Check the last line of the last hunk of a file, not the last line of
the whole patch.

Note that C git only checks that this line starts with "\ " and is at
least 12 characters long because of possible different texts when non-
English messages are used.

Change-Id: I0db81699eb3e99ed7b536a3e2b8dc97df1f58a89
Signed-off-by: Thomas Wolf <thomas.wolf@paranor.ch>

C git treats completely empty lines as empty context lines (which
traditionally have a single blank). Apparently newer GNU diff may
produce such lines; see [1]. ("Newer" meaning "since 2006"...)

[1] https://github.com/git/git/commit/b507b465f7831

Change-Id: I80c1f030edb17a46289b1dabf11a2648d2660d38
Signed-off-by: Thomas Wolf <thomas.wolf@paranor.ch>

Instead of converting the patch bytes to strings apply the patch on
byte level, like C git does. Converting the input lines and the hunk
lines from bytes to strings and then applying the patch based on
strings may give surprising results if a patch converts a text file
from one encoding to another. Moreover, in the end we don't know which
encoding to use to write the result.

Previous code just wrote the result as UTF-8, which forcibly changed
the encoding if the original input had some other encoding (even if the
patch had the same non-UTF-8 encoding). It was also wrong if the input
was UTF-8, and the patch should have changed the encoding to something
else.

So use ByteBuffers instead of Strings. This has the additional advantage
that all these ByteBuffers can share the underlying byte arrays of the
input and of the patch, so it also reduces memory consumption.

Change-Id: I450975f2ba0e7d0bec8973e3113cc2e7aea187ee
Signed-off-by: Thomas Wolf <thomas.wolf@paranor.ch>

Implement applying binary patches. Handles both literal and delta
patches. Note that C git also runs binary files through the clean
and smudge filters. Implement the same safeguards against corrupted
patches as in C git: require the full OIDs to be present in the patch
file, and apply a binary patch only if both pre- and post-image hashes
match.

Add tests for applying literal and delta patches.

Bug: 371725
Change-Id: I71dc214fe4145d7cc8e4769384fb78c7d0d6c220
Signed-off-by: Thomas Wolf <thomas.wolf@paranor.ch>

Add a new BinaryDeltaInputStream that applies a delta provided by
another InputStream to a given base. Because delta application needs
random access to the base, the base itself cannot be yet another
InputStream. But at least this enables streaming of the result.

Add a simple test using delta hunks generated by C git.

Bug: 371725
Change-Id: Ibd26fa2f49860737ad5c5387f7f4870d3e85e628
Signed-off-by: Thomas Wolf <thomas.wolf@paranor.ch>
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>

Applying a patch on Windows failed if the patch had the (normal)
single-LF line endings, but the file on disk had the usual Windows
CR-LF line endings.

Git (and JGit) compute diffs on the git-internal blob, i.e., after
CR-LF transformation and clean filtering. Applying patches to files
directly is thus incorrect and may fail if CR-LF settings don't
match, or if clean/smudge filtering is involved.

Change ApplyCommand to run the file content through the check-in
filters before applying the patch, and run the result through the
check-out filters. This makes patch application succeed even if the
patch has single-LFs, but the file has CR-LF and core.autocrlf is
true.

Add tests for various combinations of line endings in the file and in
the patch, and a test to verify the clean/smudge handling.

See also [1].

Running the file though clean/smudge may give strange results with
LFS-managed files. JGit's DiffFormatter has some extra code and
applies the smudge filter again after having run the file through
the check-in filters (CR-LF and clean). So JGit can actually produce
a diff on LFS-managed files using the normal diff machinery. (If it
doesn't run out of memory, that is. After all, LFS is intended for
_large_ files.) How such a diff would be applied with either C git
or JGit is entirely unclear; neither has any code for this special
case. Compare also [2].

Note that C git just doesn't know about LFS and always diffs after
the check-in filter chain, so for LFS files, it'll produce a diff
of the LFS pointers.

