ResolveMerger.java

/*
 * Copyright (C) 2010, Christian Halstrick <christian.halstrick@sap.com>,
 * Copyright (C) 2010-2012, Matthias Sohn <matthias.sohn@sap.com>
 * Copyright (C) 2012, Research In Motion Limited
 * Copyright (C) 2017, Obeo (mathieu.cartaud@obeo.fr)
 * Copyright (C) 2018, Thomas Wolf <thomas.wolf@paranor.ch> and others
 *
 * This program and the accompanying materials are made available under the
 * terms of the Eclipse Distribution License v. 1.0 which is available at
 * https://www.eclipse.org/org/documents/edl-v10.php.
 *
 * SPDX-License-Identifier: BSD-3-Clause
 */
package org.eclipse.jgit.merge;

import static java.nio.charset.StandardCharsets.UTF_8;
import static java.time.Instant.EPOCH;
import static org.eclipse.jgit.diff.DiffAlgorithm.SupportedAlgorithm.HISTOGRAM;
import static org.eclipse.jgit.lib.ConfigConstants.CONFIG_DIFF_SECTION;
import static org.eclipse.jgit.lib.ConfigConstants.CONFIG_KEY_ALGORITHM;
import static org.eclipse.jgit.lib.Constants.OBJ_BLOB;

import java.io.BufferedOutputStream;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.time.Instant;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.HashMap;
import java.util.Iterator;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;

import org.eclipse.jgit.attributes.Attributes;
import org.eclipse.jgit.diff.DiffAlgorithm;
import org.eclipse.jgit.diff.DiffAlgorithm.SupportedAlgorithm;
import org.eclipse.jgit.diff.RawText;
import org.eclipse.jgit.diff.RawTextComparator;
import org.eclipse.jgit.diff.Sequence;
import org.eclipse.jgit.dircache.DirCache;
import org.eclipse.jgit.dircache.DirCacheBuildIterator;
import org.eclipse.jgit.dircache.DirCacheBuilder;
import org.eclipse.jgit.dircache.DirCacheCheckout;
import org.eclipse.jgit.dircache.DirCacheCheckout.CheckoutMetadata;
import org.eclipse.jgit.dircache.DirCacheEntry;
import org.eclipse.jgit.errors.BinaryBlobException;
import org.eclipse.jgit.errors.CorruptObjectException;
import org.eclipse.jgit.errors.IncorrectObjectTypeException;
import org.eclipse.jgit.errors.IndexWriteException;
import org.eclipse.jgit.errors.MissingObjectException;
import org.eclipse.jgit.errors.NoWorkTreeException;
import org.eclipse.jgit.lib.Config;
import org.eclipse.jgit.lib.ConfigConstants;
import org.eclipse.jgit.lib.Constants;
import org.eclipse.jgit.lib.CoreConfig.EolStreamType;
import org.eclipse.jgit.lib.FileMode;
import org.eclipse.jgit.lib.ObjectId;
import org.eclipse.jgit.lib.ObjectInserter;
import org.eclipse.jgit.lib.ObjectLoader;
import org.eclipse.jgit.lib.Repository;
import org.eclipse.jgit.revwalk.RevTree;
import org.eclipse.jgit.storage.pack.PackConfig;
import org.eclipse.jgit.submodule.SubmoduleConflict;
import org.eclipse.jgit.treewalk.AbstractTreeIterator;
import org.eclipse.jgit.treewalk.CanonicalTreeParser;
import org.eclipse.jgit.treewalk.NameConflictTreeWalk;
import org.eclipse.jgit.treewalk.TreeWalk;
import org.eclipse.jgit.treewalk.TreeWalk.OperationType;
import org.eclipse.jgit.treewalk.WorkingTreeIterator;
import org.eclipse.jgit.treewalk.WorkingTreeOptions;
import org.eclipse.jgit.treewalk.filter.TreeFilter;
import org.eclipse.jgit.util.FS;
import org.eclipse.jgit.util.LfsFactory;
import org.eclipse.jgit.util.LfsFactory.LfsInputStream;
import org.eclipse.jgit.util.TemporaryBuffer;
import org.eclipse.jgit.util.io.EolStreamTypeUtil;

/**
 * A three-way merger performing a content-merge if necessary
 */
public class ResolveMerger extends ThreeWayMerger {
    /**
     * If the merge fails (means: not stopped because of unresolved conflicts)
     * this enum is used to explain why it failed
     */
    public enum MergeFailureReason {
        /** the merge failed because of a dirty index */
        DIRTY_INDEX,
        /** the merge failed because of a dirty workingtree */
        DIRTY_WORKTREE,
        /** the merge failed because of a file could not be deleted */
        COULD_NOT_DELETE
    }

    /**
     * The tree walk which we'll iterate over to merge entries.
     *
     * @since 3.4
     */
    protected NameConflictTreeWalk tw;

    /**
     * string versions of a list of commit SHA1s
     *
     * @since 3.0
     */
    protected String[] commitNames;

    /**
     * Index of the base tree within the {@link #tw tree walk}.
     *
     * @since 3.4
     */
    protected static final int T_BASE = 0;

    /**
     * Index of our tree in withthe {@link #tw tree walk}.
     *
     * @since 3.4
     */
    protected static final int T_OURS = 1;

    /**
     * Index of their tree within the {@link #tw tree walk}.
     *
     * @since 3.4
     */
    protected static final int T_THEIRS = 2;

    /**
     * Index of the index tree within the {@link #tw tree walk}.
     *
     * @since 3.4
     */
    protected static final int T_INDEX = 3;

    /**
     * Index of the working directory tree within the {@link #tw tree walk}.
     *
     * @since 3.4
     */
    protected static final int T_FILE = 4;

    /**
     * Builder to update the cache during this merge.
     *
     * @since 3.4
     */
    protected DirCacheBuilder builder;

    /**
     * merge result as tree
     *
     * @since 3.0
     */
    protected ObjectId resultTree;

