Add built-in LFS clean filter

Adds a JGit built-in implementation of the "git lfs clean" filter. This
filter should do the same as the one described in [1]. But since this
filter is written in Java and can be called by JGit without forking new
processes it should be much faster

[1]
https://github.com/github/git-lfs/blob/master/docs/man/git-lfs-clean.1.ronn

Change-Id: If60e387e97870245b4bd765eda6717eb84cffb1d

12 files changed, 616 insertions, 7 deletions

diff --git a/org.eclipse.jgit.lfs/META-INF/MANIFEST.MF b/org.eclipse.jgit.lfs/META-INF/MANIFEST.MF
index d7a2f37498..f1eeb512aa 100644
--- a/org.eclipse.jgit.lfs/META-INF/MANIFEST.MF
+++ b/org.eclipse.jgit.lfs/META-INF/MANIFEST.MF
@@ -5,11 +5,13 @@ Bundle-SymbolicName: org.eclipse.jgit.lfs
 Bundle-Version: 4.6.0.qualifier
 Bundle-Localization: plugin
 Bundle-Vendor: %provider_name
-Export-Package: org.eclipse.jgit.lfs.errors;version="4.6.0",
+Export-Package: org.eclipse.jgit.lfs;version="4.6.0",
+ org.eclipse.jgit.lfs.errors;version="4.6.0",
  org.eclipse.jgit.lfs.internal;version="4.6.0";x-friends:="org.eclipse.jgit.lfs.test",
  org.eclipse.jgit.lfs.lib;version="4.6.0"
 Bundle-RequiredExecutionEnvironment: JavaSE-1.7
-Import-Package: org.eclipse.jgit.internal.storage.file;version="[4.6.0,4.7.0)",
+Import-Package:  org.eclipse.jgit.attributes;version="[4.6.0,4.7.0)",
+ org.eclipse.jgit.internal.storage.file;version="[4.6.0,4.7.0)",
  org.eclipse.jgit.lib;version="[4.6.0,4.7.0)",
  org.eclipse.jgit.nls;version="[4.6.0,4.7.0)",
  org.eclipse.jgit.util;version="[4.6.0,4.7.0)"
diff --git a/org.eclipse.jgit.lfs/resources/org/eclipse/jgit/lfs/internal/LfsText.properties b/org.eclipse.jgit.lfs/resources/org/eclipse/jgit/lfs/internal/LfsText.properties
index 7c3aea2261..25c101f0b0 100644
--- a/org.eclipse.jgit.lfs/resources/org/eclipse/jgit/lfs/internal/LfsText.properties
+++ b/org.eclipse.jgit.lfs/resources/org/eclipse/jgit/lfs/internal/LfsText.properties
@@ -1,7 +1,8 @@
 incorrectLONG_OBJECT_ID_LENGTH=Incorrect LONG_OBJECT_ID_LENGTH.
+inconsistentMediafileLength=mediafile {0} has unexpected length; expected {1} but found {2}.
 invalidLongId=Invalid id: {0}
 invalidLongIdLength=Invalid id length {0}; should be {1}
 requiredHashFunctionNotAvailable=Required hash function {0} not available.
 repositoryNotFound=Repository {0} not found
 repositoryReadOnly=Repository {0} is read-only
-lfsUnavailable=LFS is not available for repository {0}
\ No newline at end of file
+lfsUnavailable=LFS is not available for repository {0}
diff --git a/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/CleanFilter.java b/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/CleanFilter.java
new file mode 100644
index 0000000000..f7b55e579b
--- /dev/null
+++ b/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/CleanFilter.java
@@ -0,0 +1,176 @@
+/*
+ * Copyright (C) 2016, Christian Halstrick <christian.halstrick@sap.com>
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+package org.eclipse.jgit.lfs;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.StandardOpenOption;
+import java.security.DigestOutputStream;
+
+import org.eclipse.jgit.attributes.FilterCommand;
+import org.eclipse.jgit.attributes.FilterCommandFactory;
+import org.eclipse.jgit.attributes.FilterCommandRegistry;
+import org.eclipse.jgit.lfs.errors.CorruptMediaFile;
+import org.eclipse.jgit.lfs.lib.Constants;
+import org.eclipse.jgit.lfs.lib.LongObjectId;
+import org.eclipse.jgit.lib.Repository;
+import org.eclipse.jgit.util.FileUtils;
+
+/**
+ * Built-in LFS clean filter
+ *
+ * When new content is about to be added to the git repository and this filter
+ * is configured for that content, then this filter will replace the original
+ * content with content of a so-called LFS pointer file. The pointer file
+ * content will then be added to the git repository. Additionally this filter
+ * writes the original content in a so-called 'media file' to '.git/lfs/objects/
+ * <first-two-characters-of-contentid>/<rest-of-contentid>'
+ *
+ * @see <a href="https://github.com/github/git-lfs/blob/master/docs/spec.md">Git
+ *      LFS Specification</a>
+ * @since 4.6
+ */
+public class CleanFilter extends FilterCommand {
+	/**
+	 * The factory is responsible for creating instances of {@link CleanFilter}
+	 */
+	public final static FilterCommandFactory FACTORY = new FilterCommandFactory() {
+
+		@Override
+		public FilterCommand create(Repository db, InputStream in,
+				OutputStream out) throws IOException {
+			return new CleanFilter(db, in, out);
+		}
+	};
+
+	/**
+	 * Registers this filter by calling
+	 * {@link FilterCommandRegistry#register(String, FilterCommandFactory)}
+	 */