[1] https://github.com/git/git/commit/c24f3abac
[2] https://github.com/git-lfs/git-lfs/issues/440

Bug: 571585
Change-Id: I8f71ff26313b5773ff1da612b0938ad2f18751f5
Signed-off-by: Thomas Wolf <thomas.wolf@paranor.ch>

A cookie file stores the expiration in seconds since the Linux Epoch,
not in milliseconds. Correct reading and writing cookie files; with
a backwards-compatibility hack to read files that contain a millisecond
timestamp.

Add a test, and fix tests not to rely on the actual current time so
that they will also run successfully after 2030-01-01 noon.

Bug: 571574
Change-Id: If3ba68391e574520701cdee119544eedc42a1ff2
Signed-off-by: Thomas Wolf <thomas.wolf@paranor.ch>

Due to an integer overflow bug, the current "Index file is too large
for jgit" check did not work properly and subsequently a
NegativeArraySizeException was raised.

Change-Id: I2736efb28987c29e56bc946563b7fa781898a94a
Signed-off-by: Marc Strapetz <marc.strapetz@syntevo.com>

Index format version 4 was introduced in C git in 2012. It's about
time that JGit can deal with it.

Version 4 added prefix path compression. Instead of writing the full
path for each index entry to disk, only the difference to the previous
entry's path is written: a variable-encoded int telling how many bytes
to remove from the previous entry's path to get the common prefix,
followed by the new suffix.

Also, cache entries in a version 4 index are not padded anymore.

Internally, version 3 and version 4 index entries are identical; it's
only the stored format that changes.

Implement this path compression, and make sure we write an index file
that we read previously in the same format. (Only changing from version
2 to version 3 if there are extended flags.)

Add support for the "feature.manyFiles" and the "index.version" git
configs, and honor them when writing a new index file.

Add tests, including a compatibility test that verifies that JGit can
read a version 4 index generated by C git and write an identical
version 4 index.

Bug: 565774
Change-Id: Id83241cf009e50f950eb42f8d56b834fb47da1ed
Signed-off-by: Thomas Wolf <thomas.wolf@paranor.ch>

If a hunk does not apply at the position stated in the hunk header
try to determine its position using the old lines (context and
deleted lines).

This is still a far cry from a full git apply: it doesn't do binary
patches, it doesn't handle git's whitespace options, and it's perhaps
not the fastest on big patches. C git hashes the lines and uses these
hashes to speed up matching hunks (and to do its whitespace magic).

Bug: 562348
Change-Id: Id0796bba059d84e648769d5896f497fde0b787dd
Signed-off-by: Thomas Wolf <thomas.wolf@paranor.ch>

In Git 2.10.0 the interpretation of gitattributes changed or was fixed
such that "* text=auto eol=crlf" would indeed still do auto-detection
of text vs. binary content.[1] Previously this was identical to
"* text eol=crlf", i.e., treating all files as text.

JGit still did the latter, which caused surprises because it changed
binary files.

[1] https://github.com/git/git/blob/master/Documentation/RelNotes/2.10.0.txt#L248

Bug: 561341
Change-Id: I5b6fb97b5e86fd950a98537b6b8574f768ae30e5
Signed-off-by: Thomas Wolf <thomas.wolf@paranor.ch>

When applying a patch that contains renames or copies using ApplyCommand,
also apply all hunks that apply to the renamed or copied file.

Change-Id: I9f3fa4370458bd7c14beeb2e2b49e846d70203cb
Signed-off-by: Jack Wickham <jwickham@palantir.com>

Before this change, applying a patch will fail if the destination directory
doesn't exist; after, the necessary parent directories are created.

If renaming the file fails, the directories won't be deleted, so this change
isn't atomic. However, ApplyCommand is already not atomic - if one hunk fails
to apply, other hunks still get applied - so I don't think that is a blocker.

Change-Id: Iea36138b806d4e7012176615bcc673756a82f365
Signed-off-by: Jack Wickham <jwickham@palantir.com>

Bug: 548219
Change-Id: Ibb32132a38e54508a24489322da58ddfd80a1d9a
Signed-off-by: Anton Khodos <khodosanton@gmail.com>
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>

The git config entries "http.cookieFile" and
"http.saveCookies" are correctly evaluated.

Bug: 488572
Change-Id: Icfeeea95e1a5bac3fa4438849d4ac2306d7d5562
Signed-off-by: Konrad Windszus <konrad_w@gmx.de>
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>

Add a new ssh client implementation based on Apach MINA sshd 2.0.0.

