langtools/src/jdk.compiler/share/classes/com/sun/tools/sjavac/JavacState.java
changeset 25874 83c19f00452c
parent 25299 b4a7dcd657f5
child 26107 a4a156a33c94
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/langtools/src/jdk.compiler/share/classes/com/sun/tools/sjavac/JavacState.java	Sun Aug 17 15:52:32 2014 +0100
@@ -0,0 +1,861 @@
+/*
+ * Copyright (c) 2012, 2014, Oracle and/or its affiliates. All rights reserved.
+ * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
+ *
+ * This code is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU General Public License version 2 only, as
+ * published by the Free Software Foundation.  Oracle designates this
+ * particular file as subject to the "Classpath" exception as provided
+ * by Oracle in the LICENSE file that accompanied this code.
+ *
+ * This code is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ * FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
+ * version 2 for more details (a copy is included in the LICENSE file that
+ * accompanied this code).
+ *
+ * You should have received a copy of the GNU General Public License version
+ * 2 along with this work; if not, write to the Free Software Foundation,
+ * Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * Please contact Oracle, 500 Oracle Parkway, Redwood Shores, CA 94065 USA
+ * or visit www.oracle.com if you need additional information or have any
+ * questions.
+ */
+
+package com.sun.tools.sjavac;
+
+import java.io.*;
+import java.nio.file.Path;
+import java.util.Collections;
+import java.util.Date;
+import java.util.Set;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.HashMap;
+import java.text.SimpleDateFormat;
+import java.net.URI;
+import java.util.*;
+
+import com.sun.tools.sjavac.options.Options;
+import com.sun.tools.sjavac.options.SourceLocation;
+import com.sun.tools.sjavac.server.JavacService;
+
+/**
+ * The javac state class maintains the previous (prev) and the current (now)
+ * build states and everything else that goes into the javac_state file.
+ *
+ * <p><b>This is NOT part of any supported API.
+ * If you write code that depends on this, you do so at your own
+ * risk.  This code and its internal interfaces are subject to change
+ * or deletion without notice.</b></p>
+ */
+public class JavacState
+{
+    // The arguments to the compile. If not identical, then it cannot
+    // be an incremental build!
+    String theArgs;
+    // The number of cores limits how many threads are used for heavy concurrent work.
+    int numCores;
+
+    // The bin_dir/javac_state
+    private String javacStateFilename;
+    private File javacState;
+
+    // The previous build state is loaded from javac_state
+    private BuildState prev;
+    // The current build state is constructed during the build,
+    // then saved as the new javac_state.
+    private BuildState now;
+
+    // Something has changed in the javac_state. It needs to be saved!
+    private boolean needsSaving;
+    // If this is a new javac_state file, then do not print unnecessary messages.
+    private boolean newJavacState;
+
+    // These are packages where something has changed and the package
+    // needs to be recompiled. Actions that trigger recompilation:
+    // * source belonging to the package has changed
+    // * artifact belonging to the package is lost, or its timestamp has been changed.
+    // * an unknown artifact has appeared, we simply delete it, but we also trigger a recompilation.
+    // * a package that is tainted, taints all packages that depend on it.
+    private Set<String> taintedPackages;
+    // After a compile, the pubapis are compared with the pubapis stored in the javac state file.
+    // Any packages where the pubapi differ are added to this set.
+    // Later we use this set and the dependency information to taint dependent packages.
+    private Set<String> packagesWithChangedPublicApis;
+    // When a module-info.java file is changed, taint the module,
+    // then taint all modules that depend on that that module.
+    // A module dependency can occur directly through a require, or
+    // indirectly through a module that does a public export for the first tainted module.
+    // When all modules are tainted, then taint all packages belonging to these modules.
+    // Then rebuild. It is perhaps possible (and valuable?) to do a more finegrained examination of the
+    // change in module-info.java, but that will have to wait.
+    private Set<String> taintedModules;
+    // The set of all packages that has been recompiled.
+    // Copy over the javac_state for the packages that did not need recompilation,
+    // verbatim from the previous (prev) to the new (now) build state.
