getName());
                                Files.createDirectories(target.getParent());
                                if (!Files.exists(target)) {
                                        Files.copy(jarIn, target);
                                        logger.log(TRACE, () -> "Copied source " + target);
                                } else {
                                        logger.log(TRACE, () -> target + " already exists, skipping...");
                                }
                        }
                }
                // write the changes
                if (sourceBundles) {
                        origin.appendChanges(sourceDir);
                } else {
                        origin.added.add("source code under OSGI-OPT/src");
                        origin.appendChanges(bundleDir);
                }
        }

        /** Download a Maven artifact. */
        Path downloadMaven(URL url, M2Artifact artifact) throws IOException {
                return downloadMaven(url, artifact, false);
        }

        /** Download a Maven artifact. */
        Path downloadMaven(URL url, M2Artifact artifact, boolean sources) throws IOException {
                return download(url, mavenBase, artifact.getGroupId().replace(".", "/") //
                                + '/' + artifact.getArtifactId() + '/' + artifact.getVersion() //
                                + '/' + artifact.getArtifactId() + "-" + artifact.getVersion() + (sources ? "-sources" : "") + ".jar");
        }

        /*
         * ECLIPSE ORIGIN
         */
        /** Process an archive in Eclipse format. */
        void processEclipseArchive(Path duDir) {
                try {
                        Path categoryRelativePath = descriptorsBase.relativize(duDir.getParent());
                        Path targetCategoryBase = a2Base.resolve(categoryRelativePath);
                        Files.createDirectories(targetCategoryBase);
                        // first delete all directories from previous builds
                        for (Path dir : Files.newDirectoryStream(targetCategoryBase, (p) -> Files.isDirectory(p)))
                                deleteDirectory(dir);

                        Files.createDirectories(originBase);

                        Path commonBnd = duDir.resolve(COMMON_BND);
                        Properties commonProps = new Properties();
                        try (InputStream in = Files.newInputStream(commonBnd)) {
                                commonProps.load(in);
                        }
                        String url = commonProps.getProperty(ARGEO_ORIGIN_URI.toString());
                        if (url == null) {
                                url = uris.getProperty(duDir.getFileName().toString());
                                if (url == null)
                                        throw new IllegalStateException("No url available for " + duDir);
                                commonProps.put(ARGEO_ORIGIN_URI.toString(), url);
                        }
                        Path downloaded = tryDownloadArchive(url, originBase);

                        FileSystem zipFs = FileSystems.newFileSystem(downloaded, (ClassLoader) null);

                        // filters
                        List<PathMatcher> includeMatchers = new ArrayList<>();
                        Properties includes = new Properties();
                        try (InputStream in = Files.newInputStream(duDir.resolve("includes.properties"))) {
                                includes.load(in);
                        }
                        for (Object pattern : includes.keySet()) {
                                PathMatcher pathMatcher = zipFs.getPathMatcher("glob:/" + pattern);
                                includeMatchers.add(pathMatcher);
                        }

                        List<PathMatcher> excludeMatchers = new ArrayList<>();
                        Path excludeFile = duDir.resolve("excludes.properties");
                        if (Files.exists(excludeFile)) {
                                Properties excludes = new Properties();
                                try (InputStream in = Files.newInputStream(excludeFile)) {
                                        excludes.load(in);
                                }
                                for (Object pattern : excludes.keySet()) {
                                        PathMatcher pathMatcher = zipFs.getPathMatcher("glob:/" + pattern);
                                        excludeMatchers.add(pathMatcher);
                                }
                        }

                        // keys are the bundle directories
                        Map<Path, A2Origin> origins = new HashMap<>();
                        Files.walkFileTree(zipFs.getRootDirectories().iterator().next(), new SimpleFileVisitor<Path>() {