This implementation uses JGit's own config file parser and host entry
resolver. Code inspection of the Apache MINA implementation revealed
a few bugs or idiosyncrasies that immediately would re-introduce bugs
already fixed in the past in JGit.

Apache MINA sshd is not without quirks either, and I had to configure
and override more than I had expected. But at least it was all doable
in clean ways.

Apache MINA boasts support for Bouncy Castle, so in theory this should
open the way to using more ssh key algorithms, such as ed25519.

The implementation is in a separate bundle and is still not used in
the core org.eclipse.jgit bundle. The tests re-use the ssh tests from
the core test bundle.

Bug: 520927
Change-Id: Ib35e73c35799140fe050d1ff4fb18d0d3596580e
Signed-off-by: Thomas Wolf <thomas.wolf@paranor.ch>

Add support for git-receive-pack to the ssh git server and add two
new tests for pushing.

This actually uncovered an undocumented requirement in TransportSftp:
the FTP rename operation assumes POSIX semantics, i.e., that the
target is removed. This works as written only for servers that
support and advertise the "posix-rename@openssh.com" FTP extension.

Our little Apache MINA server does not advertise this extension.

Fix the FtpChannel implementation for Jsch to handle this case in a
meaningful way so that it can pass the new "push over sftp" test.

Add more tests to test the behavior of server host key checking.

Also refactor the tests generally to separate better the test
framework from the actual tests.

Bug: 520927
Change-Id: Ia4bb85e17ddacde7b36ee8c2d5d454bbfa66dfc3
Signed-off-by: Thomas Wolf <thomas.wolf@paranor.ch>

Add a simple ssh git server based on Apache MINA sshd, and use it
in new tests that verify ssh operations and in particular a number
of bugs that had cropped up over time in JSch.

The git server supports fetching only, and sftp access.

The tests are all in an abstract base class; the concrete JschSshTest
class only provides ssh-specific test setup. So the same tests could
be run easily also with some other ssh client.

Bug: 520927
Change-Id: Ide6687b717fb497a29fc83f22b07390a26dfce1d
Signed-off-by: Thomas Wolf <thomas.wolf@paranor.ch>

The merger is now able to react to the use of the merge attribute.
The value unset and the custom value 'binary' are handled (-merge
and merge=binary)

Since the specification of the merge attribute states that when the
attribute is unset, ours version must be kept in case of a conflict, we
don't overwrite the file but keep the local version.

Bug: 517128
Change-Id: Ib5fbf17bdaf727bc5d0e106ce88f2620d9f87a6f
Signed-off-by: Mathieu Cartaud <mathieu.cartaud@obeo.fr>

Update SHA1 class to include a Java port of sha1dc[1]'s ubc_check,
which can detect the attack pattern used by the SHAttered[2] authors.

Given the shattered example files that have the same SHA-1, this
modified implementation can identify there is risk of collision given
only one file in the pair:

  $ jgit ...
  [main] WARN org.eclipse.jgit.util.sha1.SHA1 - SHA-1 collision 38762cf7f5

When JGit detects probability of a collision the SHA1 class now warns
on the logger, reporting the object's SHA-1 hash, and then throws a
Sha1CollisionException to the caller.

From the paper[3] by Marc Stevens, the probability of a false positive
identification of a collision is about 14 * 2^(-160), sufficiently low
enough for any detected collision to likely be a real collision.

git-core[4] may adopt sha1dc before the system migrates to an entirely
new hash function.  This commit enables JGit to remain compatible with
that move to sha1dc, and help protect users by warning if similar
attacks as SHAttered are identified.

Performance declined about 8% (detection off), now:

  MessageDigest        238.41 MiB/s
  MessageDigest        244.52 MiB/s
  MessageDigest        244.06 MiB/s
  MessageDigest        242.58 MiB/s

  SHA1                 216.77 MiB/s (was ~240.83 MiB/s)
  SHA1                 220.98 MiB/s
  SHA1                 221.76 MiB/s
  SHA1                 221.34 MiB/s

This decline in throughput is attributed to the step loop unrolling in
compress(), which was necessary to easily fit the UbcCheck logic into
the hash function.  Using helper functions s1-s4 reduces the code
explosion, providing acceptable throughput.

