Its confusing that a new TreeWalk() needs to have reset() invoked
on it before addTree().  This is a historical accident caused by
how TreeWalk was abused within ObjectWalk.

Drop the initial empty tree from the TreeWalk and thus remove a
number of pointless reset() operations from unit tests and some of
the internal JGit code.

Existing application code which is still calling reset() will simply
be incurring a few unnecessary field assignments, but they should
consider cleaning up their code in the future.

Change-Id: I434e94ffa43491019e7dff52ca420a4d2245f48b
Signed-off-by: Shawn O. Pearce <spearce@spearce.org>

jgit.sh <command> --help was not working for the commands Diff
and ShowCommands because of missing metaVar information. Missing
information is added here.

Change-Id: I0ab7e35006b6aa7d4326a634309dddfcdb78f2a6
Signed-off-by: Christian Halstrick <christian.halstrick@sap.com>

HistogramDiff outperforms it for any case where PatienceDiff needs to
fallback to another algorithm.  Consequently it's not worth keeping
around, because we would always want a fallback enabled.

Change-Id: I39b99cb1db4b3be74a764dd3d68cd4c9ecd91481
Signed-off-by: Shawn O. Pearce <spearce@spearce.org>

When working on a difference algorithm's implementation, its generally
more important to care about how it behaves on real-world inputs than
it does on fake inputs created for unit test cases.  Run each
implementation against a number of real-world repositories, looking at
changes between files in each commit.  This gives a better picture of
how a particular algorithm performs.

This test suite run against JGit and linux-2.6 with the current
available algorithms shows HistogramDiff always out-performs
MyersDiff, and by a wide margin on the linux-2.6 sources.  As
HistogramDiff has similar output properties as PatienceDiff, the
resulting edits are probably also more human-readable.  These test
results show that HistogramDiff is a good choice for the default
implementation, and also show that PatienceDiff isn't worth keeping.

  jgit: start at baa83ae
            2686 files,          760 commits
    N=         3 min lines,     3016 max lines
  Algorithm                     Time(ns) (  Time(ns) on   Time(ns) on )
                                         (          N=3        N=3016 )
  ---------------------------------------------------------------------
  histogram_myers              314652100 (         3900        298100 )
  histogram                    315973000 (         3800        302100 )
  patience                     774724900 (         4500        347900 )
  patience_histogram_myers     786332800 (         3700        351200 )
  myers                        819359300 (         4100        379100 )
  patience_myers               843416700 (         3800        348000 )

  linux-2.6.git: start at 85a3318
            4001 files,         2680 commits
    N=         2 min lines,    39098 max lines
  Algorithm                     Time(ns) (  Time(ns) on   Time(ns) on )
                                         (          N=2       N=39098 )
  ---------------------------------------------------------------------
  histogram_myers             1229870000 (         5900       2642700 )
  histogram                   1235654100 (         6000       2695400 )
  patience                    3856546000 (         5900       2627700 )
  patience_histogram_myers    3866728100 (         7000       2624000 )
  patience_myers              4004875300 (         8000       2651700 )
  myers                       9794679000 (         7200       2716200 )

Change-Id: I2502684d31f7851e720356820d04d8cf767f7229
Signed-off-by: Shawn O. Pearce <spearce@spearce.org>

This is the test suite I was using to help understand why we had
such a high collision rate with RawTextComparator, and to select
a replacement function.

Since its not something we will run very often, lets make it a
program in the debug package rather than a JUnit test.  This way
we can run it on demand against any corpus of files we choose,
but we aren't bottlenecking our daily builds running tests with
no assertions.

Adding a new hash function to this suite is simple, just define
a new instance member of type "Hash" with the logic applied to
the region passed in.

Change-Id: Iec0b176adb464cf95b06cda157932b79c0b59886
Signed-off-by: Shawn O. Pearce <spearce@spearce.org>

These objects should be responsible for their own formatting,
rather than delegating it to some obtuse type called ObjectInserter.