+	public final static void register() {
+		FilterCommandRegistry.register(
+				org.eclipse.jgit.lib.Constants.BUILTIN_FILTER_PREFIX
+						+ "lfs/clean", //$NON-NLS-1$
+				FACTORY);
+	}
+
+	// The OutputStream to a temporary file which will be renamed to mediafile
+	// when the operation succeeds
+	private OutputStream tmpOut;
+
+	// Used to compute the hash for the original content
+	private DigestOutputStream dOut;
+
+	private Lfs lfsUtil;
+
+	// the size of the original content
+	private long size;
+
+	// a temporary file into which the original content is written. When no
+	// errors occur this file will be renamed to the mediafile
+	private Path tmpFile;
+
+	/**
+	 * @param db
+	 *            the repository
+	 * @param in
+	 *            an {@link InputStream} providing the original content
+	 * @param out
+	 *            the {@link OutputStream} into which the content of the pointer
+	 *            file should be written. That's the content which will be added
+	 *            to the git repository
+	 * @throws IOException
+	 *             when the creation of the temporary file fails or when no
+	 *             {@link OutputStream} for this file can be created
+	 */
+	public CleanFilter(Repository db, InputStream in, OutputStream out)
+			throws IOException {
+		super(in, out);
+		lfsUtil = new Lfs(db.getDirectory().toPath().resolve("lfs")); //$NON-NLS-1$
+		Files.createDirectories(lfsUtil.getLfsTmpDir());
+		tmpFile = lfsUtil.createTmpFile();
+		tmpOut = Files.newOutputStream(tmpFile,
+				StandardOpenOption.CREATE);
+		this.dOut = new DigestOutputStream(
+				tmpOut,
+				Constants.newMessageDigest());
+	}
+
+	public int run() throws IOException {
+		try {
+			int b = in.read();
+			if (b != -1) {
+				dOut.write(b);
+				size++;
+				return 1;
+			} else {
+				dOut.close();
+				tmpOut.close();
+				LongObjectId loid = LongObjectId
+						.fromRaw(dOut.getMessageDigest().digest());
+				Path mediaFile = lfsUtil.getMediaFile(loid);
+				if (Files.isRegularFile(mediaFile)) {
+					long fsSize = Files.size(mediaFile);
+					if (fsSize != size) {
+						throw new CorruptMediaFile(mediaFile, size, fsSize);
+					}
+				} else {
+					FileUtils.mkdirs(mediaFile.getParent().toFile(), true);
+					FileUtils.rename(tmpFile.toFile(), mediaFile.toFile());
+				}
+				LfsPointer lfsPointer = new LfsPointer(loid, size);
+				lfsPointer.encode(out);
+				out.close();
+				return -1;
+			}
+		} catch (IOException e) {
+			out.close();
+			dOut.close();
+			tmpOut.close();
+			throw e;
+		}
+	}
+}
diff --git a/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/Lfs.java b/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/Lfs.java
new file mode 100644
index 0000000000..f099c5a761
--- /dev/null
+++ b/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/Lfs.java
@@ -0,0 +1,124 @@
+/*
+ * Copyright (C) 2016, Christian Halstrick <christian.halstrick@sap.com>
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+package org.eclipse.jgit.lfs;
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+
+import org.eclipse.jgit.lfs.lib.LongObjectId;
+
+/**
+ * Class which represents the lfs folder hierarchy inside a .git folder
+ *
+ * @since 4.6
+ */
+public class Lfs {
+	private Path root;
+
+	private Path objDir;
+
+	private Path tmpDir;
+
+	/**
+	 * @param root
+	 *            the path to the LFS media directory. Will be "<repo>/.git/lfs"
+	 */
+	public Lfs(Path root) {
+		this.root = root;
+	}
+
+	/**
+	 * @return the path to the LFS directory
+	 */
+	public Path getLfsRoot() {
+		return root;
+	}
+
+	/**
+	 * @return the path to the temp directory used by LFS. Will be
+	 *         "<repo>/.git/lfs/tmp"
+	 */
+	public Path getLfsTmpDir() {
+		if (tmpDir == null) {
+			tmpDir = root.resolve("tmp"); //$NON-NLS-1$
+		}
+		return tmpDir;
+	}
+
+	/**
+	 * @return the path to the object directory used by LFS. Will be
+	 *         "<repo>/.git/lfs/objects"
+	 */
+	public Path getLfsObjDir() {
+		if (objDir == null) {
+			objDir = root.resolve("objects"); //$NON-NLS-1$
+		}
+		return objDir;
+	}
+
+	/**
+	 * @param id
+	 *            the id of the mediafile
+	 * @return the file which stores the original content. This will be files
+	 *         underneath
+	 *         "<repo>/.git/lfs/objects/<firstTwoLettersOfID>/<remainingLettersOfID>"
+	 */
+	public Path getMediaFile(LongObjectId id) {
+		String idStr = LongObjectId.toString(id);
+		return getLfsObjDir().resolve(idStr.substring(0, 2))
+				.resolve(idStr.substring(2));
+	}
+
+	/**
+	 * Create a new temp file in the LFS directory
+	 *
+	 * @return a new temporary file in the LFS directory
+	 * @throws IOException
+	 *             when the temp file could not be created