+    private Set<String> recompiledPackages;
+
+    // The output directories filled with tasty artifacts.
+    private File binDir, gensrcDir, headerDir;
+
+    // The current status of the file system.
+    private Set<File> binArtifacts;
+    private Set<File> gensrcArtifacts;
+    private Set<File> headerArtifacts;
+
+    // The status of the sources.
+    Set<Source> removedSources = null;
+    Set<Source> addedSources = null;
+    Set<Source> modifiedSources = null;
+
+    // Visible sources for linking. These are the only
+    // ones that -sourcepath is allowed to see.
+    Set<URI> visibleSrcs;
+
+    // Visible classes for linking. These are the only
+    // ones that -classpath is allowed to see.
+    // It maps from a classpath root to the set of visible classes for that root.
+    // If the set is empty, then all classes are visible for that root.
+    // It can also map from a jar file to the set of visible classes for that jar file.
+    Map<URI,Set<String>> visibleClasses;
+
+    // Setup transform that always exist.
+    private CompileJavaPackages compileJavaPackages = new CompileJavaPackages();
+
+    // Where to send stdout and stderr.
+    private PrintStream out, err;
+
+    JavacState(Options options, boolean removeJavacState, PrintStream o, PrintStream e) {
+        out = o;
+        err = e;
+        numCores = options.getNumCores();
+        theArgs = options.getStateArgsString();
+        binDir = Util.pathToFile(options.getDestDir());
+        gensrcDir = Util.pathToFile(options.getGenSrcDir());
+        headerDir = Util.pathToFile(options.getHeaderDir());
+        javacStateFilename = binDir.getPath()+File.separator+"javac_state";
+        javacState = new File(javacStateFilename);
+        if (removeJavacState && javacState.exists()) {
+            javacState.delete();
+        }
+        newJavacState = false;
+        if (!javacState.exists()) {
+            newJavacState = true;
+            // If there is no javac_state then delete the contents of all the artifact dirs!
+            // We do not want to risk building a broken incremental build.
+            // BUT since the makefiles still copy things straight into the bin_dir et al,
+            // we avoid deleting files here, if the option --permit-unidentified-classes was supplied.
+            if (!options.isUnidentifiedArtifactPermitted()) {
+                deleteContents(binDir);
+                deleteContents(gensrcDir);
+                deleteContents(headerDir);
+            }
+            needsSaving = true;
+        }
+        prev = new BuildState();
+        now = new BuildState();
+        taintedPackages = new HashSet<>();
+        recompiledPackages = new HashSet<>();
+        packagesWithChangedPublicApis = new HashSet<>();
+    }
+
+    public BuildState prev() { return prev; }
+    public BuildState now() { return now; }
+
+    /**
+     * Remove args not affecting the state.
+     */
+    static String[] removeArgsNotAffectingState(String[] args) {
+        String[] out = new String[args.length];
+        int j = 0;
+        for (int i = 0; i<args.length; ++i) {
+            if (args[i].equals("-j")) {
+                // Just skip it and skip following value
+                i++;
+            } else if (args[i].startsWith("--server:")) {
+                // Just skip it.
+            } else if (args[i].startsWith("--log=")) {
+                // Just skip it.
+            } else if (args[i].equals("--compare-found-sources")) {
+                // Just skip it and skip verify file name
+                i++;
+            } else {
+                // Copy argument.
+                out[j] = args[i];
+                j++;
+            }
+        }
+        String[] ret = new String[j];
+        System.arraycopy(out, 0, ret, 0, j);
+        return ret;
+    }
+
+    /**
+     * Specify which sources are visible to the compiler through -sourcepath.
+     */
+    public void setVisibleSources(Map<String,Source> vs) {
+        visibleSrcs = new HashSet<>();
+        for (String s : vs.keySet()) {
+            Source src = vs.get(s);
+            visibleSrcs.add(src.file().toURI());
+        }
+    }
+
+    /**
+     * Specify which classes are visible to the compiler through -classpath.
