Parsing the size from a packed object header was incorrectly computing
the total inflated length when the length exceeded the range of a Java
int. The next 7 bits of size information was shifted left as an int
using a shift of 25 bits, placing the higher bits of the size into the
sign position. When this size was extended to a long to be added to
the current size accumulator the size went negative, resulting in
NegativeArraySizeException being thrown.

Fix all places where this particular pattern of code is used to read a
pack size field, or a binary delta header, as they both use the same
variable length encoding scheme.

Change-Id: I04008728ed828f18202652c3d5401cf95a441d0a

The Prefetcher may have loaded a chunk that is a fragment, if the
DhtReader is scanning the Prefetcher's chunks for a particular
object fragment chunks will be missing the index and NPE during
the findOffset() call into the index itself.

Change-Id: Ie2823724c289f745655076c5209acec32361a1ea
Signed-off-by: Shawn O. Pearce <spearce@spearce.org>

The standard Google distribution of Protocol Buffers in Java is better
maintained than TinyProtobuf, and should be faster for most uses.  It
does use slightly more memory due to many of our key types being
stored as strings in protobuf messages, but this is probably worth the
small hit to memory in exchange for better maintained code that is
easier to reuse in other applications.

Exposing all of our data members to the underlying implementation
makes it easier to develop reporting and data mining tools, or to
expand out a nested structure like RefData into a flat format in a SQL
database table.

Since the C++ `protoc` tool is necessary to convert the protobuf
script into Java code, the generated files are committed as part of
the source repository to make it easier for developers who do not have
this tool installed to still build the overall JGit package and make
use of it.  Reviewers will need to be careful to ensure that any edits
made to a *.proto file come in a commit that also updates the
generated code to match.

CQ: 5135
Change-Id: I53e11e82c186b9cf0d7b368e0276519e6a0b2893
Signed-off-by: Shawn O. Pearce <spearce@spearce.org>
Signed-off-by: Chris Aniszczyk <caniszczyk@gmail.com>

jgit.storage.dht is a storage provider implementation for JGit that
permits storing the Git repository in a distributed hashtable, NoSQL
system, or other database.  The actual underlying storage system is
undefined, and can be plugged in by implementing 7 small interfaces:

  *  Database
  *  RepositoryIndexTable
  *  RepositoryTable
  *  RefTable
  *  ChunkTable
  *  ObjectIndexTable
  *  WriteBuffer

The storage provider interface tries to assume very little about the
underlying storage system, and requires only three key features:

  *  key -> value lookup (a hashtable is suitable)
  *  atomic updates on single rows
  *  asynchronous operations (Java's ExecutorService is easy to use)

Most NoSQL database products offer all 3 of these features in their
clients, and so does any decent network based cache system like the
open source memcache product.  Relying only on key equality for data
retrevial makes it simple for the storage engine to distribute across
multiple machines.  Traditional SQL systems could also be used with a
JDBC based spi implementation.

Before submitting this change I have implemented six storage systems
for the spi layer:

  * Apache HBase[1]
  * Apache Cassandra[2]
  * Google Bigtable[3]
  * an in-memory implementation for unit testing
  * a JDBC implementation for SQL
  * a generic cache provider that can ride on top of memcache

All six systems came in with an spi layer around 1000 lines of code to
implement the above 7 interfaces.  This is a huge reduction in size
compared to prior attempts to implement a new JGit storage layer.  As
this package shows, a complete JGit storage implementation is more
than 17,000 lines of fairly complex code.

A simple cache is provided in storage.dht.spi.cache.  Implementers can
use CacheDatabase to wrap any other type of Database and perform fast
reads against a network based cache service, such as the open source
memcached[4].  An implementation of CacheService must be provided to
glue this spi onto the network cache.

[1] https://github.com/spearce/jgit_hbase
[2] https://github.com/spearce/jgit_cassandra
[3] http://labs.google.com/papers/bigtable.html
[4] http://memcached.org/

Change-Id: I0aa4072781f5ccc019ca421c036adff2c40c4295
Signed-off-by: Shawn O. Pearce <spearce@spearce.org>