We shouldn't escape non-special ASCII characters such as '@' or '~'.
These are valid in a path name on POSIX systems, and may appear as
part of a path in a GNU or Git style patch script.  Escaping them
into octal just obfuscates the user's intent, with no gain.

When parsing an escaped octal sequence, we must parse no more
than 3 digits.  That is, "\1002" is actually "@2", not the Unicode
character \u0202.

Change-Id: I3a849a0d318e69b654f03fd559f5d7f99dd63e5c
Signed-off-by: Shawn O. Pearce <spearce@spearce.org>

Sorting the array can be useful when its being used as a map of pairs
that are appended into the array and then later merge-joined against
another array of similar semantics.

Change-Id: I2e346ef5c99ed1347ec0345b44cda0bc29d03e90
Signed-off-by: Shawn O. Pearce <spearce@spearce.org>

To give the user more control on which file system abstraction
should be used on Windows, FS.detect() may be configured
to assume a Cygwin installation or nor.

Change-Id: Iffa220de76c5e180796fa46c4d67f52a1b3b2e35
Signed-off-by: Shawn O. Pearce <spearce@spearce.org>

Large delta streams are unpacked incrementally, but because a delta
can seek to a random position in the base to perform a copy we may
need to inflate the base repeatedly just to complete one delta.
So work around it by copying the base to a temporary file, and then
we can read from that temporary file using random seeks instead.
Its far more efficient because we now only need to inflate the
base once.

This is still really ugly because we have to dump to a temporary
file, but at least the code can successfully process a large
file without throwing OutOfMemoryError.  If speed is an
issue, the user will need to increase the JVM heap and ensure
core.streamFileThreshold is set to a higher value, so we don't use
this code path as often.

Unfortunately we lose the "optimization" of skipping over portions
of a delta base that we don't actually need in the final result.
This is going to cause us to inflate and write to disk useless
regions that were deleted and do not appear in the final result.
We could later improve on our code by trying to flatten delta
instruction streams before we touch the bottom base object, and
then only store the portions of the base we really need for the
final result and that appear out-of-order.  Since that is some
pretty complex code I'm punting on it for now and just doing this
simple whole-object buffering.

Because the process umask might be permitting other users to read
files we create, we put the temporary buffers into $GIT_DIR/objects.
We can reasonably assume that if a reader can read our temporary
buffer file in that directory, they can also read the base pack
file we are pulling it from and therefore its not a security breach
to expose the inflated content in a file.  This requires a reader
to have write access to the repository, but only if the file is
really big.  I'd rather err on the side of caution here and refuse
to read a very big file into /tmp than to possibly expose a secured
content because the Java 5 JVM won't let us create a protected
temporary file that only the current user can access.

Change-Id: I66fb80b08cbcaf0f65f2db0462c546a495a160dd
Signed-off-by: Shawn O. Pearce <spearce@spearce.org>

PersonIdent should be parsable for an invalid commit which
contains multiple authors, like "A <a@a.org>, B <b@b.org>".
PersonIdent(String) constructor now delegates to
RawParseUtils.parsePersonIdent().

Change-Id: Ie9798d36d9ecfcc0094ca795f5a44b003136eaf7

WorkingTreeIterator now optionally performs CRLF to LF conversion for
text files.  A basic framework is left in place to support enabling
(or disabling) this feature based on gitattributes, and also to
support the more generic smudge/clean filter system.  As there is
no gitattribute support yet in JGit this is left unimplemented,
but the mightNeedCleaning(), isBinary() and filterClean() methods
will provide reasonable places to plug that into in the future.

[sp: All bugs inside of WorkingTreeIterator are my fault, I wrote
     most of it while cherry-picking this patch and building it on
     top of Marc's original work.]

CQ: 4419
Bug: 301775
Change-Id: I0ca35cfbfe3f503729cbfc1d5034ad4abcd1097e
Signed-off-by: Shawn O. Pearce <spearce@spearce.org>

It is useful to be able to replace an existing Change-Id
in the message, for example if the user decides not to
amend the previous commit.

Bug: 321188
Change-Id: I594e7f9efd0c57d794d2bd26d55ec45f4e6a47fd
Signed-off-by: Stefan Lay <stefan.lay@sap.com>
Signed-off-by: Chris Aniszczyk <caniszczyk@gmail.com>

LockFile.commit fails if another thread concurrently reads
the base file. The problem is fixed by retrying the rename
operation if it fails.