                                @Override
                                public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) throws IOException {
                                        includeMatchers: for (PathMatcher includeMatcher : includeMatchers) {
                                                if (includeMatcher.matches(file)) {
                                                        for (PathMatcher excludeMatcher : excludeMatchers) {
                                                                if (excludeMatcher.matches(file)) {
                                                                        logger.log(TRACE, "Skipping excluded " + file);
                                                                        return FileVisitResult.CONTINUE;
                                                                }
                                                        }
                                                        if (file.getFileName().toString().contains(".source_")) {
                                                                processEclipseSourceJar(file, targetCategoryBase);
                                                                logger.log(DEBUG, () -> "Processed source " + file);
                                                        } else {
                                                                Map<String, String> map = new HashMap<>();
                                                                for (Object key : commonProps.keySet())
                                                                        map.put(key.toString(), commonProps.getProperty(key.toString()));
                                                                A2Origin origin = new A2Origin();
                                                                Path bundleDir = processBundleJar(file, targetCategoryBase, map, origin);
                                                                origins.put(bundleDir, origin);
                                                                logger.log(DEBUG, () -> "Processed " + file);
                                                        }
                                                        break includeMatchers;
                                                }
                                        }
                                        return FileVisitResult.CONTINUE;
                                }
                        });

                        DirectoryStream<Path> dirs = Files.newDirectoryStream(targetCategoryBase, (p) -> Files.isDirectory(p)
                                        && p.getFileName().toString().indexOf('.') >= 0 && !p.getFileName().toString().endsWith(".src"));
                        for (Path bundleDir : dirs) {
                                A2Origin origin = origins.get(bundleDir);
                                Objects.requireNonNull(origin, "No A2 origin found for " + bundleDir);
                                createJar(bundleDir, origin);
                        }
                } catch (IOException e) {
                        throw new RuntimeException("Cannot process " + duDir, e);
                }

        }

        /** Process sources in Eclipse format. */
        void processEclipseSourceJar(Path file, Path targetBase) throws IOException {
                try {
                        A2Origin origin = new A2Origin();
                        Path bundleDir;
                        try (JarInputStream jarIn = new JarInputStream(Files.newInputStream(file), false)) {
                                Manifest manifest = jarIn.getManifest();

                                String[] relatedBundle = manifest.getMainAttributes().getValue(ECLIPSE_SOURCE_BUNDLE.toString())
                                                .split(";");
                                String version = relatedBundle[1].substring("version=\"".length());
                                version = version.substring(0, version.length() - 1);
                                NameVersion nameVersion = new NameVersion(relatedBundle[0], version);
                                bundleDir = targetBase.resolve(nameVersion.getName() + "." + nameVersion.getBranch());

                                Path sourceDir = sourceBundles ? bundleDir.getParent().resolve(bundleDir.toString() + ".src")
                                                : bundleDir.resolve("OSGI-OPT/src");

                                Files.createDirectories(sourceDir);
                                JarEntry entry;
                                entries: while ((entry = jarIn.getNextJarEntry()) != null) {
                                        if (entry.isDirectory())
                                                continue entries;
                                        if (entry.getName().startsWith("META-INF"))// skip META-INF entries
                                                continue entries;
                                        Path target = sourceDir.resolve(entry.getName());
                                        Files.createDirectories(target.getParent());
                                        Files.copy(jarIn, target);
                                        logger.log(TRACE, () -> "Copied source " + target);
                                }

                                // write the changes
                                if (sourceBundles) {
                                        origin.appendChanges(sourceDir);
                                } else {
                                        origin.added.add("source code under OSGI-OPT/src");
                                        origin.appendChanges(bundleDir);
                                }
                        }
                } catch (IOException e) {
                        throw new IllegalStateException("Cannot process " + file, e);
                }
        }

        /*
         * COMMON PROCESSING
         */
        /** Normalise a bundle. */
        Path processBundleJar(Path file, Path targetBase, Map<String, String> entries, A2Origin origin) throws IOException {
                boolean embed = Boolean.parseBoolean(entries.getOrDefault(ARGEO_ORIGIN_EMBED.toString(), "false").toString());
                NameVersion nameVersion;
                Path bundleDir;
                // singleton
                boolean isSingleton = false;
                Manifest manifest;
                try (JarInputStream jarIn = new JarInputStream(Files.newInputStream(file), false)) {
                        Manifest sourceManifest = jarIn.getManifest();
                        manifest = sourceManifest != null ? new Manifest(sourceManifest) : new Manifest();