    /**
     * Paths that could not be merged by this merger because of an unsolvable
     * conflict.
     *
     * @since 3.4
     */
    protected List<String> unmergedPaths = new ArrayList<>();

    /**
     * Files modified during this merge operation.
     *
     * @since 3.4
     */
    protected List<String> modifiedFiles = new LinkedList<>();

    /**
     * If the merger has nothing to do for a file but check it out at the end of
     * the operation, it can be added here.
     *
     * @since 3.4
     */
    protected Map<String, DirCacheEntry> toBeCheckedOut = new HashMap<>();

    /**
     * Paths in this list will be deleted from the local copy at the end of the
     * operation.
     *
     * @since 3.4
     */
    protected List<String> toBeDeleted = new ArrayList<>();

    /**
     * Low-level textual merge results. Will be passed on to the callers in case
     * of conflicts.
     *
     * @since 3.4
     */
    protected Map<String, MergeResult<? extends Sequence>> mergeResults = new HashMap<>();

    /**
     * Paths for which the merge failed altogether.
     *
     * @since 3.4
     */
    protected Map<String, MergeFailureReason> failingPaths = new HashMap<>();

    /**
     * Updated as we merge entries of the tree walk. Tells us whether we should
     * recurse into the entry if it is a subtree.
     *
     * @since 3.4
     */
    protected boolean enterSubtree;

    /**
     * Set to true if this merge should work in-memory. The repos dircache and
     * workingtree are not touched by this method. Eventually needed files are
     * created as temporary files and a new empty, in-memory dircache will be
     * used instead the repo's one. Often used for bare repos where the repo
     * doesn't even have a workingtree and dircache.
     * @since 3.0
     */
    protected boolean inCore;

    /**
     * Set to true if this merger should use the default dircache of the
     * repository and should handle locking and unlocking of the dircache. If
     * this merger should work in-core or if an explicit dircache was specified
     * during construction then this field is set to false.
     * @since 3.0
     */
    protected boolean implicitDirCache;

    /**
     * Directory cache
     * @since 3.0
     */
    protected DirCache dircache;

    /**
     * The iterator to access the working tree. If set to <code>null</code> this
     * merger will not touch the working tree.
     * @since 3.0
     */
    protected WorkingTreeIterator workingTreeIterator;

    /**
     * our merge algorithm
     * @since 3.0
     */
    protected MergeAlgorithm mergeAlgorithm;

    /**
     * The {@link WorkingTreeOptions} are needed to determine line endings for
     * merged files.
     *
     * @since 4.11
     */
    protected WorkingTreeOptions workingTreeOptions;

    /**
     * The size limit (bytes) which controls a file to be stored in {@code Heap}
     * or {@code LocalFile} during the merge.
     */
    private int inCoreLimit;

    /**
     * Keeps {@link CheckoutMetadata} for {@link #checkout()} and
     * {@link #cleanUp()}.
     */
    private Map<String, CheckoutMetadata> checkoutMetadata;

    private static MergeAlgorithm getMergeAlgorithm(Config config) {
        SupportedAlgorithm diffAlg = config.getEnum(
                CONFIG_DIFF_SECTION, null, CONFIG_KEY_ALGORITHM,
                HISTOGRAM);
        return new MergeAlgorithm(DiffAlgorithm.getAlgorithm(diffAlg));
    }

    private static int getInCoreLimit(Config config) {
        return config.getInt(
                ConfigConstants.CONFIG_MERGE_SECTION, ConfigConstants.CONFIG_KEY_IN_CORE_LIMIT, 10 << 20);
    }

    private static String[] defaultCommitNames() {
        return new String[] { "BASE", "OURS", "THEIRS" }; //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
    }

    private static final Attributes NO_ATTRIBUTES = new Attributes();

    /**
     * Constructor for ResolveMerger.
     *
     * @param local
     *            the {@link org.eclipse.jgit.lib.Repository}.
     * @param inCore
     *            a boolean.
     */
    protected ResolveMerger(Repository local, boolean inCore) {
        super(local);
        Config config = local.getConfig();
        mergeAlgorithm = getMergeAlgorithm(config);
        inCoreLimit = getInCoreLimit(config);
        commitNames = defaultCommitNames();
        this.inCore = inCore;

        if (inCore) {
            implicitDirCache = false;
            dircache = DirCache.newInCore();
        } else {
            implicitDirCache = true;
            workingTreeOptions = local.getConfig().get(WorkingTreeOptions.KEY);
        }
    }

    /**
     * Constructor for ResolveMerger.
     *
     * @param local
     *            the {@link org.eclipse.jgit.lib.Repository}.
     */
    protected ResolveMerger(Repository local) {
        this(local, false);
    }

    /**
     * Constructor for ResolveMerger.
     *
     * @param inserter
     *            an {@link org.eclipse.jgit.lib.ObjectInserter} object.
     * @param config
     *            the repository configuration
     * @since 4.8
     */
    protected ResolveMerger(ObjectInserter inserter, Config config) {
        super(inserter);
        mergeAlgorithm = getMergeAlgorithm(config);
        commitNames = defaultCommitNames();
        inCore = true;
        implicitDirCache = false;
        dircache = DirCache.newInCore();
    }

    /** {@inheritDoc} */
    @Override
    protected boolean mergeImpl() throws IOException {
        if (implicitDirCache) {
            dircache = nonNullRepo().lockDirCache();
        }
        if (!inCore) {
            checkoutMetadata = new HashMap<>();
        }
        try {
            return mergeTrees(mergeBase(), sourceTrees[0], sourceTrees[1],
                    false);
        } finally {
            checkoutMetadata = null;
            if (implicitDirCache) {
                dircache.unlock();
            }
        }
    }

    private void checkout() throws NoWorkTreeException, IOException {
        // Iterate in reverse so that "folder/file" is deleted before
        // "folder". Otherwise this could result in a failing path because
        // of a non-empty directory, for which delete() would fail.
        for (int i = toBeDeleted.size() - 1; i >= 0; i--) {
            String fileName = toBeDeleted.get(i);
            File f = new File(nonNullRepo().getWorkTree(), fileName);
            if (!f.delete())
                if (!f.isDirectory())
                    failingPaths.put(fileName,
                            MergeFailureReason.COULD_NOT_DELETE);
            modifiedFiles.add(fileName);
        }
        for (Map.Entry<String, DirCacheEntry> entry : toBeCheckedOut
                .entrySet()) {
            DirCacheEntry cacheEntry = entry.getValue();
            if (cacheEntry.getFileMode() == FileMode.GITLINK) {
                new File(nonNullRepo().getWorkTree(), entry.getKey()).mkdirs();
            } else {
                DirCacheCheckout.checkoutEntry(db, cacheEntry, reader, false,
                        checkoutMetadata.get(entry.getKey()));
                modifiedFiles.add(entry.getKey());
            }
        }
    }