While we are at it, simplify the way we insert these into a database.
Passing in the type and calling format in application code turned
out to be a huge mistake in terms of ease-of-use of the insert API.

Change-Id: Id5bb95ee56aa2a002243e9b7853b84ec8df1d7bf
Signed-off-by: Shawn O. Pearce <spearce@spearce.org>

Since these types no longer support reading, calling them a Builder
is a better description of what they do.  They help the caller to
build a commit or a tag object.

Change-Id: I53cae5a800a66ea1721b0fe5e702599df31da05d
Signed-off-by: Shawn O. Pearce <spearce@spearce.org>

ObjectReader implementations may wish to use multiple threads in
order to evaluate object reuse faster.  Let the reader make that
decision by passing the iteration down into the reader.

Because the work is pushed into the reader, it may need to locate a
given ObjectToPack given its ObjectId.  This can easily occur if the
reader has sent a list of ObjectIds to the object database and gets
back information keyed only by ObjectId, without the ObjectToPack
handle.  Expose lookup using the PackWriter's own internal map,
so the reader doesn't need to build a redundant copy to track the
assocation of ObjectId back to ObjectToPack.

Change-Id: I0c536405a55034881fb5db92a2d2a99534faed34
Signed-off-by: Shawn O. Pearce <spearce@spearce.org>

The Commit class now only supports the creation of a commit object.
To read a commit, applictions should use RevCommit.  This permits
us to have exactly one implementation, and RevCommit's is faster
and more bug-free.

Change-Id: Ib573f7e15f36855112815269385c21dea532e2cf
Signed-off-by: Shawn O. Pearce <spearce@spearce.org>

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>

This is a horribly crude application, it doesn't even verify that
the object its dumping is delta encoded.  Its method of getting the
delta is pretty abusive to the public PackWriter API, because right
now we don't want to expose the real internal low-level methods
actually required to do this.

Change-Id: I437a17ceb98708b5603a2061126eb251e82f4ed4
Signed-off-by: Shawn O. Pearce <spearce@spearce.org>

Instead of creating the DirCache from a static factory method, use
an instance method on Repository, permitting the implementation to
override the method with a completely different type of DirCache
reading and writing.  This would better support a repository in the
cloud strategy, or even just an in-memory unit test environment.

Change-Id: I6399894b12d6480c4b3ac84d10775dfd1b8d13e7
Signed-off-by: Shawn O. Pearce <spearce@spearce.org>

Update a number of calling sites of RevWalk to ensure the walker's
internal ObjectReader is released after the walk is no longer used.
Because the ObjectReader is likely to hold onto a native resource
like an Inflater, we don't want to leak them outside of their
useful scope.

Where possible we also try to share ObjectReaders across several
walk pools, or between a walker and a PackWriter.  This permits
the ObjectReader to actually do some caching if it felt inclined
to do so.

Not everything was updated, we'll probably need to come back and
update even more call sites, but these are some of the biggest
offenders.  Test cases in particular aren't updated.  My plan is to
move most storage-agnostic tests onto some purely in-memory storage
solution that doesn't do compression.

Change-Id: I04087ec79faeea208b19848939898ad7172b6672
Signed-off-by: Shawn O. Pearce <spearce@spearce.org>

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>

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

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>

This commit actually does three major changes to the way references
are handled within JGit.  Unfortunately they were easier to do as
a single massive commit than to break them up into smaller units.

Disambiguate symbolic references:
---------------------------------

  Reporting a symbolic reference such as HEAD as though it were
  any other normal reference like refs/heads/master causes subtle
  programming errors.  We have been bitten by this error on several
  occasions, as have some downstream applications written by myself.

  Instead of reporting HEAD as a reference whose name differs from
  its "original name", report it as an actual SymbolicRef object
  that the application can test the type and examine the target of.

  With this change, Ref is now an abstract type with different
  subclasses for the different types.