+     */
+    public void setVisibleClasses(Map<String,Source> vs) {
+        visibleSrcs = new HashSet<>();
+        for (String s : vs.keySet()) {
+            Source src = vs.get(s);
+            visibleSrcs.add(src.file().toURI());
+        }
+    }
+    /**
+     * Returns true if this is an incremental build.
+     */
+    public boolean isIncremental() {
+        return !prev.sources().isEmpty();
+    }
+
+    /**
+     * Find all artifacts that exists on disk.
+     */
+    public void findAllArtifacts() {
+        binArtifacts = findAllFiles(binDir);
+        gensrcArtifacts = findAllFiles(gensrcDir);
+        headerArtifacts = findAllFiles(headerDir);
+    }
+
+    /**
+     * Lookup the artifacts generated for this package in the previous build.
+     */
+    private Map<String,File> fetchPrevArtifacts(String pkg) {
+        Package p = prev.packages().get(pkg);
+        if (p != null) {
+            return p.artifacts();
+        }
+        return new HashMap<>();
+    }
+
+    /**
+     * Delete all prev artifacts in the currently tainted packages.
+     */
+    public void deleteClassArtifactsInTaintedPackages() {
+        for (String pkg : taintedPackages) {
+            Map<String,File> arts = fetchPrevArtifacts(pkg);
+            for (File f : arts.values()) {
+                if (f.exists() && f.getName().endsWith(".class")) {
+                    f.delete();
+                }
+            }
+        }
+    }
+
+    /**
+     * Mark the javac_state file to be in need of saving and as a side effect,
+     * it gets a new timestamp.
+     */
+    private void needsSaving() {
+        needsSaving = true;
+    }
+
+    /**
+     * Save the javac_state file.
+     */
+    public void save() throws IOException {
+        if (!needsSaving) return;
+        try (FileWriter out = new FileWriter(javacStateFilename)) {
+            StringBuilder b = new StringBuilder();
+            long millisNow = System.currentTimeMillis();
+            Date d = new Date(millisNow);
+            SimpleDateFormat df =
+                new SimpleDateFormat("yyyy-MM-dd HH:mm:ss SSS");
+            b.append("# javac_state ver 0.3 generated "+millisNow+" "+df.format(d)+"\n");
+            b.append("# This format might change at any time. Please do not depend on it.\n");
+            b.append("# M module\n");
+            b.append("# P package\n");
+            b.append("# S C source_tobe_compiled timestamp\n");
+            b.append("# S L link_only_source timestamp\n");
+            b.append("# G C generated_source timestamp\n");
+            b.append("# A artifact timestamp\n");
+            b.append("# D dependency\n");
+            b.append("# I pubapi\n");
+            b.append("# R arguments\n");
+            b.append("R ").append(theArgs).append("\n");
+
+            // Copy over the javac_state for the packages that did not need recompilation.
+            now.copyPackagesExcept(prev, recompiledPackages, new HashSet<String>());
+            // Save the packages, ie package names, dependencies, pubapis and artifacts!
+            // I.e. the lot.
+            Module.saveModules(now.modules(), b);
+
+            String s = b.toString();
+            out.write(s, 0, s.length());
+        }
+    }
+
+    /**
+     * Load a javac_state file.