+	 */
+	public Path createTmpFile() throws IOException {
+		return Files.createTempFile(getLfsTmpDir(), null, null);
+	}
+
+}
diff --git a/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/LfsPointer.java b/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/LfsPointer.java
new file mode 100644
index 0000000000..2521e63163
--- /dev/null
+++ b/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/LfsPointer.java
@@ -0,0 +1,121 @@
+/*
+ * Copyright (C) 2016, Christian Halstrick <christian.halstrick@sap.com>
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+package org.eclipse.jgit.lfs;
+
+import java.io.OutputStream;
+import java.io.PrintStream;
+
+import org.eclipse.jgit.lfs.lib.Constants;
+import org.eclipse.jgit.lfs.lib.LongObjectId;
+
+/**
+ * Represents an LFS pointer file
+ *
+ * @since 4.6
+ */
+public class LfsPointer {
+	/**
+	 * The version of the LfsPointer file format
+	 */
+	public static final String VERSION = "https://git-lfs.github.com/spec/v1"; //$NON-NLS-1$
+
+	/**
+	 * The name of the hash function as used in the pointer files. This will
+	 * evaluate to "sha256"
+	 */
+	public static final String HASH_FUNCTION_NAME = Constants.LONG_HASH_FUNCTION
+			.toLowerCase().replace("-", ""); //$NON-NLS-1$ //$NON-NLS-2$
+
+	private LongObjectId oid;
+
+	private long size;
+
+	/**
+	 * @param oid
+	 *            the id of the content
+	 * @param size
+	 *            the size of the content
+	 */
+	public LfsPointer(LongObjectId oid, long size) {
+		this.oid = oid;
+		this.size = size;
+	}
+
+	/**
+	 * @return the id of the content
+	 */
+	public LongObjectId getOid() {
+		return oid;
+	}
+
+	/**
+	 * @return the size of the content
+	 */
+	public long getSize() {
+		return size;
+	}
+
+	/**
+	 * Encode this object into the LFS format defined by {@link #VERSION}
+	 *
+	 * @param out
+	 *            the {@link OutputStream} into which the encoded data should be
+	 *            written
+	 */
+	public void encode(OutputStream out) {
+		try (PrintStream ps = new PrintStream(out)) {
+			ps.print("version "); //$NON-NLS-1$
+			ps.println(VERSION);
+			ps.print("oid " + HASH_FUNCTION_NAME + ":"); //$NON-NLS-1$ //$NON-NLS-2$
+			ps.println(LongObjectId.toString(oid));
+			ps.print("size "); //$NON-NLS-1$
+			ps.println(size);
+		}
+	}
+
+	@Override
+	public String toString() {
+		return "LfsPointer: oid=" + LongObjectId.toString(oid) + ", size=" //$NON-NLS-1$ //$NON-NLS-2$
+				+ size;
+	}
+}
\ No newline at end of file
diff --git a/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/errors/CorruptMediaFile.java b/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/errors/CorruptMediaFile.java
new file mode 100644
index 0000000000..f2b51c0442
--- /dev/null
+++ b/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/errors/CorruptMediaFile.java
@@ -0,0 +1,100 @@
+/*
+ * Copyright (C) 2016, Christian Halstrick <christian.halstrick@sap.com>
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+package org.eclipse.jgit.lfs.errors;
+
+import java.io.IOException;
+import java.nio.file.Path;
+import java.text.MessageFormat;
+
+import org.eclipse.jgit.lfs.internal.LfsText;
+
+/**
+ * Thrown when a LFS mediafile is found which doesn't have the expected size
+ *
+ * @since 4.6
+ */
+public class CorruptMediaFile extends IOException {
+	private static final long serialVersionUID = 1L;
+
+	private Path mediaFile;
+
+	private long expectedSize;
+
+	private long size;
+
+	/**
+	 * @param mediaFile
+	 * @param expectedSize
+	 * @param size
+	 */
+	@SuppressWarnings("boxing")
+	public CorruptMediaFile(Path mediaFile, long expectedSize,
+			long size) {
+		super(MessageFormat.format(LfsText.get().inconsistentMediafileLength,
+				mediaFile, expectedSize, size));
+		this.mediaFile = mediaFile;
+		this.expectedSize = expectedSize;
+		this.size = size;
+	}
+
+	/**
+	 * @return the media file which seems to be corrupt
+	 */
+	public Path getMediaFile() {
+		return mediaFile;
+	}
+
+	/**
+	 * @return the expected size of the media file
+	 */
+	public long getExpectedSize() {
+		return expectedSize;
+	}
+
+	/**
+	 * @return the actual size of the media file in the file system
+	 */
+	public long getSize() {
+		return size;
+	}
+}
diff --git a/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/internal/LfsText.java b/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/internal/LfsText.java
index 365eaa1727..0aad5c9dac 100644
--- a/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/internal/LfsText.java
+++ b/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/internal/LfsText.java
@@ -58,6 +58,7 @@ public class LfsText extends TranslationBundle {
 	}
 