    /**
     * Reverts the worktree after an unsuccessful merge. We know that for all
     * modified files the old content was in the old index and the index
     * contained only stage 0. In case if inCore operation just clear the
     * history of modified files.
     *
     * @throws java.io.IOException
     * @throws org.eclipse.jgit.errors.CorruptObjectException
     * @throws org.eclipse.jgit.errors.NoWorkTreeException
     * @since 3.4
     */
    protected void cleanUp() throws NoWorkTreeException,
            CorruptObjectException,
            IOException {
        if (inCore) {
            modifiedFiles.clear();
            return;
        }

        DirCache dc = nonNullRepo().readDirCache();
        Iterator<String> mpathsIt=modifiedFiles.iterator();
        while(mpathsIt.hasNext()) {
            String mpath = mpathsIt.next();
            DirCacheEntry entry = dc.getEntry(mpath);
            if (entry != null) {
                DirCacheCheckout.checkoutEntry(db, entry, reader, false,
                        checkoutMetadata.get(mpath));
            }
            mpathsIt.remove();
        }
    }

    /**
     * adds a new path with the specified stage to the index builder
     *
     * @param path
     * @param p
     * @param stage
     * @param lastMod
     * @param len
     * @return the entry which was added to the index
     */
    private DirCacheEntry add(byte[] path, CanonicalTreeParser p, int stage,
            Instant lastMod, long len) {
        if (p != null && !p.getEntryFileMode().equals(FileMode.TREE)) {
            DirCacheEntry e = new DirCacheEntry(path, stage);
            e.setFileMode(p.getEntryFileMode());
            e.setObjectId(p.getEntryObjectId());
            e.setLastModified(lastMod);
            e.setLength(len);
            builder.add(e);
            return e;
        }
        return null;
    }

    /**
     * adds a entry to the index builder which is a copy of the specified
     * DirCacheEntry
     *
     * @param e
     *            the entry which should be copied
     *
     * @return the entry which was added to the index
     */
    private DirCacheEntry keep(DirCacheEntry e) {
        DirCacheEntry newEntry = new DirCacheEntry(e.getRawPath(),
                e.getStage());
        newEntry.setFileMode(e.getFileMode());
        newEntry.setObjectId(e.getObjectId());
        newEntry.setLastModified(e.getLastModifiedInstant());
        newEntry.setLength(e.getLength());
        builder.add(newEntry);
        return newEntry;
    }

    /**
     * Remembers the {@link CheckoutMetadata} for the given path; it may be
     * needed in {@link #checkout()} or in {@link #cleanUp()}.
     *
     * @param path
     *            of the current node
     * @param attributes
     *            for the current node
     * @throws IOException
     *             if the smudge filter cannot be determined
     * @since 5.1
     */
    protected void addCheckoutMetadata(String path, Attributes attributes)
            throws IOException {
        if (checkoutMetadata != null) {
            EolStreamType eol = EolStreamTypeUtil.detectStreamType(
                    OperationType.CHECKOUT_OP, workingTreeOptions, attributes);
            CheckoutMetadata data = new CheckoutMetadata(eol,
                    tw.getFilterCommand(Constants.ATTR_FILTER_TYPE_SMUDGE));
            checkoutMetadata.put(path, data);
        }
    }

    /**
     * Adds a {@link DirCacheEntry} for direct checkout and remembers its
     * {@link CheckoutMetadata}.
     *
     * @param path
     *            of the entry
     * @param entry
     *            to add
     * @param attributes
     *            for the current entry
     * @throws IOException
     *             if the {@link CheckoutMetadata} cannot be determined
     * @since 5.1
     */
    protected void addToCheckout(String path, DirCacheEntry entry,
            Attributes attributes) throws IOException {
        toBeCheckedOut.put(path, entry);
        addCheckoutMetadata(path, attributes);
    }

    /**
     * Remember a path for deletion, and remember its {@link CheckoutMetadata}
     * in case it has to be restored in {@link #cleanUp()}.
     *
     * @param path
     *            of the entry
     * @param isFile
     *            whether it is a file
     * @param attributes
     *            for the entry
     * @throws IOException
     *             if the {@link CheckoutMetadata} cannot be determined
     * @since 5.1
     */
    protected void addDeletion(String path, boolean isFile,
            Attributes attributes) throws IOException {
        toBeDeleted.add(path);
        if (isFile) {
            addCheckoutMetadata(path, attributes);
        }
    }