+     */
+    public static JavacState load(Options options, PrintStream out, PrintStream err) {
+        JavacState db = new JavacState(options, false, out, err);
+        Module  lastModule = null;
+        Package lastPackage = null;
+        Source  lastSource = null;
+        boolean noFileFound = false;
+        boolean foundCorrectVerNr = false;
+        boolean newCommandLine = false;
+        boolean syntaxError = false;
+
+        try (BufferedReader in = new BufferedReader(new FileReader(db.javacStateFilename))) {
+            for (;;) {
+                String l = in.readLine();
+                if (l==null) break;
+                if (l.length()>=3 && l.charAt(1) == ' ') {
+                    char c = l.charAt(0);
+                    if (c == 'M') {
+                        lastModule = db.prev.loadModule(l);
+                    } else
+                    if (c == 'P') {
+                        if (lastModule == null) { syntaxError = true; break; }
+                        lastPackage = db.prev.loadPackage(lastModule, l);
+                    } else
+                    if (c == 'D') {
+                        if (lastModule == null || lastPackage == null) { syntaxError = true; break; }
+                        lastPackage.loadDependency(l);
+                    } else
+                    if (c == 'I') {
+                        if (lastModule == null || lastPackage == null) { syntaxError = true; break; }
+                        lastPackage.loadPubapi(l);
+                    } else
+                    if (c == 'A') {
+                        if (lastModule == null || lastPackage == null) { syntaxError = true; break; }
+                        lastPackage.loadArtifact(l);
+                    } else
+                    if (c == 'S') {
+                        if (lastModule == null || lastPackage == null) { syntaxError = true; break; }
+                        lastSource = db.prev.loadSource(lastPackage, l, false);
+                    } else
+                    if (c == 'G') {
+                        if (lastModule == null || lastPackage == null) { syntaxError = true; break; }
+                        lastSource = db.prev.loadSource(lastPackage, l, true);
+                    } else
+                    if (c == 'R') {
+                        String ncmdl = "R "+db.theArgs;
+                        if (!l.equals(ncmdl)) {
+                            newCommandLine = true;
+                        }
+                    } else
+                         if (c == '#') {
+                        if (l.startsWith("# javac_state ver ")) {
+                            int sp = l.indexOf(" ", 18);
+                            if (sp != -1) {
+                                String ver = l.substring(18,sp);
+                                if (!ver.equals("0.3")) {
+                    break;
+                                 }
+                foundCorrectVerNr = true;
+                            }
+                        }
+                    }
+                }
+            }
+        } catch (FileNotFoundException e) {
+            // Silently create a new javac_state file.
+            noFileFound = true;
+        } catch (IOException e) {
+            Log.info("Dropping old javac_state because of errors when reading it.");
+            db = new JavacState(options, true, out, err);
+            foundCorrectVerNr = true;
+            newCommandLine = false;
+            syntaxError = false;
+    }
+        if (foundCorrectVerNr == false && !noFileFound) {
+            Log.info("Dropping old javac_state since it is of an old version.");
+            db = new JavacState(options, true, out, err);
+        } else
+        if (newCommandLine == true && !noFileFound) {
+            Log.info("Dropping old javac_state since a new command line is used!");
+            db = new JavacState(options, true, out, err);
+        } else
+        if (syntaxError == true) {
+            Log.info("Dropping old javac_state since it contains syntax errors.");
+            db = new JavacState(options, true, out, err);
+        }
+        db.prev.calculateDependents();
+        return db;
+    }
+
+    /**
+     * Mark a java package as tainted, ie it needs recompilation.
+     */
+    public void taintPackage(String name, String because) {
+        if (!taintedPackages.contains(name)) {
+            if (because != null) Log.debug("Tainting "+Util.justPackageName(name)+" because "+because);
+            // It has not been tainted before.
+            taintedPackages.add(name);
+            needsSaving();
+            Package nowp = now.packages().get(name);
+            if (nowp != null) {
+                for (String d : nowp.dependents()) {
+                    taintPackage(d, because);
+                }
+            }
+        }
+    }
+
+    /**
+     * This packages need recompilation.
+     */
+    public Set<String> taintedPackages() {
+        return taintedPackages;
+    }
+
+    /**
+     * Clean out the tainted package set, used after the first round of compiles,
+     * prior to propagating dependencies.
+     */
+    public void clearTaintedPackages() {
+        taintedPackages = new HashSet<>();
+    }
+
+    /**
+     * Go through all sources and check which have been removed, added or modified
+     * and taint the corresponding packages.
+     */
+    public void checkSourceStatus(boolean check_gensrc) {
+        removedSources = calculateRemovedSources();
+        for (Source s : removedSources) {
+            if (!s.isGenerated() || check_gensrc) {
+                taintPackage(s.pkg().name(), "source "+s.name()+" was removed");
+            }
+        }
+
+        addedSources = calculateAddedSources();
+        for (Source s : addedSources) {
+            String msg = null;
+            if (isIncremental()) {
+                // When building from scratch, there is no point
+                // printing "was added" for every file since all files are added.