                        String rawSourceSymbolicName = manifest.getMainAttributes().getValue(BUNDLE_SYMBOLICNAME.toString());
                        if (rawSourceSymbolicName != null) {
                                // make sure there is no directive
                                String[] arr = rawSourceSymbolicName.split(";");
                                for (int i = 1; i < arr.length; i++) {
                                        if (arr[i].trim().equals("singleton:=true"))
                                                isSingleton = true;
                                        logger.log(DEBUG, file.getFileName() + " is a singleton");
                                }
                        }
                        // remove problematic entries in MANIFEST
                        manifest.getEntries().clear();

                        String ourSymbolicName = entries.get(BUNDLE_SYMBOLICNAME.toString());
                        String ourVersion = entries.get(BUNDLE_VERSION.toString());

                        if (ourSymbolicName != null && ourVersion != null) {
                                nameVersion = new NameVersion(ourSymbolicName, ourVersion);
                        } else {
                                nameVersion = nameVersionFromManifest(manifest);
                                if (ourVersion != null && !nameVersion.getVersion().equals(ourVersion)) {
                                        logger.log(WARNING,
                                                        "Original version is " + nameVersion.getVersion() + " while new version is " + ourVersion);
                                        entries.put(BUNDLE_VERSION.toString(), ourVersion);
                                }
                                if (ourSymbolicName != null) {
                                        // we always force our symbolic name
                                        nameVersion.setName(ourSymbolicName);
                                }
                        }
                        bundleDir = targetBase.resolve(nameVersion.getName() + "." + nameVersion.getBranch());

                        if (sourceManifest != null) {// copy original MANIFEST
                                Path originalManifest = bundleDir.resolve(A2_ORIGIN).resolve("MANIFEST.MF");
                                Files.createDirectories(originalManifest.getParent());
                                try (OutputStream out = Files.newOutputStream(originalManifest)) {
                                        sourceManifest.write(out);
                                }
                                origin.added.add("original MANIFEST (" + bundleDir.relativize(originalManifest) + ")");
                        }

                        // force Java 9 module name
                        entries.put(ManifestConstants.AUTOMATIC_MODULE_NAME.toString(), nameVersion.getName());

                        boolean isNative = false;
                        String os = null;
                        String arch = null;
                        if (bundleDir.startsWith(a2LibBase)) {
                                isNative = true;
                                Path libRelativePath = a2LibBase.relativize(bundleDir);
                                os = libRelativePath.getName(0).toString();
                                arch = libRelativePath.getName(1).toString();
                        }

                        if (!embed) {
                                // copy entries
                                JarEntry entry;
                                entries: while ((entry = jarIn.getNextJarEntry()) != null) {
                                        if (entry.isDirectory())
                                                continue entries;
                                        if (entry.getName().endsWith(".RSA") || entry.getName().endsWith(".SF")) {
                                                origin.deleted.add("cryptographic signatures");
                                                continue entries;
                                        }
                                        if (entry.getName().endsWith("module-info.class")) { // skip Java 9 module info
                                                origin.deleted.add("Java module information (module-info.class)");
                                                continue entries;
                                        }
                                        if (entry.getName().startsWith("META-INF/versions/")) { // skip multi-version
                                                origin.deleted.add("additional Java versions (META-INF/versions)");
                                                continue entries;
                                        }
                                        if (entry.getName().startsWith("META-INF/maven/")) {
                                                origin.deleted.add("Maven information (META-INF/maven)");
                                                continue entries;
                                        }
                                        // skip file system providers as they cause issues with native image
                                        if (entry.getName().startsWith("META-INF/services/java.nio.file.spi.FileSystemProvider")) {
                                                origin.deleted
                                                                .add("file system providers (META-INF/services/java.nio.file.spi.FileSystemProvider)");
                                                continue entries;
                                        }
                                        if (entry.getName().startsWith("OSGI-OPT/src/")) { // skip embedded sources
                                                origin.deleted.add("embedded sources");
                                                continue entries;
                                        }
                                        Path target = bundleDir.resolve(entry.getName());
                                        Files.createDirectories(target.getParent());
                                        Files.copy(jarIn, target);