    /**
     * Processes one path and tries to merge taking git attributes in account.
     * This method will do all trivial (not content) merges and will also detect
     * if a merge will fail. The merge will fail when one of the following is
     * true
     * <ul>
     * <li>the index entry does not match the entry in ours. When merging one
     * branch into the current HEAD, ours will point to HEAD and theirs will
     * point to the other branch. It is assumed that the index matches the HEAD
     * because it will only not match HEAD if it was populated before the merge
     * operation. But the merge commit should not accidentally contain
     * modifications done before the merge. Check the <a href=
     * "http://www.kernel.org/pub/software/scm/git/docs/git-read-tree.html#_3_way_merge"
     * >git read-tree</a> documentation for further explanations.</li>
     * <li>A conflict was detected and the working-tree file is dirty. When a
     * conflict is detected the content-merge algorithm will try to write a
     * merged version into the working-tree. If the file is dirty we would
     * override unsaved data.</li>
     * </ul>
     *
     * @param base
     *            the common base for ours and theirs
     * @param ours
     *            the ours side of the merge. When merging a branch into the
     *            HEAD ours will point to HEAD
     * @param theirs
     *            the theirs side of the merge. When merging a branch into the
     *            current HEAD theirs will point to the branch which is merged
     *            into HEAD.
     * @param index
     *            the index entry
     * @param work
     *            the file in the working tree
     * @param ignoreConflicts
     *            see
     *            {@link org.eclipse.jgit.merge.ResolveMerger#mergeTrees(AbstractTreeIterator, RevTree, RevTree, boolean)}
     * @param attributes
     *            the attributes defined for this entry
     * @return <code>false</code> if the merge will fail because the index entry
     *         didn't match ours or the working-dir file was dirty and a
     *         conflict occurred
     * @throws org.eclipse.jgit.errors.MissingObjectException
     * @throws org.eclipse.jgit.errors.IncorrectObjectTypeException
     * @throws org.eclipse.jgit.errors.CorruptObjectException
     * @throws java.io.IOException
     * @since 4.9
     */
    protected boolean processEntry(CanonicalTreeParser base,
            CanonicalTreeParser ours, CanonicalTreeParser theirs,
            DirCacheBuildIterator index, WorkingTreeIterator work,
            boolean ignoreConflicts, Attributes attributes)
            throws MissingObjectException, IncorrectObjectTypeException,
            CorruptObjectException, IOException {
        enterSubtree = true;
        final int modeO = tw.getRawMode(T_OURS);
        final int modeT = tw.getRawMode(T_THEIRS);
        final int modeB = tw.getRawMode(T_BASE);
        boolean gitLinkMerging = isGitLink(modeO) || isGitLink(modeT)
                || isGitLink(modeB);
        if (modeO == 0 && modeT == 0 && modeB == 0)
            // File is either untracked or new, staged but uncommitted
            return true;

        if (isIndexDirty())
            return false;

        DirCacheEntry ourDce = null;

        if (index == null || index.getDirCacheEntry() == null) {
            // create a fake DCE, but only if ours is valid. ours is kept only
            // in case it is valid, so a null ourDce is ok in all other cases.
            if (nonTree(modeO)) {
                ourDce = new DirCacheEntry(tw.getRawPath());
                ourDce.setObjectId(tw.getObjectId(T_OURS));
                ourDce.setFileMode(tw.getFileMode(T_OURS));
            }
        } else {
            ourDce = index.getDirCacheEntry();
        }

        if (nonTree(modeO) && nonTree(modeT) && tw.idEqual(T_OURS, T_THEIRS)) {
            // OURS and THEIRS have equal content. Check the file mode
            if (modeO == modeT) {
                // content and mode of OURS and THEIRS are equal: it doesn't
                // matter which one we choose. OURS is chosen. Since the index
                // is clean (the index matches already OURS) we can keep the existing one
                keep(ourDce);
                // no checkout needed!
                return true;
            }
            // same content but different mode on OURS and THEIRS.
            // Try to merge the mode and report an error if this is
            // not possible.
            int newMode = mergeFileModes(modeB, modeO, modeT);
            if (newMode != FileMode.MISSING.getBits()) {
                if (newMode == modeO) {
                    // ours version is preferred
                    keep(ourDce);
                } else {
                    // the preferred version THEIRS has a different mode
                    // than ours. Check it out!
                    if (isWorktreeDirty(work, ourDce)) {
                        return false;
                    }
                    // we know about length and lastMod only after we have
                    // written the new content.
                    // This will happen later. Set these values to 0 for know.
                    DirCacheEntry e = add(tw.getRawPath(), theirs,
                            DirCacheEntry.STAGE_0, EPOCH, 0);
                    addToCheckout(tw.getPathString(), e, attributes);
                }
                return true;
            }
            // FileModes are not mergeable. We found a conflict on modes.
            // For conflicting entries we don't know lastModified and
            // length.
            add(tw.getRawPath(), base, DirCacheEntry.STAGE_1, EPOCH, 0);
            add(tw.getRawPath(), ours, DirCacheEntry.STAGE_2, EPOCH, 0);
            add(tw.getRawPath(), theirs, DirCacheEntry.STAGE_3, EPOCH, 0);
            unmergedPaths.add(tw.getPathString());
            mergeResults.put(tw.getPathString(),
                    new MergeResult<>(Collections.<RawText> emptyList()));
            return true;
        }

        if (modeB == modeT && tw.idEqual(T_BASE, T_THEIRS)) {
            // THEIRS was not changed compared to BASE. All changes must be in
            // OURS. OURS is chosen. We can keep the existing entry.
            if (ourDce != null)
                keep(ourDce);
            // no checkout needed!
            return true;
        }

        if (modeB == modeO && tw.idEqual(T_BASE, T_OURS)) {
            // OURS was not changed compared to BASE. All changes must be in
            // THEIRS. THEIRS is chosen.

            // Check worktree before checking out THEIRS
            if (isWorktreeDirty(work, ourDce))
                return false;
            if (nonTree(modeT)) {
                // we know about length and lastMod only after we have written
                // the new content.
                // This will happen later. Set these values to 0 for know.
                DirCacheEntry e = add(tw.getRawPath(), theirs,
                        DirCacheEntry.STAGE_0, EPOCH, 0);
                if (e != null) {
                    addToCheckout(tw.getPathString(), e, attributes);
                }
                return true;
            }
            // we want THEIRS ... but THEIRS contains a folder or the
            // deletion of the path. Delete what's in the working tree,
            // which we know to be clean.
            if (tw.getTreeCount() > T_FILE && tw.getRawMode(T_FILE) == 0) {
                // Not present in working tree, so nothing to delete
                return true;
            }
            if (modeT != 0 && modeT == modeB) {
                // Base, ours, and theirs all contain a folder: don't delete
                return true;
            }
            addDeletion(tw.getPathString(), nonTree(modeO), attributes);
            return true;
        }