Change-Id: I6bb76ea7f2e6e90e3ddc45f9dd4d69bd1b6fa1eb
Bug: 308506
Signed-off-by: Jens Baumgart <jens.baumgart@sap.com>

GitIndex.write fails if another thread concurrently reads
the index file. The problem is fixed by retrying the rename
operation if it fails.

Bug: 311051
Change-Id: Ib243d2a90adae312712d02521de4834d06804944
Signed-off-by: Jens Baumgart <jens.baumgart@sap.com>

If the heap limit was set to something smaller than 8 KiB, we were
still allocating the full 8 KiB block size, and accepting up to
the amount we allocated by.  Instead actually put a hard cap on
the limit.

Change-Id: Id1da26fde2102e76510b1da4ede8493928a981cc
Signed-off-by: Shawn O. Pearce <spearce@spearce.org>

It is possible that StreamCopyThread will not flush everything
from it's src to it's dst.  In most cases StreamCopyThread works
like this:

  in loop:
    n = src.read(buf);
    dst.write(buf, 0, n);

and when we want to flush, we interrupt() StreamCopyThread and it
flushes everything it wrote to dst.

The problem is that our interrupt() could interrupt reading. In this
case we will flush everything we wrote to dst, but not everything
we wrote to src.

Change-Id: Ifaf4d8be87535c7364dd59b217dfc631460018ff
Signed-off-by: Shawn O. Pearce <spearce@spearce.org>

JGit did not have support for skipping whitespace when comparing
lines in RawText objects. I added a subclass of RawText that skips
whitespace in its equals and hashCode methods. I used a subclass
rather than adding functionality into RawText so that performance
would not be impacted by extra logic.

This class only supports ignoring all whitespace. Others will follow
that allow other forms of whitespace ignoring.

Change-Id: Ic2f79e85215e48d3fd53ec1b4ad13373dd183a4a

This move isolates all of the local file specific implementation code
into a single package, where their package-private methods and support
classes are properly hidden away from the rest of the core library.

Because of the sheer number of files impacted, I have limited this
change to only the renames and the updated imports.

Change-Id: Icca4884e1a418f83f8b617d0c4c78b73d8a4bd17
Signed-off-by: Shawn O. Pearce <spearce@spearce.org>

Output of selected reuses is refactored to use a new ObjectReuseAsIs
interface that extends the ObjectReader.  This interface allows the
reader to control how it performs the reuse into the output stream,
but also allows it to throw an exception to request the writer to
find a different candidate representation.

The PackFile reuse code was overhauled, cleaning up the APIs so they
aren't exposed in the object loader, but instead are now a single
method on the PackFile itself.  The reuse algorithm was changed to do
a data verification pass, followed by the copy pass to the output.
This permits us to work around a corrupt object in a pack file by
seeking another copy of that object when this one is bad.

The reuse code was also optimized for the common case, where the
in-pack representation is under 16 KiB.  In these smaller cases
data is sent to the pack writer more directly, avoiding some copying.

Change-Id: I6350c2b444118305e8446ce1dfd049259832bcca
Signed-off-by: Shawn O. Pearce <spearce@spearce.org>

The ObjectInserter API permits ObjectDatabase implementations to
control their own object insertion behavior, rather than forcing
it to always be a new loose file created in the local filesystem.
Inserted objects can also be queued and written asynchronously to
the main application, such as by appending into a pack file that
is later closed and added to the repository.

This change also starts to open the door to non-file based object
storage, such as an in-memory HashMap for unit testing, or a more
complex system built on top of a distributed hash table.

To help existing application code port to the newer interface we
are keeping ObjectWriter as a delegation wrapper to the new API.
Each ObjectWriter instances holds a reference to an ObjectInserter
for the Repository's top-level ObjectDatabase, and it flushes and
releases that instance on each object processed.

Change-Id: I413224fb95563e7330c82748deb0aada4e0d6ace
Signed-off-by: Shawn O. Pearce <spearce@spearce.org>

If UploadPack invokes flush() on the output stream we pass it, its
most likely the progress messages coming down the side band stream.
As pack generation can take a while, we want to push that down
at the client as early as we can, to keep the connection alive,
and to let the user know we are still working on their behalf.

Ensure we dump the temporary buffer whenever flush() is invoked,
otherwise the messages don't get sent in a timely fashion to the
user agent (in this case, git fetch).