 	// @formatter:off
+	/***/ public String inconsistentMediafileLength;
 	/***/ public String incorrectLONG_OBJECT_ID_LENGTH;
 	/***/ public String invalidLongId;
 	/***/ public String invalidLongIdLength;
diff --git a/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/lib/Constants.java b/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/lib/Constants.java
index d2464126cc..269cbc3a83 100644
--- a/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/lib/Constants.java
+++ b/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/lib/Constants.java
@@ -55,8 +55,12 @@ import org.eclipse.jgit.lfs.internal.LfsText;
  **/
 @SuppressWarnings("nls")
 public final class Constants {
-	/** Hash function used natively by Git LFS extension for large objects. */
-	private static final String LONG_HASH_FUNCTION = "SHA-256";
+	/**
+	 * Hash function used natively by Git LFS extension for large objects.
+	 *
+	 * @since 4.6
+	 */
+	public static final String LONG_HASH_FUNCTION = "SHA-256";
 
 	/**
 	 * A Git LFS large object hash is 256 bits, i.e. 32 bytes.
diff --git a/org.eclipse.jgit.pgm/META-INF/MANIFEST.MF b/org.eclipse.jgit.pgm/META-INF/MANIFEST.MF
index 3366d378cf..7c2462b806 100644
--- a/org.eclipse.jgit.pgm/META-INF/MANIFEST.MF
+++ b/org.eclipse.jgit.pgm/META-INF/MANIFEST.MF
@@ -39,6 +39,7 @@ Import-Package: javax.servlet;version="[3.1.0,4.0.0)",
  org.eclipse.jgit.internal.storage.file;version="[4.6.0,4.7.0)",
  org.eclipse.jgit.internal.storage.pack;version="[4.6.0,4.7.0)",
  org.eclipse.jgit.internal.storage.reftree;version="[4.6.0,4.7.0)",
+ org.eclipse.jgit.lfs;version="[4.6.0,4.7.0)",
  org.eclipse.jgit.lfs.lib;version="[4.6.0,4.7.0)",
  org.eclipse.jgit.lfs.server;version="[4.6.0,4.7.0)",
  org.eclipse.jgit.lfs.server.fs;version="[4.6.0,4.7.0)",
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Main.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Main.java
index d701f22c38..654573b2a4 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Main.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Main.java
@@ -57,6 +57,7 @@ import java.util.List;
 import org.eclipse.jgit.awtui.AwtAuthenticator;
 import org.eclipse.jgit.awtui.AwtCredentialsProvider;
 import org.eclipse.jgit.errors.TransportException;
+import org.eclipse.jgit.lfs.CleanFilter;
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.lib.RepositoryBuilder;
 import org.eclipse.jgit.pgm.internal.CLIText;
@@ -97,6 +98,7 @@ public class Main {
 	 */
 	public Main() {
 		HttpTransport.setConnectionFactory(new HttpClientConnectionFactory());
+		CleanFilter.register();
 	}
 