        if (tw.isSubtree()) {
            // file/folder conflicts: here I want to detect only file/folder
            // conflict between ours and theirs. file/folder conflicts between
            // base/index/workingTree and something else are not relevant or
            // detected later
            if (nonTree(modeO) != nonTree(modeT)) {
                if (ignoreConflicts) {
                    // In case of merge failures, ignore this path instead of reporting unmerged, so
                    // a caller can use virtual commit. This will not result in files with conflict
                    // markers in the index/working tree. The actual diff on the path will be
                    // computed directly on children.
                    enterSubtree = false;
                    return true;
                }
                if (nonTree(modeB))
                    add(tw.getRawPath(), base, DirCacheEntry.STAGE_1, EPOCH, 0);
                if (nonTree(modeO))
                    add(tw.getRawPath(), ours, DirCacheEntry.STAGE_2, EPOCH, 0);
                if (nonTree(modeT))
                    add(tw.getRawPath(), theirs, DirCacheEntry.STAGE_3, EPOCH, 0);
                unmergedPaths.add(tw.getPathString());
                enterSubtree = false;
                return true;
            }

            // ours and theirs are both folders or both files (and treewalk
            // tells us we are in a subtree because of index or working-dir).
            // If they are both folders no content-merge is required - we can
            // return here.
            if (!nonTree(modeO))
                return true;

            // ours and theirs are both files, just fall out of the if block
            // and do the content merge
        }

        if (nonTree(modeO) && nonTree(modeT)) {
            // Check worktree before modifying files
            boolean worktreeDirty = isWorktreeDirty(work, ourDce);
            if (!attributes.canBeContentMerged() && worktreeDirty) {
                return false;
            }

            if (gitLinkMerging && ignoreConflicts) {
                // Always select 'ours' in case of GITLINK merge failures so
                // a caller can use virtual commit.
                add(tw.getRawPath(), ours, DirCacheEntry.STAGE_0, EPOCH, 0);
                return true;
            } else if (gitLinkMerging) {
                add(tw.getRawPath(), base, DirCacheEntry.STAGE_1, EPOCH, 0);
                add(tw.getRawPath(), ours, DirCacheEntry.STAGE_2, EPOCH, 0);
                add(tw.getRawPath(), theirs, DirCacheEntry.STAGE_3, EPOCH, 0);
                MergeResult<SubmoduleConflict> result = createGitLinksMergeResult(
                        base, ours, theirs);
                result.setContainsConflicts(true);
                mergeResults.put(tw.getPathString(), result);
                unmergedPaths.add(tw.getPathString());
                return true;
            } else if (!attributes.canBeContentMerged()) {
                add(tw.getRawPath(), base, DirCacheEntry.STAGE_1, EPOCH, 0);
                add(tw.getRawPath(), ours, DirCacheEntry.STAGE_2, EPOCH, 0);
                add(tw.getRawPath(), theirs, DirCacheEntry.STAGE_3, EPOCH, 0);

                // attribute merge issues are conflicts but not failures
                unmergedPaths.add(tw.getPathString());
                return true;
            }

            // Check worktree before modifying files
            if (worktreeDirty) {
                return false;
            }

            MergeResult<RawText> result = contentMerge(base, ours, theirs,
                    attributes);
            if (ignoreConflicts) {
                result.setContainsConflicts(false);
            }
            updateIndex(base, ours, theirs, result, attributes);
            String currentPath = tw.getPathString();
            if (result.containsConflicts() && !ignoreConflicts) {
                unmergedPaths.add(currentPath);
            }
            modifiedFiles.add(currentPath);
            addCheckoutMetadata(currentPath, attributes);
        } else if (modeO != modeT) {
            // OURS or THEIRS has been deleted
            if (((modeO != 0 && !tw.idEqual(T_BASE, T_OURS)) || (modeT != 0 && !tw
                    .idEqual(T_BASE, T_THEIRS)))) {
                if (gitLinkMerging && ignoreConflicts) {
                    add(tw.getRawPath(), ours, DirCacheEntry.STAGE_0, EPOCH, 0);
                } else if (gitLinkMerging) {
                    add(tw.getRawPath(), base, DirCacheEntry.STAGE_1, EPOCH, 0);
                    add(tw.getRawPath(), ours, DirCacheEntry.STAGE_2, EPOCH, 0);
                    add(tw.getRawPath(), theirs, DirCacheEntry.STAGE_3, EPOCH, 0);
                    MergeResult<SubmoduleConflict> result = createGitLinksMergeResult(
                            base, ours, theirs);
                    result.setContainsConflicts(true);
                    mergeResults.put(tw.getPathString(), result);
                    unmergedPaths.add(tw.getPathString());
                } else {
                    MergeResult<RawText> result = contentMerge(base, ours,
                            theirs, attributes);

                    if (ignoreConflicts) {
                        // In case a conflict is detected the working tree file
                        // is again filled with new content (containing conflict
                        // markers). But also stage 0 of the index is filled
                        // with that content.
                        result.setContainsConflicts(false);
                        updateIndex(base, ours, theirs, result, attributes);
                    } else {
                        add(tw.getRawPath(), base, DirCacheEntry.STAGE_1, EPOCH,
                                0);
                        add(tw.getRawPath(), ours, DirCacheEntry.STAGE_2, EPOCH,
                                0);
                        DirCacheEntry e = add(tw.getRawPath(), theirs,
                                DirCacheEntry.STAGE_3, EPOCH, 0);

                        // OURS was deleted checkout THEIRS
                        if (modeO == 0) {
                            // Check worktree before checking out THEIRS
                            if (isWorktreeDirty(work, ourDce)) {
                                return false;
                            }
                            if (nonTree(modeT)) {
                                if (e != null) {
                                    addToCheckout(tw.getPathString(), e,
                                            attributes);
                                }
                            }
                        }

                        unmergedPaths.add(tw.getPathString());

