Adds the file content merge alorithm and tests for merge to jgit.
The merge algorithm:

- Gets as input parameters the common base, the two new contents
  called "ours" and "theirs".

- Computes the Edits from base to ours and from base to theirs with
  the help of MyersDiff.

- Iterates over the edits.

- Independent edits from ours or from theirs will just be applied
  to the result.

- For conflicting edits we first harmonize the ranges of the edits
  so that in the end we have exactly two edits starting and ending
  at the same points in the common base. Then we write the two
  conclicting contents into the result stream.

Change-Id: I411862393e7bf416b6f33ca55ec5af608ff4663
Signed-off-by: Christian Halstrick <christian.halstrick@sap.com>
[sp: Fixed up two awkard comments in documentation.]
Signed-off-by: Shawn O. Pearce <spearce@spearce.org>

Add some tests which make sure that the diff algorithm really behaves in the
promised O(N*D) manner. This tests compute diffs between multiple big chunks
of data, measure time for computing the diffs and fail if the measured times
are off O(N*D) by more than a factor 10

Signed-off-by: Christian Halstrick <christian.halstrick@sap.com>
Change-Id: I8e1e0be60299472828718371b231f1d8a9dc21a7
Signed-off-by: Robin Rosenberg <robin.rosenberg@dewire.com>

Bug: 291083
Eclipse-CQ: 3559
Change-Id: I5a10946637438052e7596489b9f9de3a0c6b2066
Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Signed-off-by: Shawn O. Pearce <spearce@spearce.org>

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>

Only one test class actually needs this function, so instead of
us inheriting it down into every test, move it to that one class.

Change-Id: I5700ca48df4177153f2b3861dec7c538c621e775
Signed-off-by: Shawn O. Pearce <spearce@spearce.org>

This test doesn't work because it requires a pack file which we have
lost to the ages.  We couldn't include it because the pack was actually
a copy of the GPL'd C git.git project, and was there to test some sort
of corner case that the test never documented properly.

Change-Id: I282ee1c6a637a8654df93a3847507a6c60e4cfab
Signed-off-by: Shawn O. Pearce <spearce@spearce.org>

Honor the configuration parameter core.logAllRefUpdates when writing
reflogs.  Instead of writing reflog entries always only write
reflogs if this parameter is set to true or if the corresponding
file in the <git-dir>/logs directory already exists. In other words:
if you are updating a ref and this parameter is set to false and
there is no file corresponding to your ref in the <git-dir>/logs
folder then no reflog will be written.

This is a fix for the issue http://code.google.com/p/egit/issues/detail?id=4



Change-Id: I908e4c77e3630dc3223b2d2a47cb4534dbe4ed42
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>
Signed-off-by: Christian Halstrick <christian.halstrick@sap.com>
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 3a2dd9921c8a08740a9e02c421469e5b1a9e47cb.

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