+                // However for an incremental build it makes sense.
+                msg = "source "+s.name()+" was added";
+            }
+            if (!s.isGenerated() || check_gensrc) {
+                taintPackage(s.pkg().name(), msg);
+            }
+        }
+
+        modifiedSources = calculateModifiedSources();
+        for (Source s : modifiedSources) {
+            if (!s.isGenerated() || check_gensrc) {
+                taintPackage(s.pkg().name(), "source "+s.name()+" was modified");
+            }
+        }
+    }
+
+    /**
+     * Acquire the compile_java_packages suffix rule for .java files.
+     */
+    public Map<String,Transformer> getJavaSuffixRule() {
+        Map<String,Transformer> sr = new HashMap<>();
+        sr.put(".java", compileJavaPackages);
+        return sr;
+    }
+
+
+    /**
+     * If artifacts have gone missing, force a recompile of the packages
+     * they belong to.
+     */
+    public void taintPackagesThatMissArtifacts() {
+        for (Package pkg : prev.packages().values()) {
+            for (File f : pkg.artifacts().values()) {
+                if (!f.exists()) {
+                    // Hmm, the artifact on disk does not exist! Someone has removed it....
+                    // Lets rebuild the package.
+                    taintPackage(pkg.name(), ""+f+" is missing.");
+                }
+            }
+        }
+    }
+
+    /**
+     * Propagate recompilation through the dependency chains.
+     * Avoid re-tainting packages that have already been compiled.
+     */
+    public void taintPackagesDependingOnChangedPackages(Set<String> pkgs, Set<String> recentlyCompiled) {
+        for (Package pkg : prev.packages().values()) {
+            for (String dep : pkg.dependencies()) {
+                if (pkgs.contains(dep) && !recentlyCompiled.contains(pkg.name())) {
+                    taintPackage(pkg.name(), " its depending on "+dep);
+                }
+            }
+        }
+    }
+
+    /**
+     * Scan all output dirs for artifacts and remove those files (artifacts?)
+     * that are not recognized as such, in the javac_state file.
+     */
+    public void removeUnidentifiedArtifacts() {
+        Set<File> allKnownArtifacts = new HashSet<>();
+        for (Package pkg : prev.packages().values()) {
+            for (File f : pkg.artifacts().values()) {
+                allKnownArtifacts.add(f);
+            }
+        }
+        // Do not forget about javac_state....
+        allKnownArtifacts.add(javacState);
+
+        for (File f : binArtifacts) {
+            if (!allKnownArtifacts.contains(f)) {
+                Log.debug("Removing "+f.getPath()+" since it is unknown to the javac_state.");
+                f.delete();
+            }
+        }
+        for (File f : headerArtifacts) {
+            if (!allKnownArtifacts.contains(f)) {
+                Log.debug("Removing "+f.getPath()+" since it is unknown to the javac_state.");
+                f.delete();
+            }
+        }
+        for (File f : gensrcArtifacts) {
+            if (!allKnownArtifacts.contains(f)) {
+                Log.debug("Removing "+f.getPath()+" since it is unknown to the javac_state.");
+                f.delete();
+            }
+        }
+    }
+
+    /**
+     * Remove artifacts that are no longer produced when compiling!
+     */
+    public void removeSuperfluousArtifacts(Set<String> recentlyCompiled) {
+        // Nothing to do, if nothing was recompiled.
+        if (recentlyCompiled.size() == 0) return;
+
+        for (String pkg : now.packages().keySet()) {
+            // If this package has not been recompiled, skip the check.
+            if (!recentlyCompiled.contains(pkg)) continue;
+            Collection<File> arts = now.artifacts().values();
+            for (File f : fetchPrevArtifacts(pkg).values()) {
+                if (!arts.contains(f)) {
+                    Log.debug("Removing "+f.getPath()+" since it is now superfluous!");
+                    if (f.exists()) f.delete();
+                }
+            }
+        }
+    }
+
+    /**
+     * Return those files belonging to prev, but not now.