                        // generate a MergeResult for the deleted file
                        mergeResults.put(tw.getPathString(), result);
                    }
                }
            }
        }
        return true;
    }

    private static MergeResult<SubmoduleConflict> createGitLinksMergeResult(
            CanonicalTreeParser base, CanonicalTreeParser ours,
            CanonicalTreeParser theirs) {
        return new MergeResult<>(Arrays.asList(
                new SubmoduleConflict(
                        base == null ? null : base.getEntryObjectId()),
                new SubmoduleConflict(
                        ours == null ? null : ours.getEntryObjectId()),
                new SubmoduleConflict(
                        theirs == null ? null : theirs.getEntryObjectId())));
    }

    /**
     * Does the content merge. The three texts base, ours and theirs are
     * specified with {@link CanonicalTreeParser}. If any of the parsers is
     * specified as <code>null</code> then an empty text will be used instead.
     *
     * @param base
     * @param ours
     * @param theirs
     * @param attributes
     *
     * @return the result of the content merge
     * @throws IOException
     */
    private MergeResult<RawText> contentMerge(CanonicalTreeParser base,
            CanonicalTreeParser ours, CanonicalTreeParser theirs,
            Attributes attributes)
            throws IOException {
        RawText baseText;
        RawText ourText;
        RawText theirsText;

        try {
            baseText = base == null ? RawText.EMPTY_TEXT : getRawText(
                            base.getEntryObjectId(), attributes);
            ourText = ours == null ? RawText.EMPTY_TEXT : getRawText(
                            ours.getEntryObjectId(), attributes);
            theirsText = theirs == null ? RawText.EMPTY_TEXT : getRawText(
                            theirs.getEntryObjectId(), attributes);
        } catch (BinaryBlobException e) {
            MergeResult<RawText> r = new MergeResult<>(Collections.<RawText>emptyList());
            r.setContainsConflicts(true);
            return r;
        }
        return (mergeAlgorithm.merge(RawTextComparator.DEFAULT, baseText,
                ourText, theirsText));
    }

    private boolean isIndexDirty() {
        if (inCore)
            return false;

        final int modeI = tw.getRawMode(T_INDEX);
        final int modeO = tw.getRawMode(T_OURS);

        // Index entry has to match ours to be considered clean
        final boolean isDirty = nonTree(modeI)
                && !(modeO == modeI && tw.idEqual(T_INDEX, T_OURS));
        if (isDirty)
            failingPaths
                    .put(tw.getPathString(), MergeFailureReason.DIRTY_INDEX);
        return isDirty;
    }

    private boolean isWorktreeDirty(WorkingTreeIterator work,
            DirCacheEntry ourDce) throws IOException {
        if (work == null)
            return false;

        final int modeF = tw.getRawMode(T_FILE);
        final int modeO = tw.getRawMode(T_OURS);

        // Worktree entry has to match ours to be considered clean
        boolean isDirty;
        if (ourDce != null)
            isDirty = work.isModified(ourDce, true, reader);
        else {
            isDirty = work.isModeDifferent(modeO);
            if (!isDirty && nonTree(modeF))
                isDirty = !tw.idEqual(T_FILE, T_OURS);
        }

        // Ignore existing empty directories
        if (isDirty && modeF == FileMode.TYPE_TREE
                && modeO == FileMode.TYPE_MISSING)
            isDirty = false;
        if (isDirty)
            failingPaths.put(tw.getPathString(),
                    MergeFailureReason.DIRTY_WORKTREE);
        return isDirty;
    }

    /**
     * Updates the index after a content merge has happened. If no conflict has
     * occurred this includes persisting the merged content to the object
     * database. In case of conflicts this method takes care to write the
     * correct stages to the index.
     *
     * @param base
     * @param ours
     * @param theirs
     * @param result
     * @param attributes
     * @throws FileNotFoundException
     * @throws IOException
     */
    private void updateIndex(CanonicalTreeParser base,
            CanonicalTreeParser ours, CanonicalTreeParser theirs,
            MergeResult<RawText> result, Attributes attributes)
            throws FileNotFoundException,
            IOException {
        TemporaryBuffer rawMerged = null;
        try {
            rawMerged = doMerge(result);
            File mergedFile = inCore ? null
                    : writeMergedFile(rawMerged, attributes);
            if (result.containsConflicts()) {
                // A conflict occurred, the file will contain conflict markers
                // the index will be populated with the three stages and the
                // workdir (if used) contains the halfway merged content.
                add(tw.getRawPath(), base, DirCacheEntry.STAGE_1, EPOCH, 0);
                add(tw.getRawPath(), ours, DirCacheEntry.STAGE_2, EPOCH, 0);
                add(tw.getRawPath(), theirs, DirCacheEntry.STAGE_3, EPOCH, 0);
                mergeResults.put(tw.getPathString(), result);
                return;
            }

            // No conflict occurred, the file will contain fully merged content.
            // The index will be populated with the new merged version.
            DirCacheEntry dce = new DirCacheEntry(tw.getPathString());

            // Set the mode for the new content. Fall back to REGULAR_FILE if
            // we can't merge modes of OURS and THEIRS.
            int newMode = mergeFileModes(tw.getRawMode(0), tw.getRawMode(1),
                    tw.getRawMode(2));
            dce.setFileMode(newMode == FileMode.MISSING.getBits()
                    ? FileMode.REGULAR_FILE : FileMode.fromBits(newMode));
            if (mergedFile != null) {
                dce.setLastModified(
                        nonNullRepo().getFS().lastModifiedInstant(mergedFile));
                dce.setLength((int) mergedFile.length());
            }
            dce.setObjectId(insertMergeResult(rawMerged, attributes));
            builder.add(dce);
        } finally {
            if (rawMerged != null) {
                rawMerged.destroy();
            }
        }
    }