With detection enabled (default):

  SHA1 detectCollision 180.12 MiB/s
  SHA1 detectCollision 181.59 MiB/s
  SHA1 detectCollision 181.64 MiB/s
  SHA1 detectCollision 182.24 MiB/s

  sha1dc (native C)   ~206.28 MiB/s
  sha1dc (native C)   ~204.47 MiB/s
  sha1dc (native C)   ~203.74 MiB/s

Average time across 100,000 calls to hash 4100 bytes (such as a commit
or tree) for the various algorithms available to JGit also shows SHA1
is slower than MessageDigest, but by an acceptable margin:

  MessageDigest        17 usec
  SHA1                 18 usec
  SHA1 detectCollision 22 usec

Time to index-pack for git.git (217982 objects, 69 MiB) has increased:

  MessageDigest   SHA1 w/ detectCollision
  -------------   -----------------------
         20.12s   25.25s
         19.87s   25.48s
         20.04s   25.26s

    avg  20.01s   25.33s    +26%

Being implemented in Java with these additional safety checks is
clearly a penalty, but throughput is still acceptable given the
increased security against object name collisions.

[1] https://github.com/cr-marcstevens/sha1collisiondetection
[2] https://shattered.it/
[3] https://marc-stevens.nl/research/papers/C13-S.pdf
[4] https://public-inbox.org/git/20170223230621.43anex65ndoqbgnf@sigill.intra.peff.net/

Change-Id: I9fe4c6d8fc5e5a661af72cd3246c9e67b1b9fee6

Symlinks on MacOS are written as UTF-8 NFD, but
readSymbolicLink().toString() converts to NFC with potentially fewer
bytes. May occur in particular if the link target has non-ASCII
characters for which the NFC and NFD encodings differ. This may lead
to an EOFException: Short read of block.

This causes all kinds of weird effects in EGit, ranging from failing
rebases (which report the exception to the user) to EGit decorations in
the navigator silently disappearing (and never coming back).

* Rename readContentAsNormalizedString() to readSymlinkTarget() as it's
  called only for symlinks. Also make it protected.
* Fix by allowing the read to succeed even if less than the expected
  number of bytes are returned by the entry's input stream.
* Override in FileTreeIterator to use fs.readSymlink() directly.

Includes a new MacOS-only test.

Change-Id: I264c5972d67b1cbb1ed690580f5706e671b9affd
Signed-off-by: Thomas Wolf <thomas.wolf@paranor.ch>
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>

git-apply allows modifying file modes in patched files using either
"new mode" or "new file mode" headers. This patch adds support for
setting files as executables and vice-versa.

Change-Id: I24848966b46f686f540a8efa8150b42e0d9c3ad1
Signed-off-by: Nadav Cohen <nadavcoh@gmail.com>

Such hunks are identifiable by a zero value for "new start line". Prior
to the fix, JGit throws and ArrayIndexOutOfBoundsException on such
patches.

Change-Id: I4f3deb5e5f41a08af965fcc178d678c77270cddb
Signed-off-by: Jonathan Schneider <jkschneider@gmail.com>
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>

Bug: 483943
Change-Id: If28f64053d20ab1bee54245f223e952dc2fe392c
Signed-off-by: XinTong Wang <xintong@ca.ibm.com>
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>

Previously the result of an application would have been \r\r\n in the
case of windows line endings, as RawText does not touch the \r, and
ApplyCommand adds "\r\n" if this is the ending of the first line in the
target file. Only always adding \n should be ok, since \r\n would be the
result if the file and the patch include windows line endings.

Also add according test.

Change-Id: Ibd4c4948d81bd1c511ecf5fd6c906444930d236e

Otherwise applying will fail with a FileNotFoundException, because
File.createNewFile() fails with missing parents.

Contains change & according test.

Change-Id: I970522b549b8bb260ca6720da11f12c57ee8a492
Signed-off-by: Chris Aniszczyk <zx@twitter.com>

Bug: 361548
CQ: 6243
Change-Id: I08e1369e142bb19f42a8d7bbb5a7d062cc8533fc
Signed-off-by: Chris Aniszczyk <zx@twitter.com>

The test was never run from maven, because its name did not end
in a way that was recognized by the pom. After rename it failed
because it did not find its resources.