We specifically don't implement flush() for ReceivePack right now,
as that protocol currently does not provide progress messages to
the user, but it does invoke flush several times, as the different
streams include '0000' type flush-pkts to denote various end points.

Change-Id: I797c90a2c562a416223dc0704785f61ac64e0220
Signed-off-by: Shawn O. Pearce <spearce@spearce.org>

On Windows, FS_Win32_Cygwin has been used if a Cygwin Git installation
is present in the PATH. Assuming that the user works with the Cygwin
Git installation may result in unnecessary overhead if he actually
does not.

Applications built on top of jgit may have more knowledge on the
actually used Git client (Cygwin or not) and hence should be able to
configure which FS to use accordingly.

Change-Id: Ifc4278078b298781d55cf5421e9647a21fa5db24

A Change-Id helps tools like Gerrit Code Review to keeps different
versions of a patch together. The Change-Id is computed as a SHA-1
hash of some of the same basic information as a commit id on the first
commit intended to solve a particular problem and then reused for
updated solutions.

Change-Id: I04334f84e76e83a4185283cb72ea0308b1cb4182
Signed-off-by: Robin Rosenberg <robin.rosenberg@dewire.com>

The J2SE NIO APIs require that FileChannel close the underlying file
descriptor if a thread is interrupted while it is inside of a read or
write operation on that channel.  This is insane, because it means we
cannot share the file descriptor between threads.  If a thread is in
the middle of the FileChannel variant of IO.readFully() and it
receives an interrupt, the pack will be automatically closed on us.
This causes the other threads trying to use that same FileChannel to
receive IOExceptions, which leads to the pack getting marked as
invalid.  Once the pack is marked invalid, JGit loses access to its
entire contents and starts to report MissingObjectExceptions.

Because PackWriter must ensure that the chosen pack file stays
available until the current object's data is fully copied to the
output, JGit cannot simply reopen the pack when its automatically
closed due to an interrupt being sent at the wrong time.  The pack may
have been deleted by a concurrent `git gc` process, and that open file
descriptor might be the last reference to the inode on disk.  Once its
closed, the PackWriter loses access to that object representation, and
it cannot complete sending the object the client.

Fortunately, RandomAccessFile's readFully method does not have this
problem.  Interrupts during readFully() are ignored.  However, it
requires us to first seek to the offset we need to read, then issue
the read call.  This requires locking around the file descriptor to
prevent concurrent threads from moving the pointer before the read.

This reduces the concurrency level, as now only one window can be
paged in at a time from each pack.  However, the WindowCache should
already be holding most of the pages required to handle the working
set for a process, and its own internal locking was already limiting
us on the number of concurrent loads possible.  Provided that most
concurrent accesses are getting hits in the WindowCache, or are for
different repositories on the same server, we shouldn't see a major
performance hit due to the more serialized loading.

I would have preferred to use a pool of RandomAccessFiles for each
pack, with threads borrowing an instance dedicated to that thread
whenever they needed to page in a window.  This would permit much
higher levels of concurrency by using multiple file descriptors (and
file pointers) for each pack.  However the code became too complex to
develop in any reasonable period of time, so I've chosen to retrofit
the existing code with more serialization instead.

Bug: 308945
Change-Id: I2e6e11c6e5a105e5aef68871b66200fd725134c9
Signed-off-by: Shawn O. Pearce <spearce@spearce.org>

The strings are externalized into the root resource bundles.
The resource bundles are stored under the new "resources" source
folder to get proper maven build.

Strings from tests are, in general, not externalized. Only in
cases where it was necessary to make the test pass the strings
were externalized. This was typically necessary in cases where
e.getMessage() was used in assert and the exception message was
slightly changed due to reuse of the externalized strings.

Change-Id: Ic0f29c80b9a54fcec8320d8539a3e112852a1f7b
Signed-off-by: Sasa Zivkov <sasa.zivkov@sap.com>

In close() method of SshFetchConnection and SshPushConnection
errorThread.join() can wait forever if JSch will not close the
channel's error stream.  Join with a timeout, and interrupt the
copy thread if its blocked on data that will never arrive.

Bug: 312863
Change-Id: I763081267653153eed9cd7763a015059338c2df8
Reported-by: Dmitry Neverov <dmitry.neverov@gmail.com>
Signed-off-by: Shawn O. Pearce <spearce@spearce.org>

If we get an interrupt during an IO operation (src.read or dst.write)
caused by the flush() method incrementing the flush counter, ensure
we restart the proper section of code.  Just ignore the interrupt
and continue running.