    /**
     * Writes merged file content to the working tree.
     *
     * @param rawMerged
     *            the raw merged content
     * @param attributes
     *            the files .gitattributes entries
     * @return the working tree file to which the merged content was written.
     * @throws FileNotFoundException
     * @throws IOException
     */
    private File writeMergedFile(TemporaryBuffer rawMerged,
            Attributes attributes)
            throws FileNotFoundException, IOException {
        File workTree = nonNullRepo().getWorkTree();
        FS fs = nonNullRepo().getFS();
        File of = new File(workTree, tw.getPathString());
        File parentFolder = of.getParentFile();
        if (!fs.exists(parentFolder)) {
            parentFolder.mkdirs();
        }
        EolStreamType streamType = EolStreamTypeUtil.detectStreamType(
                OperationType.CHECKOUT_OP, workingTreeOptions,
                attributes);
        try (OutputStream os = EolStreamTypeUtil.wrapOutputStream(
                new BufferedOutputStream(new FileOutputStream(of)),
                streamType)) {
            rawMerged.writeTo(os, null);
        }
        return of;
    }

    private TemporaryBuffer doMerge(MergeResult<RawText> result)
            throws IOException {
        TemporaryBuffer.LocalFile buf = new TemporaryBuffer.LocalFile(
                db != null ? nonNullRepo().getDirectory() : null, inCoreLimit);
        boolean success = false;
        try {
            new MergeFormatter().formatMerge(buf, result,
                    Arrays.asList(commitNames), UTF_8);
            buf.close();
            success = true;
        } finally {
            if (!success) {
                buf.destroy();
            }
        }
        return buf;
    }

    private ObjectId insertMergeResult(TemporaryBuffer buf,
            Attributes attributes) throws IOException {
        InputStream in = buf.openInputStream();
        try (LfsInputStream is = LfsFactory.getInstance().applyCleanFilter(
                getRepository(), in,
                buf.length(), attributes.get(Constants.ATTR_MERGE))) {
            return getObjectInserter().insert(OBJ_BLOB, is.getLength(), is);
        }
    }

    /**
     * Try to merge filemodes. If only ours or theirs have changed the mode
     * (compared to base) we choose that one. If ours and theirs have equal
     * modes return that one. If also that is not the case the modes are not
     * mergeable. Return {@link FileMode#MISSING} int that case.
     *
     * @param modeB
     *            filemode found in BASE
     * @param modeO
     *            filemode found in OURS
     * @param modeT
     *            filemode found in THEIRS
     *
     * @return the merged filemode or {@link FileMode#MISSING} in case of a
     *         conflict
     */
    private int mergeFileModes(int modeB, int modeO, int modeT) {
        if (modeO == modeT)
            return modeO;
        if (modeB == modeO)
            // Base equal to Ours -> chooses Theirs if that is not missing
            return (modeT == FileMode.MISSING.getBits()) ? modeO : modeT;
        if (modeB == modeT)
            // Base equal to Theirs -> chooses Ours if that is not missing
            return (modeO == FileMode.MISSING.getBits()) ? modeT : modeO;
        return FileMode.MISSING.getBits();
    }

    private RawText getRawText(ObjectId id,
            Attributes attributes)
            throws IOException, BinaryBlobException {
        if (id.equals(ObjectId.zeroId()))
            return new RawText(new byte[] {});

        ObjectLoader loader = LfsFactory.getInstance().applySmudgeFilter(
                getRepository(), reader.open(id, OBJ_BLOB),
                attributes.get(Constants.ATTR_MERGE));
        int threshold = PackConfig.DEFAULT_BIG_FILE_THRESHOLD;
        return RawText.load(loader, threshold);
    }

    private static boolean nonTree(int mode) {
        return mode != 0 && !FileMode.TREE.equals(mode);
    }

    private static boolean isGitLink(int mode) {
        return FileMode.GITLINK.equals(mode);
    }

    /** {@inheritDoc} */
    @Override
    public ObjectId getResultTreeId() {
        return (resultTree == null) ? null : resultTree.toObjectId();
    }

    /**
     * Set the names of the commits as they would appear in conflict markers
     *
     * @param commitNames
     *            the names of the commits as they would appear in conflict
     *            markers
     */
    public void setCommitNames(String[] commitNames) {
        this.commitNames = commitNames;
    }

    /**
     * Get the names of the commits as they would appear in conflict markers.
     *
     * @return the names of the commits as they would appear in conflict
     *         markers.
     */
    public String[] getCommitNames() {
        return commitNames;
    }

    /**
     * Get the paths with conflicts. This is a subset of the files listed by
     * {@link #getModifiedFiles()}
     *
     * @return the paths with conflicts. This is a subset of the files listed by
     *         {@link #getModifiedFiles()}
     */
    public List<String> getUnmergedPaths() {
        return unmergedPaths;
    }

    /**
     * Get the paths of files which have been modified by this merge.
     *
     * @return the paths of files which have been modified by this merge. A file
     *         will be modified if a content-merge works on this path or if the
     *         merge algorithm decides to take the theirs-version. This is a
     *         superset of the files listed by {@link #getUnmergedPaths()}.
     */
    public List<String> getModifiedFiles() {
        return modifiedFiles;
    }

    /**
     * Get a map which maps the paths of files which have to be checked out
     * because the merge created new fully-merged content for this file into the
     * index.
     *
     * @return a map which maps the paths of files which have to be checked out
     *         because the merge created new fully-merged content for this file
     *         into the index. This means: the merge wrote a new stage 0 entry
     *         for this path.
     */
    public Map<String, DirCacheEntry> getToBeCheckedOut() {
        return toBeCheckedOut;
    }

    /**
     * Get the mergeResults
     *
     * @return the mergeResults
     */
    public Map<String, MergeResult<? extends Sequence>> getMergeResults() {
        return mergeResults;
    }

    /**
     * Get list of paths causing this merge to fail (not stopped because of a
     * conflict).
     *
     * @return lists paths causing this merge to fail (not stopped because of a
     *         conflict). <code>null</code> is returned if this merge didn't
     *         fail.
     */
    public Map<String, MergeFailureReason> getFailingPaths() {
        return failingPaths.isEmpty() ? null : failingPaths;
    }

