Rather than implementing the file reading logic ourselves, and
wind up leaking the FileInputStream's file descriptor until the
next GC, use IO.readFully(File) which wraps the read loop inside
of a try/finally to ensure the stream is closed before it exits.

Change-Id: I85a3fe87d5eff88fa788962004aebe19d2e91bb4
Signed-off-by: Shawn O. Pearce <spearce@spearce.org>
Reviewed-by: Roland Grunberg <rgrunber@redhat.com>

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>

This change only fixes warnings of the eclipse build regarding missing javadocs.
Some comments where just missing, so they have been added. Other comments where
at the wrong (from eclipse point of view) place, so eclipse was complaining.
Also two method which existed for debugging purposes have been removed to get
rid of Eclipse warngins about unused code.

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>

This commit contains fixes provided by Christian Halstrick.

Bug: 291083
Eclipse-CQ: 3559
Change-Id: If8d187e70a51f31040f99098489e513791dc6415
Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Signed-off-by: Shawn O. Pearce <spearce@spearce.org>

Bug: 291083
Eclipse-CQ: 3559
Change-Id: Ia02f346a96b5f1e24f8bc9676bd428b968a41222
Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Signed-off-by: Shawn O. Pearce <spearce@spearce.org>

Myers' algorithm is the standard way to generate diff scripts in
an efficient manner (especially memory-wise).

The source contains extensive documentation about the principal
ideas of the algorithm.

Bug: 291083
Eclipse-CQ: 3559
Change-Id: Id873e7c2c204692cb4a1a05d24b733154b9ed49c
Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
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>