+     */
+    private Set<Source> calculateRemovedSources() {
+        Set<Source> removed = new HashSet<>();
+        for (String src : prev.sources().keySet()) {
+            if (now.sources().get(src) == null) {
+                removed.add(prev.sources().get(src));
+            }
+        }
+        return removed;
+    }
+
+    /**
+     * Return those files belonging to now, but not prev.
+     */
+    private Set<Source> calculateAddedSources() {
+        Set<Source> added = new HashSet<>();
+        for (String src : now.sources().keySet()) {
+            if (prev.sources().get(src) == null) {
+                added.add(now.sources().get(src));
+            }
+        }
+        return added;
+    }
+
+    /**
+     * Return those files where the timestamp is newer.
+     * If a source file timestamp suddenly is older than what is known
+     * about it in javac_state, then consider it modified, but print
+     * a warning!
+     */
+    private Set<Source> calculateModifiedSources() {
+        Set<Source> modified = new HashSet<>();
+        for (String src : now.sources().keySet()) {
+            Source n = now.sources().get(src);
+            Source t = prev.sources().get(src);
+            if (prev.sources().get(src) != null) {
+                if (t != null) {
+                    if (n.lastModified() > t.lastModified()) {
+                        modified.add(n);
+                    } else if (n.lastModified() < t.lastModified()) {
+                        modified.add(n);
+                        Log.warn("The source file "+n.name()+" timestamp has moved backwards in time.");
+                    }
+                }
+            }
+        }
+        return modified;
+    }
+
+    /**
+     * Recursively delete a directory and all its contents.
+     */
+    private static void deleteContents(File dir) {
+        if (dir != null && dir.exists()) {
+            for (File f : dir.listFiles()) {
+                if (f.isDirectory()) {
+                    deleteContents(f);
+                }
+                f.delete();
+            }
+        }
+    }
+
+    /**
+     * Run the copy translator only.
+     */
+    public void performCopying(File binDir, Map<String,Transformer> suffixRules) {
+        Map<String,Transformer> sr = new HashMap<>();
+        for (Map.Entry<String,Transformer> e : suffixRules.entrySet()) {
+            if (e.getValue().getClass().equals(CopyFile.class)) {
+                sr.put(e.getKey(), e.getValue());
+            }
+        }
+        perform(null, binDir, sr);
+    }
+
+    /**
+     * Run all the translators that translate into java source code.
+     * I.e. all translators that are not copy nor compile_java_source.
+     */
+    public void performTranslation(File gensrcDir, Map<String,Transformer> suffixRules) {
+        Map<String,Transformer> sr = new HashMap<>();
+        for (Map.Entry<String,Transformer> e : suffixRules.entrySet()) {
+            Class<?> trClass = e.getValue().getClass();
+            if (trClass == CompileJavaPackages.class || trClass == CopyFile.class)
+                continue;
+
+            sr.put(e.getKey(), e.getValue());
+        }
+        perform(null, gensrcDir, sr);
+    }
+
+    /**
+     * Compile all the java sources. Return true, if it needs to be called again!
+     */
+    public boolean performJavaCompilations(JavacService javacService,
+                                           Options args,
+                                           Set<String> recentlyCompiled,
+                                           boolean[] rcValue) {
+        Map<String,Transformer> suffixRules = new HashMap<>();
+        suffixRules.put(".java", compileJavaPackages);
+        compileJavaPackages.setExtra(args);
+
+        rcValue[0] = perform(javacService, binDir, suffixRules);
+        recentlyCompiled.addAll(taintedPackages());
+        clearTaintedPackages();
+        boolean again = !packagesWithChangedPublicApis.isEmpty();
+        taintPackagesDependingOnChangedPackages(packagesWithChangedPublicApis, recentlyCompiled);
+        packagesWithChangedPublicApis = new HashSet<>();
+        return again && rcValue[0];
+    }
+
+    /**
+     * Store the source into the set of sources belonging to the given transform.