                                        // native libraries
                                        if (isNative && (entry.getName().endsWith(".so") || entry.getName().endsWith(".dll")
                                                        || entry.getName().endsWith(".jnilib"))) {
                                                Path categoryDir = bundleDir.getParent();
                                                boolean copyDll = false;
                                                Path targetDll = categoryDir.resolve(bundleDir.relativize(target));
                                                if (nameVersion.getName().equals("com.sun.jna")) {
                                                        if (arch.equals("x86_64"))
                                                                arch = "x86-64";
                                                        if (os.equals("macosx"))
                                                                os = "darwin";
                                                        if (target.getParent().getFileName().toString().equals(os + "-" + arch)) {
                                                                copyDll = true;
                                                        }
                                                        targetDll = categoryDir.resolve(target.getFileName());
                                                } else {
                                                        copyDll = true;
                                                }
                                                if (copyDll) {
                                                        Files.createDirectories(targetDll.getParent());
                                                        if (Files.exists(targetDll))
                                                                Files.delete(targetDll);
                                                        Files.copy(target, targetDll);
                                                }
                                                Files.delete(target);
                                                origin.deleted.add(bundleDir.relativize(target).toString());
                                        }
                                        logger.log(TRACE, () -> "Copied " + target);
                                }
                        }
                }

                // copy MANIFEST
                Path manifestPath = bundleDir.resolve("META-INF/MANIFEST.MF");
                Files.createDirectories(manifestPath.getParent());

                if (isSingleton && entries.containsKey(BUNDLE_SYMBOLICNAME.toString())) {
                        entries.put(BUNDLE_SYMBOLICNAME.toString(),
                                        entries.get(BUNDLE_SYMBOLICNAME.toString()) + ";singleton:=true");
                }

                if (embed) {// copy embedded jar
                        Files.copy(file, bundleDir.resolve(file.getFileName()));
                        entries.put(ManifestConstants.BUNDLE_CLASSPATH.toString(), file.getFileName().toString());
                }

                // Final MANIFEST decisions
                // This also where we check the original OSGi metadata and compare with our
                // changes
                for (String key : entries.keySet()) {
                        String value = entries.get(key);
                        String previousValue = manifest.getMainAttributes().getValue(key);
                        boolean wasDifferent = previousValue != null && !previousValue.equals(value);
                        boolean keepPrevious = false;
                        if (wasDifferent) {
                                if (SPDX_LICENSE_IDENTIFIER.toString().equals(key) && previousValue != null)
                                        keepPrevious = true;
                                else if (BUNDLE_VERSION.toString().equals(key) && wasDifferent)
                                        if (previousValue.equals(value + ".0")) // typically a Maven first release
                                                keepPrevious = true;

                                if (keepPrevious) {
                                        if (logger.isLoggable(DEBUG))
                                                logger.log(DEBUG, file.getFileName() + ": " + key + " was NOT modified, value kept is "
                                                                + previousValue + ", not overriden with " + value);
                                        value = previousValue;
                                }
                        }

                        manifest.getMainAttributes().putValue(key, value);
                        if (wasDifferent && !keepPrevious) {
                                if (IMPORT_PACKAGE.toString().equals(key) || EXPORT_PACKAGE.toString().equals(key))
                                        logger.log(TRACE, () -> file.getFileName() + ": " + key + " was modified");
                                else
                                        logger.log(WARNING,
                                                        file.getFileName() + ": " + key + " was " + previousValue + ", overridden with " + value);
                        }

                        // de-pollute MANIFEST
                        switch (key) {
                        case "Archiver-Version":
                        case "Build-By":
                        case "Created-By":
                        case "Originally-Created-By":
                        case "Tool":
                        case "Bnd-LastModified":
                                manifest.getMainAttributes().remove(key);
                                break;
                        default: // do nothing
                        }

                        // !! hack to remove unresolvable
                        if (key.equals("Provide-Capability") || key.equals("Require-Capability"))
                                if (nameVersion.getName().equals("osgi.core") || nameVersion.getName().equals("osgi.cmpn")) {
                                        manifest.getMainAttributes().remove(key);
                                }
                }