Bug: 313082
Change-Id: Ib2b37901af8141289bbac9807cacf42b4e2461bd
Signed-off-by: Shawn O. Pearce <spearce@spearce.org>

If a flush() gets delivered at the same time that we are blocking
while writing to an interruptable stream, the copy thread will
abort assuming its a stream error.  Instead ignore the interrupt,
and retry the write.

Change-Id: Icbf62d1b8abe0fabbb532dbee088020eecf4c6c2
Signed-off-by: Shawn O. Pearce <spearce@spearce.org>

It is possible to miss flush() invocation in StreamCopyThread.
In this case some data will not be sent to remote host and we will
wait forever (or until timeout) in src.read().

Use a counter to keep track of the flush requests.

Change-Id: Ia818be9b109a1674d9e2a9c78e125ab248cfb75b
Signed-off-by: Shawn O. Pearce <spearce@spearce.org>

RawParseUtils.parsePersonIdent handles now those invalid byte sequences
which would result in IndexOutOfBoundsException and returns null in this
case.

Any messages received on side band #2 that aren't scraped as a
progress message into our ProgressMonitor are now forwarded to a
buffer which is later included into the OperationResult object.
Application callers can use this buffer to present the additional
messages from the remote peer after the push or fetch operation
has concluded.

The smart push connections using the native send-pack/receive-pack
protocol now request side-band-64k capability if it is available
and forward any messages received through that channel onto this
message buffer.  This makes hook messages available over smart HTTP,
or even over SSH.

The SSH transport was modified to redirect the remote command's
stderr stream into the message buffer, interleaved with any data
received over side band #2.  Due to buffering between these two
different channels in the SSH channel mux itself the order of any
writes between the two cannot be ensured, but it tries to stay close.

The local fork transport was also modified to redirect the local
receive-pack's stderr into the message buffer, rather than going to
the invoking JVM's System.err.  This gives applications a chance
to log the local error messages, rather than needing to redirect
their JVM's stderr before startup.

To keep things simple, the application has to wait for the entire
operation to complete before it can see the messages.  This may
be a downside if the user is trying to debug a remote hook that is
blocking indefinitely, the user would need to abort the connection
before they can inspect the message buffer in any sort of UI built
on top of JGit.

Change-Id: Ibc215f4569e63071da5b7e5c6674ce924ae39e11
Signed-off-by: Shawn O. Pearce <spearce@spearce.org>

These types can be used by RefDatabase implementations to manage
the collection.

A RefList stores items sorted by their name, and is an immutable
type using copy-on-write semantics to perform modifications to
the collection.  Binary search is used to locate an existing item
by name, or to locate the proper insertion position if an item does
not exist.

A RefMap can merge up to 3 RefList collections at once during its
entry iteration, allowing items in the resolved or loose RefList
to override items by the same name in the packed RefList.

The RefMap's goal is O(log N) lookup time, and O(N) iteration time,
which is suitable for returning from a RefDatabase.  By relying on
the immutable RefList we might be able to make map construction
nearly constant, making Repository.getAllRefs() an inexpensive
operation if the caches are current.  Since modification is not
common, changes require up to O(N + log N) time to copy the internal
list and collapse or expand the list's array.  As most changes
are made to the loose collection and not the packed collection,
in practice most changes would require less than the full O(N)
time, due to a significantly smaller N in the loose list.

Almost complete test coverage is included in the corresponding
unit tests.  A handful of methods on RefMap are not tested in this
change, as writing the proper test depends on a future refactoring
of how the Ref class represents symbolic reference names.

Change-Id: Ic2095274000336556f719edd75a5c5dd6dd1d857
Signed-off-by: Shawn O. Pearce <spearce@spearce.org>

During fetch over http:// clients now try to take advantage of
the info/refs?service=git-upload-pack URL to determine if the
remote side will support a standard upload-pack command stream.
If so each block of 32 have lines is sent in one POST request,
prefixed by all of the 'want' lines and any previously discovered
common bases as 'have' lines.

During push over http:// clients now try to take advantage of
the info/refs?service=git-receive-pack URL to determine if the
remote side will support a standard receive-pack command stream.
If so, commands are sent along with their pack in a single HTTP
POST request.