Rename test class and move resources to the resources folder

Change-Id: I74a7ef1373cd902e1d05ff6ea38f8648b5fc5700
Signed-off-by: Robin Rosenberg <robin.rosenberg@dewire.com>

If the 'TREE' extension contains an invalid subtree that has
been removed, DirCacheIterator still tried to access it due to
an invalid childCnt field within the parent DirCacheTree object.
This is easy for a user to do, they just need to move all files
out of a subdirectory.

For example, the input for the JUnit test case for this bug was
built using the following C Git sequence:

  mkdir -p a/b
  touch a/b/c q
  git add a/b/c q
  git write-tree
  git mv a/b/c a/a

After the last step, the subdirectory a/b is empty, as its only
file was moved into the parent directory.  Because of the earlier
`git write-tree` operation, there is a 'TREE' extension present, but
the a and a/b subdirectories have been marked invalid by the rename.

When JGit tried to iterate over the a tree, it tried to correct
childCnt to be zero as a/b no longer exists, but it failed to
update childCnt.

Change-Id: I7a0f78fc48a36b1a83252d354618f6807fca0426
Signed-off-by: Shawn O. Pearce <spearce@spearce.org>

Extended flags are processed and available via DirCacheEntry's
new isSkipWorkTree() and isIntentToAdd() methods.  "resolve-undo"
information is completely ignored since its an optional extension.

Change-Id: Ie6e9c6784c9f265ca3c013c6dc0e6bd29d3b7233

The working tree iterator has perfect knowledge of the path structure
as well as immediate information about whether or not an ignore file
even exists at this level.  We can exploit that to simplify the
logic and running time for testing ignored file status by pushing
all of the checks down into the iterator itself.

Change-Id: I22ff534853e8c5672cc5c2d9444aeb14e294070e
Signed-off-by: Shawn O. Pearce <spearce@spearce.org>
CC: Charley Wang <chwang@redhat.com>
CC: Chris Aniszczyk <caniszczyk@gmail.com>
CC: Stefan Lay <stefan.lay@sap.com>
CC: Matthias Sohn <matthias.sohn@sap.com>

This patch adds ignore compatibility to jgit. It encompasses
exclude files as well as .gitignore. Uses TreeWalk and
FileTreeIterator to find nodes and parses .gitignore
files when required. The patch includes a simple cache that
can be used to save results and avoid excessive gitignore
parsing.

CQ: 4302
Bug: 303925
Change-Id: Iebd7e5bb534accca4bf00d25bbc1f561d7cad11b
Signed-off-by: Chris Aniszczyk <caniszczyk@gmail.com>
Signed-off-by: Stefan Lay <stefan.lay@sap.com>
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>

We didn't skip the correct number of bytes when we skipped over an
unrecognized but optional dircache extension.  We missed skipping
the 8 byte header that makes up the extension's name and length.

We also didn't include the skipped extension's payload as part of
our index checksum, resuting in a checksum failure when the index
was done reading.  So ensure we always scan through a skipped
section and include it in the checksum computation.

Add a test case for a currently unsupported index extension, 'ZZZZ',
to verify we can still read the DirCache object even though we
don't know what 'ZZZZ' is supposed to mean.

Bug: 301287
Change-Id: I4bdde94576fffe826d0782483fd98cab1ea628fa
Signed-off-by: Shawn O. Pearce <spearce@spearce.org>

The test data is expected to have unix new lines by tests, but it
is converted to crlf on Windows platform (with msys git). As result
DiffFormatterReflowTest tests fail. To prevent this problem,
crlf conversion is disbled for test data related to that test.

Bug: 295077
Change-Id: I67d3ed543fcc38647041896146de12b1781ec6be
Signed-off-by: Constantine Plotnikov <constantine.plotnikov@gmail.com>

Per CQ 3448 this is the initial contribution of the JGit project
to eclipse.org.  It is derived from the historical JGit repository
at commit 3a2dd9921c.

Signed-off-by: Shawn O. Pearce <spearce@spearce.org>