                // license checks
                String spdxLicenceId = manifest.getMainAttributes().getValue(SPDX_LICENSE_IDENTIFIER.toString());
                String bundleLicense = manifest.getMainAttributes().getValue(BUNDLE_LICENSE.toString());
                if (spdxLicenceId == null) {
                        logger.log(ERROR, file.getFileName() + ": " + SPDX_LICENSE_IDENTIFIER + " not available, " + BUNDLE_LICENSE
                                        + " is " + bundleLicense);
                } else {
                        if (!licensesUsed.containsKey(spdxLicenceId))
                                licensesUsed.put(spdxLicenceId, new TreeSet<>());
                        licensesUsed.get(spdxLicenceId).add(nameVersion.toString());
                }

                origin.modified.add("jar MANIFEST (META-INF/MANIFEST.MF)");
                // write the MANIFEST
                try (OutputStream out = Files.newOutputStream(manifestPath)) {
                        manifest.write(out);
                }
                return bundleDir;
        }

        /*
         * UTILITIES
         */
        /** Recursively deletes a directory. */
        static void deleteDirectory(Path path) throws IOException {
                if (!Files.exists(path))
                        return;
                Files.walkFileTree(path, new SimpleFileVisitor<Path>() {
                        @Override
                        public FileVisitResult postVisitDirectory(Path directory, IOException e) throws IOException {
                                if (e != null)
                                        throw e;
                                Files.delete(directory);
                                return CONTINUE;
                        }

                        @Override
                        public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) throws IOException {
                                Files.delete(file);
                                return CONTINUE;
                        }
                });
        }

        /** Extract name/version from a MANIFEST. */
        NameVersion nameVersionFromManifest(Manifest manifest) {
                Attributes attrs = manifest.getMainAttributes();
                // symbolic name
                String symbolicName = attrs.getValue(ManifestConstants.BUNDLE_SYMBOLICNAME.toString());
                if (symbolicName == null)
                        return null;
                // make sure there is no directive
                symbolicName = symbolicName.split(";")[0];

                String version = attrs.getValue(ManifestConstants.BUNDLE_VERSION.toString());
                return new NameVersion(symbolicName, version);
        }

        /** Try to download from an URI. */
        Path tryDownloadArchive(String uri, Path dir) throws IOException {
                // find mirror
                List<String> urlBases = null;
                String uriPrefix = null;
                uriPrefixes: for (String uriPref : mirrors.keySet()) {
                        if (uri.startsWith(uriPref)) {
                                if (mirrors.get(uriPref).size() > 0) {
                                        urlBases = mirrors.get(uriPref);
                                        uriPrefix = uriPref;
                                        break uriPrefixes;
                                }
                        }
                }
                if (urlBases == null)
                        try {
                                return downloadArchive(new URL(uri), dir);
                        } catch (FileNotFoundException e) {
                                throw new FileNotFoundException("Cannot find " + uri);
                        }

                // try to download
                for (String urlBase : urlBases) {
                        String relativePath = uri.substring(uriPrefix.length());
                        URL url = new URL(urlBase + relativePath);
                        try {
                                return downloadArchive(url, dir);
                        } catch (FileNotFoundException e) {
                                logger.log(WARNING, "Cannot download " + url + ", trying another mirror");
                        }
                }
                throw new FileNotFoundException("Cannot find " + uri);
        }

        /**
         * Effectively download. Synchronised in order to avoid downloading twice in
         * parallel.
         */
        synchronized Path downloadArchive(URL url, Path dir) throws IOException {
                return download(url, dir, (String) null);
        }

        /** Effectively download. */
        Path download(URL url, Path dir, String name) throws IOException {

                Path dest;
                if (name == null) {
                        // We use also use parent directory in case the archive itself has a fixed name
                        String[] segments = url.getPath().split("/");
                        name = segments.length > 1 ? segments[segments.length - 2] + '-' + segments[segments.length - 1]
                                        : segments[segments.length - 1];
                }

                dest = dir.resolve(name);
                if (Files.exists(dest)) {
                        logger.log(TRACE, () -> "File " + dest + " already exists for " + url + ", not downloading again");
                        return dest;
                } else {
                        Files.createDirectories(dest.getParent());
                }

                try (InputStream in = url.openStream()) {
                        Files.copy(in, dest);
                        logger.log(DEBUG, () -> "Downloaded " + dest + " from " + url);
                }
                return dest;
        }