+     */
+    private void addFileToTransform(Map<Transformer,Map<String,Set<URI>>> gs, Transformer t, Source s) {
+        Map<String,Set<URI>> fs = gs.get(t);
+        if (fs == null) {
+            fs = new HashMap<>();
+            gs.put(t, fs);
+        }
+        Set<URI> ss = fs.get(s.pkg().name());
+        if (ss == null) {
+            ss = new HashSet<>();
+            fs.put(s.pkg().name(), ss);
+        }
+        ss.add(s.file().toURI());
+    }
+
+    /**
+     * For all packages, find all sources belonging to the package, group the sources
+     * based on their transformers and apply the transformers on each source code group.
+     */
+    private boolean perform(JavacService javacService,
+                            File outputDir,
+                            Map<String,Transformer> suffixRules)
+    {
+        boolean rc = true;
+        // Group sources based on transforms. A source file can only belong to a single transform.
+        Map<Transformer,Map<String,Set<URI>>> groupedSources = new HashMap<>();
+        for (Source src : now.sources().values()) {
+            Transformer t = suffixRules.get(src.suffix());
+               if (t != null) {
+                if (taintedPackages.contains(src.pkg().name()) && !src.isLinkedOnly()) {
+                    addFileToTransform(groupedSources, t, src);
+                }
+            }
+        }
+        // Go through the transforms and transform them.
+        for (Map.Entry<Transformer,Map<String,Set<URI>>> e : groupedSources.entrySet()) {
+            Transformer t = e.getKey();
+            Map<String,Set<URI>> srcs = e.getValue();
+            // These maps need to be synchronized since multiple threads will be writing results into them.
+            Map<String,Set<URI>> packageArtifacts =
+                    Collections.synchronizedMap(new HashMap<String,Set<URI>>());
+            Map<String,Set<String>> packageDependencies =
+                    Collections.synchronizedMap(new HashMap<String,Set<String>>());
+            Map<String,String> packagePublicApis =
+                    Collections.synchronizedMap(new HashMap<String, String>());
+
+            boolean  r = t.transform(javacService,
+                                     srcs,
+                                     visibleSrcs,
+                                     visibleClasses,
+                                     prev.dependents(),
+                                     outputDir.toURI(),
+                                     packageArtifacts,
+                                     packageDependencies,
+                                     packagePublicApis,
+                                     0,
+                                     isIncremental(),
+                                     numCores,
+                                     out,
+                                     err);
+            if (!r) rc = false;
+
+            for (String p : srcs.keySet()) {
+                recompiledPackages.add(p);
+            }
+            // The transform is done! Extract all the artifacts and store the info into the Package objects.
+            for (Map.Entry<String,Set<URI>> a : packageArtifacts.entrySet()) {
+                Module mnow = now.findModuleFromPackageName(a.getKey());
+                mnow.addArtifacts(a.getKey(), a.getValue());
+            }
+            // Extract all the dependencies and store the info into the Package objects.
+            for (Map.Entry<String,Set<String>> a : packageDependencies.entrySet()) {
+                Set<String> deps = a.getValue();
+                Module mnow = now.findModuleFromPackageName(a.getKey());
+                mnow.setDependencies(a.getKey(), deps);
+            }
+            // Extract all the pubapis and store the info into the Package objects.
+            for (Map.Entry<String,String> a : packagePublicApis.entrySet()) {
+                Module mprev = prev.findModuleFromPackageName(a.getKey());
+                List<String> pubapi = Package.pubapiToList(a.getValue());
+                Module mnow = now.findModuleFromPackageName(a.getKey());
+                mnow.setPubapi(a.getKey(), pubapi);
+                if (mprev.hasPubapiChanged(a.getKey(), pubapi)) {
+                    // Aha! The pubapi of this package has changed!
+                    // It can also be a new compile from scratch.
+                    if (mprev.lookupPackage(a.getKey()).existsInJavacState()) {
+                        // This is an incremental compile! The pubapi
+                        // did change. Trigger recompilation of dependents.