Bug: 291002
Change-Id: I8c69b16ac15c442e1a4c3bd60b4ea1a47882b851
Signed-off-by: Shawn O. Pearce <spearce@spearce.org>

This is a simple HTTP server that provides the minimum server side
support required for dumb (non-git aware) transport clients.

We produce the info/refs and objects/info/packs file on the fly
from the local repository state, but otherwise serve data as raw
files from the on-disk structure.

In the future we could better optimize the FileSender class and the
servlets that use it to take advantage of direct file to network
APIs in more advanced servlet containers like Jetty.

Our glue package borrows the idea of a micro embedded DSL from
Google Guice and uses it to configure a collection of Filters
and HttpServlets, all of which are matched against requests using
regular expressions.  If a subgroup exists in the pattern, it is
extracted and used for the path info component of the request.

Change-Id: Ia0f1a425d07d035e344ae54faf8aeb04763e7487
Signed-off-by: Shawn O. Pearce <spearce@spearce.org>

Later we are going to add support for smart HTTP, which requires us to
buffer at least some of the request created by a client before we ship
it to the server.  For many requests, we can fit it completely into a
1 MiB buffer, but if it doesn't we can drop back to using the chunked
transfer encoding to send an unknown stream length.

Rather than recoding the block based memory buffer, we refactor the
local file overflow strategy into a subclass, allowing the HTTP client
code to replace this portion of the logic with its own approach to
start the chunked encoding request.

Change-Id: Iac61ea1017b14e0ad3c4425efc3d75718b71bb8e
Signed-off-by: Shawn O. Pearce <sop@google.com>

Change-Id: Idd98530d5f6fca4de8631aa865e4bcd6e6cf9306
Signed-off-by: Shawn O. Pearce <spearce@spearce.org>

The UnionInputStream utility class combines multiple sequential
InputStreams so they appear to the caller as a single stream with
no gaps.  This can be used to concentate streams coming from multiple
independent HTTP connections (for example).

The companion unit test covers the class's full functionality.

Change-Id: I0676c7b5e082a5886bf0e8f43f9fd6c46a666228
Signed-off-by: Shawn O. Pearce <sop@google.com>

This makes it easier to swap out authenticator implementations and
yet still rely upon being able to configure at least one Authenticator
instance in the JVM and program it with data obtained from outside
of the user interface.

Change-Id: I8c1a0eb8acee1d306f4c3b40a790b7fa0c3abb70
Signed-off-by: Shawn O. Pearce <spearce@spearce.org>

According the javadoc, and implied by the name of the class, NB
is about network byte order. The purpose of moving the IO only,
and non-byte order related functions to another class is to
make it easier for new contributors to understand that they
can use these functions in general and it's also makes it easier
to understand where to put new IO related utility functions

Change-Id: I4a9f6b39d5564bc8a694b366e7ff3cc758c5181b
Signed-off-by: Robin Rosenberg <robin.rosenberg@dewire.com>
Signed-off-by: Shawn O. Pearce <spearce@spearce.org>

As discussed on the egit-dev mailing list, we prefer not to have
trailing whitespace in our source code.  Correct all currently
offending lines by trimming them.

Change-Id: I002b1d1980071084c0bc53242c8f5900970e6845
Signed-off-by: Shawn O. Pearce <spearce@spearce.org>

MyersDiff was crashing with ArrayIndexOutOfBoundsException when
diffing huge files. This was because the snake data (begin and
end position while processing chunks of the text) was sequeezed
into a single int. But with longer texts to diff these values
exceeded the range of java int values. It is fixed by squeezing
the two ints into a long and by adding the LongList helper
class.

Change-Id: Iacb9082e1b076e994d1486aa8e512342ad7432b3
Signed-off-by: Christian Halstrick <christian.halstrick@sap.com>

Some applications may wish to modify an int list.

Bug: 291083
Eclipse-CQ: 3559
Change-Id: Iea871443ec661230aec92397229f1eda6c74216f
Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Signed-off-by: Shawn O. Pearce <spearce@spearce.org>

This is the last chunk of code in jgit-core which references the awtui
package.  Moving it to the only consumer in jgit-pgm allows us to move
the awtui package over to the jgit-awtui module.

Change-Id: I2fd81be2076117b2f2c5f8ed45de7f29272af6cf
Signed-off-by: Shawn O. Pearce <spearce@spearce.org>

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>