        /** Create a JAR file from a directory. */
        Path createJar(Path bundleDir, A2Origin origin) throws IOException {
                // write changes
                origin.appendChanges(bundleDir);
                // Create the jar
                Path jarPath = bundleDir.getParent().resolve(bundleDir.getFileName() + ".jar");
                Path manifestPath = bundleDir.resolve("META-INF/MANIFEST.MF");
                Manifest manifest;
                try (InputStream in = Files.newInputStream(manifestPath)) {
                        manifest = new Manifest(in);
                }
                try (JarOutputStream jarOut = new JarOutputStream(Files.newOutputStream(jarPath), manifest)) {
                        jarOut.setLevel(Deflater.DEFAULT_COMPRESSION);
                        Files.walkFileTree(bundleDir, new SimpleFileVisitor<Path>() {

                                @Override
                                public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) throws IOException {
                                        if (file.getFileName().toString().equals("MANIFEST.MF"))
                                                return super.visitFile(file, attrs);
                                        JarEntry entry = new JarEntry(
                                                        bundleDir.relativize(file).toString().replace(File.separatorChar, '/'));
                                        jarOut.putNextEntry(entry);
                                        Files.copy(file, jarOut);
                                        return super.visitFile(file, attrs);
                                }

                        });
                }
                deleteDirectory(bundleDir);

                if (sourceBundles) {
                        Path bundleCategoryDir = bundleDir.getParent();
                        Path sourceDir = bundleCategoryDir.resolve(bundleDir.toString() + ".src");
                        if (!Files.exists(sourceDir)) {
                                logger.log(WARNING, sourceDir + " does not exist, skipping...");
                                return jarPath;

                        }

                        Path relPath = a2Base.relativize(bundleCategoryDir);
                        Path srcCategoryDir = a2SrcBase.resolve(relPath);
                        Path srcJarP = srcCategoryDir.resolve(sourceDir.getFileName() + ".jar");
                        Files.createDirectories(srcJarP.getParent());

                        String bundleSymbolicName = manifest.getMainAttributes().getValue("Bundle-SymbolicName").toString();
                        // in case there are additional directives
                        bundleSymbolicName = bundleSymbolicName.split(";")[0];
                        Manifest srcManifest = new Manifest();
                        srcManifest.getMainAttributes().put(MANIFEST_VERSION, "1.0");
                        srcManifest.getMainAttributes().putValue(BUNDLE_SYMBOLICNAME.toString(), bundleSymbolicName + ".src");
                        srcManifest.getMainAttributes().putValue(BUNDLE_VERSION.toString(),
                                        manifest.getMainAttributes().getValue(BUNDLE_VERSION.toString()).toString());
                        srcManifest.getMainAttributes().putValue(ECLIPSE_SOURCE_BUNDLE.toString(), bundleSymbolicName
                                        + ";version=\"" + manifest.getMainAttributes().getValue(BUNDLE_VERSION.toString()));

                        try (JarOutputStream srcJarOut = new JarOutputStream(Files.newOutputStream(srcJarP), srcManifest)) {
                                srcJarOut.setLevel(Deflater.BEST_COMPRESSION);
                                Files.walkFileTree(sourceDir, new SimpleFileVisitor<Path>() {

                                        @Override
                                        public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) throws IOException {
                                                if (file.getFileName().toString().equals("MANIFEST.MF"))
                                                        return super.visitFile(file, attrs);
                                                JarEntry entry = new JarEntry(
                                                                sourceDir.relativize(file).toString().replace(File.separatorChar, '/'));
                                                srcJarOut.putNextEntry(entry);
                                                Files.copy(file, srcJarOut);
                                                return super.visitFile(file, attrs);
                                        }