 	/**
diff --git a/org.eclipse.jgit.test/META-INF/MANIFEST.MF b/org.eclipse.jgit.test/META-INF/MANIFEST.MF
index c336037157..04bb247bee 100644
--- a/org.eclipse.jgit.test/META-INF/MANIFEST.MF
+++ b/org.eclipse.jgit.test/META-INF/MANIFEST.MF
@@ -28,6 +28,7 @@ Import-Package: com.googlecode.javaewah;version="[0.7.9,0.8.0)",
  org.eclipse.jgit.internal.storage.pack;version="[4.6.0,4.7.0)",
  org.eclipse.jgit.internal.storage.reftree;version="[4.6.0,4.7.0)",
  org.eclipse.jgit.junit;version="[4.6.0,4.7.0)",
+ org.eclipse.jgit.lfs;version="[4.6.0,4.7.0)",
  org.eclipse.jgit.lib;version="[4.6.0,4.7.0)",
  org.eclipse.jgit.merge;version="[4.6.0,4.7.0)",
  org.eclipse.jgit.nls;version="[4.6.0,4.7.0)",
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/AddCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/AddCommandTest.java
index 42601aaa9f..a3cae4b056 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/AddCommandTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/AddCommandTest.java
@@ -62,6 +62,7 @@ import org.eclipse.jgit.dircache.DirCacheBuilder;
 import org.eclipse.jgit.dircache.DirCacheEntry;
 import org.eclipse.jgit.junit.JGitTestUtil;
 import org.eclipse.jgit.junit.RepositoryTestCase;
+import org.eclipse.jgit.lfs.CleanFilter;
 import org.eclipse.jgit.lib.*;
 import org.eclipse.jgit.revwalk.RevCommit;
 import org.eclipse.jgit.storage.file.FileRepositoryBuilder;
@@ -70,8 +71,22 @@ import org.eclipse.jgit.treewalk.WorkingTreeOptions;
 import org.eclipse.jgit.util.FS;
 import org.eclipse.jgit.util.FileUtils;
 import org.junit.Test;
+import org.junit.experimental.theories.DataPoints;
+import org.junit.experimental.theories.Theories;
+import org.junit.experimental.theories.Theory;
+import org.junit.runner.RunWith;
 
+@RunWith(Theories.class)
 public class AddCommandTest extends RepositoryTestCase {
+	@DataPoints
+	public static boolean[] smudge = { true, false };
+
+
+	@Override
+	public void setUp() throws Exception {
+		CleanFilter.register();
+		super.setUp();
+	}
 