+                        packagesWithChangedPublicApis.add(a.getKey());
+                        Log.info("The pubapi of "+Util.justPackageName(a.getKey())+" has changed!");
+                    }
+                }
+            }
+        }
+        return rc;
+    }
+
+    /**
+     * Utility method to recursively find all files below a directory.
+     */
+    private static Set<File> findAllFiles(File dir) {
+        Set<File> foundFiles = new HashSet<>();
+        if (dir == null) {
+            return foundFiles;
+        }
+        recurse(dir, foundFiles);
+        return foundFiles;
+    }
+
+    private static void recurse(File dir, Set<File> foundFiles) {
+        for (File f : dir.listFiles()) {
+            if (f.isFile()) {
+                foundFiles.add(f);
+            } else if (f.isDirectory()) {
+                recurse(f, foundFiles);
+            }
+        }
+    }
+
+    /**
+     * Compare the calculate source list, with an explicit list, usually supplied from the makefile.
+     * Used to detect bugs where the makefile and sjavac have different opinions on which files
+     * should be compiled.
+     */
+    public void compareWithMakefileList(File makefileSourceList)
+            throws ProblemException
+    {
+        // If we are building on win32 using for example cygwin the paths in the makefile source list
+        // might be /cygdrive/c/.... which does not match c:\....
+        // We need to adjust our calculated sources to be identical, if necessary.
+        boolean mightNeedRewriting = File.pathSeparatorChar == ';';
+
+        if (makefileSourceList == null) return;
+
+        Set<String> calculatedSources = new HashSet<>();
+        Set<String> listedSources = new HashSet<>();
+
+        // Create a set of filenames with full paths.
+        for (Source s : now.sources().values()) {
+            // Don't include link only sources when comparing sources to compile
+            if (!s.isLinkedOnly()) {
+                String path = s.file().getPath();
+                if (mightNeedRewriting)
+                    path = Util.normalizeDriveLetter(path);
+                calculatedSources.add(path);
+            }
+        }
+        // Read in the file and create another set of filenames with full paths.
+        try {
+            BufferedReader in = new BufferedReader(new FileReader(makefileSourceList));
+            for (;;) {
+                String l = in.readLine();
+                if (l==null) break;
+                l = l.trim();
+                if (mightNeedRewriting) {
+                    if (l.indexOf(":") == 1 && l.indexOf("\\") == 2) {
+                        // Everything a-ok, the format is already C:\foo\bar
+                    } else if (l.indexOf(":") == 1 && l.indexOf("/") == 2) {
+                        // The format is C:/foo/bar, rewrite into the above format.
+                        l = l.replaceAll("/","\\\\");
+                    } else if (l.charAt(0) == '/' && l.indexOf("/",1) != -1) {
+                        // The format might be: /cygdrive/c/foo/bar, rewrite into the above format.
+                        // Do not hardcode the name cygdrive here.
+                        int slash = l.indexOf("/",1);
+                        l = l.replaceAll("/","\\\\");
+                        l = ""+l.charAt(slash+1)+":"+l.substring(slash+2);
+                    }
+                    if (Character.isLowerCase(l.charAt(0))) {
+                        l = Character.toUpperCase(l.charAt(0))+l.substring(1);
+                    }
+                }
+                listedSources.add(l);
+            }
+        } catch (FileNotFoundException e) {
+            throw new ProblemException("Could not open "+makefileSourceList.getPath()+" since it does not exist!");
+        } catch (IOException e) {
+            throw new ProblemException("Could not read "+makefileSourceList.getPath());
+        }
+
+        for (String s : listedSources) {
+            if (!calculatedSources.contains(s)) {
+                 throw new ProblemException("The makefile listed source "+s+" was not calculated by the smart javac wrapper!");
+            }
+        }
+
+        for (String s : calculatedSources) {
+            if (!listedSources.contains(s)) {
+                throw new ProblemException("The smart javac wrapper calculated source "+s+" was not listed by the makefiles!");
+            }
+        }
+    }
+}