  In the classical example of "HEAD" being a symbolic reference to
  branch "refs/heads/master", the Repository.getAllRefs() method
  will now return:

      Map<String, Ref> all = repository.getAllRefs();
      SymbolicRef HEAD = (SymbolicRef) all.get("HEAD");
      ObjectIdRef master = (ObjectIdRef) all.get("refs/heads/master");

      assertSame(master,               HEAD.getTarget());
      assertSame(master.getObjectId(), HEAD.getObjectId());

      assertEquals("HEAD",              HEAD.getName());
      assertEquals("refs/heads/master", master.getName());

  A nice side-effect of this change is the storage type of the
  symbolic reference is no longer ambiguous with the storge type
  of the underlying reference it targets.  In the above example,
  if master was only available in the packed-refs file, then the
  following is also true:

      assertSame(Ref.Storage.LOOSE,  HEAD.getStorage());
      assertSame(Ref.Storage.PACKED, master.getStorage());

  (Prior to this change we returned the ambiguous storage of
   LOOSE_PACKED for HEAD, which was confusing since it wasn't
   actually true on disk).

  Another nice side-effect of this change is all intermediate
  symbolic references are preserved, and are therefore visible
  to the application when they walk the target chain.  We can
  now correctly inspect chains of symbolic references.

  As a result of this change the Ref.getOrigName() method has been
  removed from the API.  Applications should identify a symbolic
  reference by testing for isSymbolic() and not by using an arcane
  string comparsion between properties.

Abstract the RefDatabase storage:
---------------------------------

  RefDatabase is now abstract, similar to ObjectDatabase, and a
  new concrete implementation called RefDirectory is used for the
  traditional on-disk storage layout.  In the future we plan to
  support additional implementations, such as a pure in-memory
  RefDatabase for unit testing purposes.

Optimize RefDirectory:
----------------------

  The implementation of the in-memory reference cache, reading, and
  update routines has been completely rewritten.  Much of the code
  was heavily borrowed or cribbed from the prior implementation,
  so copyright notices have been left intact as much as possible.

  The RefDirectory cache no longer confuses symbolic references
  with normal references.  This permits the cache to resolve the
  value of a symbolic reference as late as possible, ensuring it
  is always current, without needing to maintain reverse pointers.

  The cache is now 2 sorted RefLists, rather than 3 HashMaps.
  Using sorted lists allows the implementation to reduce the
  in-memory footprint when storing many refs.  Using specialized
  types for the elements allows the code to avoid additional map
  lookups for auxiliary stat information.

  To improve scan time during getRefs(), the lists are returned via
  a copy-on-write contract.  Most callers of getRefs() do not modify
  the returned collections, so the copy-on-write semantics improves
  access on repositories with a large number of packed references.

  Iterator traversals of the returned Map<String,Ref> are performed
  using a simple merge-join of the two cache lists, ensuring we can
  perform the entire traversal in linear time as a function of the
  number of references: O(PackedRefs + LooseRefs).

  Scans of the loose reference space to update the cache run in
  O(LooseRefs log LooseRefs) time, as the directory contents
  are sorted before being merged against the in-memory cache.
  Since the majority of stable references are kept packed, there
  typically are only a handful of reference names to be sorted,
  so the sorting cost should not be very high.

  Locking is reduced during getRefs() by taking advantage of the
  copy-on-write semantics of the improved cache data structure.
  This permits concurrent readers to pull back references without
  blocking each other.  If there is contention updating the cache
  during a scan, one or more updates are simply skipped and will
  get picked up again in a future scan.

  Writing to the $GIT_DIR/packed-refs during reference delete is
  now fully atomic.  The file is locked, reparsed fresh, and written
  back out if a change is necessary.  This avoids all race conditions
  with concurrent external updates of the packed-refs file.

  The RefLogWriter class has been fully folded into RefDirectory
  and is therefore deleted.  Maintaining the reference's log is
  the responsiblity of the database implementation, and not all
  implementations will use java.io for access.

  Future work still remains to be done to abstract the ReflogReader
  class away from local disk IO.

Change-Id: I26b9287c45a4b2d2be35ba2849daa316f5eec85d
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>