                                });
                        }
                        deleteDirectory(sourceDir);
                }

                return jarPath;
        }

        /** MANIFEST headers. */
        enum ManifestConstants {
                // OSGi
                /** OSGi bundle symbolic name. */
                BUNDLE_SYMBOLICNAME("Bundle-SymbolicName"), //
                /** OSGi bundle version. */
                BUNDLE_VERSION("Bundle-Version"), //
                /** OSGi bundle license. */
                BUNDLE_LICENSE("Bundle-License"), //
                /** OSGi exported packages list. */
                EXPORT_PACKAGE("Export-Package"), //
                /** OSGi imported packages list. */
                IMPORT_PACKAGE("Import-Package"), //
                /** OSGi path to embedded jar. */
                BUNDLE_CLASSPATH("Bundle-Classpath"), //
                // Java
                /** Java module name. */
                AUTOMATIC_MODULE_NAME("Automatic-Module-Name"), //
                // Eclipse
                /** Eclipse source bundle. */
                ECLIPSE_SOURCE_BUNDLE("Eclipse-SourceBundle"), //
                // SPDX
                /**
                 * SPDX license identifier.
                 * 
                 * @see https://spdx.org/licenses/
                 */
                SPDX_LICENSE_IDENTIFIER("SPDX-License-Identifier"), //
                // Argeo Origin
                /**
                 * Maven coordinates of the origin, possibly partial when using common.bnd or
                 * merge.bnd.
                 */
                ARGEO_ORIGIN_M2("Argeo-Origin-M2"), //
                /** List of Maven coordinates to merge. */
                ARGEO_ORIGIN_M2_MERGE("Argeo-Origin-M2-Merge"), //
                /** Maven repository, if not the default one. */
                ARGEO_ORIGIN_M2_REPO("Argeo-Origin-M2-Repo"), //
                /**
                 * Do not perform BND analysis of the origin component. Typically IMport_package
                 * and Export-Package will be kept untouched.
                 */
                ARGEO_ORIGIN_MANIFEST_NOT_MODIFIED("Argeo-Origin-ManifestNotModified"), //
                /**
                 * Embed the original jar without modifying it (may be required by some
                 * proprietary licenses, such as JCR Day License).
                 */
                ARGEO_ORIGIN_EMBED("Argeo-Origin-Embed"), //
                /**
                 * Origin (non-Maven) URI of the component. It may be anything (jar, archive,
                 * etc.).
                 */
                ARGEO_ORIGIN_URI("Argeo-Origin-URI"), //
                ;

                final String value;

                private ManifestConstants(String value) {
                        this.value = value;
                }

                @Override
                public String toString() {
                        return value;
                }
        }
}

/**
 * Gathers modifications performed on the original binaries and sources,
 * especially in order to comply with their license requirements.
 */
class A2Origin {
        Set<String> modified = new TreeSet<>();
        Set<String> deleted = new TreeSet<>();
        Set<String> added = new TreeSet<>();
        Set<String> moved = new TreeSet<>();

        /** Append changes to the A2-ORIGIN/changes file. */
        void appendChanges(Path baseDirectory) throws IOException {
                Path changesFile = baseDirectory.resolve("A2-ORIGIN/changes");
                Files.createDirectories(changesFile.getParent());
                try (BufferedWriter writer = Files.newBufferedWriter(changesFile, StandardOpenOption.APPEND,
                                StandardOpenOption.CREATE)) {
                        for (String msg : added)
                                writer.write("- Added " + msg + ".\n");
                        for (String msg : modified)
                                writer.write("- Modified " + msg + ".\n");
                        for (String msg : moved)
                                writer.write("- Moved " + msg + ".\n");
                        for (String msg : deleted)
                                writer.write("- Deleted " + msg + ".\n");
                }
        }
}

/** Simple representation of an M2 artifact. */
class M2Artifact extends CategoryNameVersion {
        private String classifier;

        M2Artifact(String m2coordinates) {
                this(m2coordinates, null);
        }

        M2Artifact(String m2coordinates, String classifier) {
                String[] parts = m2coordinates.split(":");
                setCategory(parts[0]);
                setName(parts[1]);
                if (parts.length > 2) {
                        setVersion(parts[2]);
                }
                this.classifier = classifier;
        }

        String getGroupId() {
                return super.getCategory();
        }

        String getArtifactId() {
                return super.getName();
        }

        String toM2Coordinates() {
                return getCategory() + ":" + getName() + (getVersion() != null ? ":" + getVersion() : "");
        }

        String getClassifier() {
                return classifier != null ? classifier : "";
        }

        String getExtension() {
                return "jar";
        }
}

/** Utilities around Maven (conventions based). */
class M2ConventionsUtils {
        final static String MAVEN_CENTRAL_BASE_URL = "https://repo1.maven.org/maven2/";