    /**
     * Returns whether this merge failed (i.e. not stopped because of a
     * conflict)
     *
     * @return <code>true</code> if a failure occurred, <code>false</code>
     *         otherwise
     */
    public boolean failed() {
        return !failingPaths.isEmpty();
    }

    /**
     * Sets the DirCache which shall be used by this merger. If the DirCache is
     * not set explicitly and if this merger doesn't work in-core, this merger
     * will implicitly get and lock a default DirCache. If the DirCache is
     * explicitly set the caller is responsible to lock it in advance. Finally
     * the merger will call {@link org.eclipse.jgit.dircache.DirCache#commit()}
     * which requires that the DirCache is locked. If the {@link #mergeImpl()}
     * returns without throwing an exception the lock will be released. In case
     * of exceptions the caller is responsible to release the lock.
     *
     * @param dc
     *            the DirCache to set
     */
    public void setDirCache(DirCache dc) {
        this.dircache = dc;
        implicitDirCache = false;
    }

    /**
     * Sets the WorkingTreeIterator to be used by this merger. If no
     * WorkingTreeIterator is set this merger will ignore the working tree and
     * fail if a content merge is necessary.
     * <p>
     * TODO: enhance WorkingTreeIterator to support write operations. Then this
     * merger will be able to merge with a different working tree abstraction.
     *
     * @param workingTreeIterator
     *            the workingTreeIt to set
     */
    public void setWorkingTreeIterator(WorkingTreeIterator workingTreeIterator) {
        this.workingTreeIterator = workingTreeIterator;
    }


    /**
     * The resolve conflict way of three way merging
     *
     * @param baseTree
     *            a {@link org.eclipse.jgit.treewalk.AbstractTreeIterator}
     *            object.
     * @param headTree
     *            a {@link org.eclipse.jgit.revwalk.RevTree} object.
     * @param mergeTree
     *            a {@link org.eclipse.jgit.revwalk.RevTree} object.
     * @param ignoreConflicts
     *            Controls what to do in case a content-merge is done and a
     *            conflict is detected. The default setting for this should be
     *            <code>false</code>. In this case the working tree file is
     *            filled with new content (containing conflict markers) and the
     *            index is filled with multiple stages containing BASE, OURS and
     *            THEIRS content. Having such non-0 stages is the sign to git
     *            tools that there are still conflicts for that path.
     *            <p>
     *            If <code>true</code> is specified the behavior is different.
     *            In case a conflict is detected the working tree file is again
     *            filled with new content (containing conflict markers). But
     *            also stage 0 of the index is filled with that content. No
     *            other stages are filled. Means: there is no conflict on that
     *            path but the new content (including conflict markers) is
     *            stored as successful merge result. This is needed in the
     *            context of {@link org.eclipse.jgit.merge.RecursiveMerger}
     *            where when determining merge bases we don't want to deal with
     *            content-merge conflicts.
     * @return whether the trees merged cleanly
     * @throws java.io.IOException
     * @since 3.5
     */
    protected boolean mergeTrees(AbstractTreeIterator baseTree,
            RevTree headTree, RevTree mergeTree, boolean ignoreConflicts)
            throws IOException {

        builder = dircache.builder();
        DirCacheBuildIterator buildIt = new DirCacheBuildIterator(builder);

        tw = new NameConflictTreeWalk(db, reader);
        tw.addTree(baseTree);
        tw.addTree(headTree);
        tw.addTree(mergeTree);
        int dciPos = tw.addTree(buildIt);
        if (workingTreeIterator != null) {
            tw.addTree(workingTreeIterator);
            workingTreeIterator.setDirCacheIterator(tw, dciPos);
        } else {
            tw.setFilter(TreeFilter.ANY_DIFF);
        }

        if (!mergeTreeWalk(tw, ignoreConflicts)) {
            return false;
        }

        if (!inCore) {
            // No problem found. The only thing left to be done is to
            // checkout all files from "theirs" which have been selected to
            // go into the new index.
            checkout();

            // All content-merges are successfully done. If we can now write the
            // new index we are on quite safe ground. Even if the checkout of
            // files coming from "theirs" fails the user can work around such
            // failures by checking out the index again.
            if (!builder.commit()) {
                cleanUp();
                throw new IndexWriteException();
            }
            builder = null;

        } else {
            builder.finish();
            builder = null;
        }

        if (getUnmergedPaths().isEmpty() && !failed()) {
            resultTree = dircache.writeTree(getObjectInserter());
            return true;
        }
        resultTree = null;
        return false;
    }

    /**
     * Process the given TreeWalk's entries.
     *
     * @param treeWalk
     *            The walk to iterate over.
     * @param ignoreConflicts
     *            see
     *            {@link org.eclipse.jgit.merge.ResolveMerger#mergeTrees(AbstractTreeIterator, RevTree, RevTree, boolean)}
     * @return Whether the trees merged cleanly.
     * @throws java.io.IOException
     * @since 3.5
     */
    protected boolean mergeTreeWalk(TreeWalk treeWalk, boolean ignoreConflicts)
            throws IOException {
        boolean hasWorkingTreeIterator = tw.getTreeCount() > T_FILE;
        boolean hasAttributeNodeProvider = treeWalk
                .getAttributesNodeProvider() != null;
        while (treeWalk.next()) {
            if (!processEntry(
                    treeWalk.getTree(T_BASE, CanonicalTreeParser.class),
                    treeWalk.getTree(T_OURS, CanonicalTreeParser.class),
                    treeWalk.getTree(T_THEIRS, CanonicalTreeParser.class),
                    treeWalk.getTree(T_INDEX, DirCacheBuildIterator.class),
                    hasWorkingTreeIterator ? treeWalk.getTree(T_FILE,
                            WorkingTreeIterator.class) : null,
                    ignoreConflicts, hasAttributeNodeProvider
                            ? treeWalk.getAttributes()
                            : NO_ATTRIBUTES)) {
                cleanUp();
                return false;
            }
            if (treeWalk.isSubtree() && enterSubtree)
                treeWalk.enterSubtree();
        }
        return true;
    }
}