 	@Test
 	public void testAddNothing() throws GitAPIException {
@@ -110,8 +125,7 @@ public class AddCommandTest extends RepositoryTestCase {
 	}
 
 	@Test
-	public void testCleanFilter() throws IOException,
-			GitAPIException {
+	public void testCleanFilter() throws IOException, GitAPIException {
 		writeTrashFile(".gitattributes", "*.txt filter=tstFilter");
 		writeTrashFile("src/a.tmp", "foo");
 		// Caution: we need a trailing '\n' since sed on mac always appends
@@ -134,6 +148,68 @@ public class AddCommandTest extends RepositoryTestCase {
 		}
 	}
 
+	@Theory
+	public void testBuiltinFilter(boolean doSmudge)
+			throws IOException,
+			GitAPIException, InterruptedException {
+		writeTrashFile(".gitattributes", "*.txt filter=lfs");
+		writeTrashFile("src/a.tmp", "foo");
+		// Caution: we need a trailing '\n' since sed on mac always appends
+		// linefeeds if missing
+		File script = writeTempFile("sed s/o/e/g");
+		File f = writeTrashFile("src/a.txt", "foo\n");
+
+		try (Git git = new Git(db)) {
+			if (!doSmudge) {
+				fsTick(f);
+			}
+			git.add().addFilepattern(".gitattributes").call();
+			StoredConfig config = git.getRepository().getConfig();
+			config.setString("filter", "lfs", "clean",
+					"sh " + slashify(script.getPath()));
+			config.setString("filter", "lfs", "smudge",
+					"sh " + slashify(script.getPath()));
+			config.setBoolean("filter", "lfs", "useJGitBuiltin", true);
+			config.save();
+
+			if (!doSmudge) {
+				fsTick(f);
+			}
+			git.add().addFilepattern("src/a.txt").addFilepattern("src/a.tmp")
+					.addFilepattern(".gitattributes").call();
+
+			assertEquals(
+					"[.gitattributes, mode:100644, content:*.txt filter=lfs][src/a.tmp, mode:100644, content:foo][src/a.txt, mode:100644, content:version https://git-lfs.github.com/spec/v1\noid sha256:b5bb9d8014a0f9b1d61e21e796d78dccdf1352f23cd32812f4850b878ae4944c\nsize 4\n]",
+					indexState(CONTENT));
+
+			RevCommit c1 = git.commit().setMessage("c1").call();
+			assertTrue(git.status().call().isClean());
+			f = writeTrashFile("src/a.txt", "foobar\n");
+			if (!doSmudge) {
+				fsTick(f);
+			}
+			git.add().addFilepattern("src/a.txt").call();
+			git.commit().setMessage("c2").call();
+			assertTrue(git.status().call().isClean());
+			assertEquals(
+					"[.gitattributes, mode:100644, content:*.txt filter=lfs][src/a.tmp, mode:100644, content:foo][src/a.txt, mode:100644, content:version https://git-lfs.github.com/spec/v1\noid sha256:aec070645fe53ee3b3763059376134f058cc337247c978add178b6ccdfb0019f\nsize 7\n]",
+					indexState(CONTENT));
+			assertEquals("foobar\n", read("src/a.txt"));
+			git.checkout().setName(c1.getName()).call();
+			assertEquals(
+					"[.gitattributes, mode:100644, content:*.txt filter=lfs][src/a.tmp, mode:100644, content:foo][src/a.txt, mode:100644, content:version https://git-lfs.github.com/spec/v1\noid sha256:b5bb9d8014a0f9b1d61e21e796d78dccdf1352f23cd32812f4850b878ae4944c\nsize 4\n]",
+					indexState(CONTENT));
+			// due to lfs clean filter but dummy smudge filter we expect strange
+			// content. The smudge filter converts from real content to pointer
+			// file content (starting with "version ") but the smudge filter
+			// replaces 'o' by 'e' which results in a text starting with
+			// "versien "
+			assertEquals(
+					"versien https://git-lfs.github.cem/spec/v1\neid sha256:b5bb9d8014a0f9b1d61e21e796d78dccdf1352f23cd32812f4850b878ae4944c\nsize 4\n",
+					read("src/a.txt"));
+		}
+	}
+
 	@Test
 	public void testAttributesWithTreeWalkFilter()
 			throws IOException, GitAPIException {