        /** The file name of this artifact when stored */
        static String artifactFileName(M2Artifact artifact) {
                return artifact.getArtifactId() + '-' + artifact.getVersion()
                                + (artifact.getClassifier().equals("") ? "" : '-' + artifact.getClassifier()) + '.'
                                + artifact.getExtension();
        }

        /** Absolute path to the file */
        static String artifactPath(String artifactBasePath, M2Artifact artifact) {
                return artifactParentPath(artifactBasePath, artifact) + '/' + artifactFileName(artifact);
        }

        /** Absolute path to the file */
        static String artifactUrl(String repoUrl, M2Artifact artifact) {
                if (repoUrl.endsWith("/"))
                        return repoUrl + artifactPath("/", artifact).substring(1);
                else
                        return repoUrl + artifactPath("/", artifact);
        }

        /** Absolute path to the file */
        static URL mavenRepoUrl(String repoBase, M2Artifact artifact) {
                String url = artifactUrl(repoBase == null ? MAVEN_CENTRAL_BASE_URL : repoBase, artifact);
                try {
                        return new URL(url);
                } catch (MalformedURLException e) {
                        // it should not happen
                        throw new IllegalStateException(e);
                }
        }

        /** Absolute path to the directories where the files will be stored */
        static String artifactParentPath(String artifactBasePath, M2Artifact artifact) {
                return artifactBasePath + (artifactBasePath.endsWith("/") ? "" : "/") + artifactParentPath(artifact);
        }

        /** Relative path to the directories where the files will be stored */
        static String artifactParentPath(M2Artifact artifact) {
                return artifact.getGroupId().replace('.', '/') + '/' + artifact.getArtifactId() + '/' + artifact.getVersion();
        }

        /** Singleton */
        private M2ConventionsUtils() {
        }
}

/** Combination of a category, a name and a version. */
class CategoryNameVersion extends NameVersion {
        private String category;

        CategoryNameVersion() {
        }

        CategoryNameVersion(String category, String name, String version) {
                super(name, version);
                this.category = category;
        }

        CategoryNameVersion(String category, NameVersion nameVersion) {
                super(nameVersion);
                this.category = category;
        }

        String getCategory() {
                return category;
        }

        void setCategory(String category) {
                this.category = category;
        }

        @Override
        public String toString() {
                return category + ":" + super.toString();
        }

}

/** Combination of a name and a version. */
class NameVersion implements Comparable<NameVersion> {
        private String name;
        private String version;

        NameVersion() {
        }

        /** Interprets string in OSGi-like format my.module.name;version=0.0.0 */
        NameVersion(String nameVersion) {
                int index = nameVersion.indexOf(";version=");
                if (index < 0) {
                        setName(nameVersion);
                        setVersion(null);
                } else {
                        setName(nameVersion.substring(0, index));
                        setVersion(nameVersion.substring(index + ";version=".length()));
                }
        }

        NameVersion(String name, String version) {
                this.name = name;
                this.version = version;
        }

        NameVersion(NameVersion nameVersion) {
                this.name = nameVersion.getName();
                this.version = nameVersion.getVersion();
        }

        String getName() {
                return name;
        }

        void setName(String name) {
                this.name = name;
        }

        String getVersion() {
                return version;
        }

        void setVersion(String version) {
                this.version = version;
        }

        String getBranch() {
                String[] parts = getVersion().split("\\.");
                if (parts.length < 2)
                        throw new IllegalStateException("Version " + getVersion() + " cannot be interpreted as branch.");
                return parts[0] + "." + parts[1];
        }

        @Override
        public boolean equals(Object obj) {
                if (obj instanceof NameVersion) {
                        NameVersion nameVersion = (NameVersion) obj;
                        return name.equals(nameVersion.getName()) && version.equals(nameVersion.getVersion());
                } else
                        return false;
        }

        @Override
        public int hashCode() {
                return name.hashCode();
        }

        @Override
        public String toString() {
                return name + ":" + version;
        }

        public int compareTo(NameVersion o) {
                if (o.getName().equals(name))
                        return version.compareTo(o.getVersion());
                else
                        return name.compareTo(o.getName());
        }
}