Currently there is no way to determine the precise changes done
to the working tree by a JGit command. Only the CheckoutCommand
actually provides access to the lists of modified, deleted, and
to-be-deleted files, but those lists may be inaccurate (since they
are determined up-front before the working tree is modified) if
the actual checkout then fails halfway through. Moreover, other
JGit commands that modify the working tree do not offer any way to
figure out which files were changed.

This poses problems for EGit, which may need to refresh parts of the
Eclipse workspace when JGit has done java.io file operations.

Provide the foundations for better file change tracking: the working
tree is modified exclusively in DirCacheCheckout. Make it emit a new
type of RepositoryEvent that lists all files that were modified or
deleted, even if the checkout failed halfway through. We update the
'updated' and 'removed' lists determined up-front in case of file
system problems to reflect the actual state of changes made.

EGit thus can register a listener for these events and then knows
exactly which parts of the Eclipse workspace may need to be refreshed.

Two commands manage checking out individual DirCacheEntries themselves:
checkout specific paths, and applying a stash with untracked files.
Make those two also emit such a new WorkingTreeModifiedEvent.

Furthermore, merges may modify files, and clean, rm, and stash create
may delete files.

CQ: 13969
Bug: 500106
Change-Id: I7a100aee315791fa1201f43bbad61fbae60b35cb
Signed-off-by: Thomas Wolf <thomas.wolf@paranor.ch>

Set missingOverrideAnnotation=warning in Eclipse compiler preferences
which enables the warning:

  The method <method> of type <type> should be tagged with @Override
  since it actually overrides a superclass method

Justification for this warning is described in:

  http://stackoverflow.com/a/94411/381622

Enabling this causes in excess of 1000 warnings across the entire
code-base. They are very easy to fix automatically with Eclipse's
"Quick Fix" tool.

Fix all of them except 2 which cause compilation failure when the
project is built with mvn; add TODO comments on those for further
investigation.

Change-Id: I5772061041fd361fe93137fd8b0ad356e748a29c
Signed-off-by: David Pursehouse <david.pursehouse@gmail.com>

If there are untracked changes, apply only the untracked tree
after a successful merge. The merge tree from merging untracked
with HEAD would also contain files already reset before (changes
in tracked files) and try to reset those again,leading to false
checkout conflicts.

Bug: 505804
Change-Id: Iaced4d277623334d11e3d1cca5969590d7c5093e
Signed-off-by: Thomas Wolf <thomas.wolf@paranor.ch>

There was a bug regarding how JGit handled untracked files when applying
a stash. Problem was that untracked files are applied by doing a merge
of HEAD and untrackedFiles commit with a merge base of the stashed HEAD.
That's wrong because the untrackedFiles commit has no parent and
contains only the untracked files. Using stashed HEAD as merge base
leads to unneccessary conflicts on files not event included in the
untrackedFiles commit.

Imagine this graph directly before you want to apply a stash which was
based on 0. You want to apply the stash on current HEAD commit 5.

  5 (HEAD,master)
 /
0---+
 \   \
  1---3 (WIP on master)
     /
    2 (untracked files on master)

Imagine for a specific (tracked) file f
- commit 0 contains X
- HEAD contains Y
- commit 2 (the untracked files) does not contain file f

A merge of 2 and 5 with a merge base of 0 leads to a conflict. The 5
commit wants to modify the file and the 2 commit wants to delete the
file -> conflict.

If no merge base is set then the semantic is correct.

Thanks to Bow for finding this bug and providing the test case.

Bug: 485467
Change-Id: I453fa6ec337f81b2a52c4f51f23044faeec409e6
Also-by: Bow Ruggeri <bow@bow.net>
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>

TreeWalk provides the new method getEolStreamType. This new method can
be used with EolStreamTypeUtil in order to create a wrapped InputStream
or OutputStream when reading / writing files. The implementation
implements support for the git configuration options core.crlf, core.eol
and the .gitattributes "text", "eol" and "binary"

CQ: 10896
Bug: 486563
Change-Id: Ie4f6367afc2a6aec1de56faf95120fff0339a358
Signed-off-by: Ivan Motsch <ivan.motsch@bsiag.com>
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>

If the checkout path is currently a non-empty directory (and was a link
or a regular file before), this directory will be removed before
performing checkout, but only if the checkout path is specified.

Bug: 474973
Change-Id: Ifc6c61592d9b54d26c66367163acdebea369145c
Signed-off-by: Andrey Loskutov <loskutov@gmx.de>

Change-Id: I7fa180db0c59e4a317a0c99ec48574cb0e5ac2f2
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>

- use try-with-resource where possible
- replace use of deprecated release() by close()

Change-Id: I0f139c3535679087b7fa09649166bca514750b81
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>

Entries should only be written to the working tree managed by the
Repository. Simplify callers by passing only the entry and computing
the work tree location inside of the checkoutEntry method.

Change-Id: I574e41280d0407f1853fda12f4bd0d30f75d74e7

The TreeWalk constructor doesn't throw in a meaninful way that
requires cleanup of the not-yet-created TreeWalk.

Hoist the constructor outside of the try/finally and remove the
now unnecessary != null check during the finally.

Change-Id: If5b8bb91562715df0699726648123a47426b9850

Change-Id: I73f38492b6a2e7fd6e77005efd0a8a8c65763e74

Unstashed changes are saved in a commit which is added as an additional
parent to the stash commit.
This behaviour is fully compatible with C Git stashing of untracked
files.

Bug: 434411
Change-Id: I2af784deb0c2320bb57bc4fd472a8daad8674e7d
Signed-off-by: Andreas Hermann <a.v.hermann@gmail.com>

Signed-off-by: Laurent Goubet <laurent.goubet@obeo.fr>
Change-Id: I84e9d7b4b772b4ad7d3e7010aad78291d4d178fe

This feature was introduced in native git with version 1.8.4.

Bug: 422951
Change-Id: I42f194174d64d7ada6631e2156c2a7bf93b5e91c
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>

Applying a stash on another commit failed because the merge base for the
cherry-pick of the stashed index state was not corectly set.

Bug: 422684
Change-Id: I9355352b2b9a7abefa3248ca3c17a9301177d0d6
Signed-off-by: Stefan Lay <stefan.lay@sap.com>

Change-Id: I2d1076b46695dac84961b8ae663bfc5cb123b3a3
Signed-off-by: Chris Aniszczyk <caniszczyk@gmail.com>

Use recursive merge as the default strategy since it can successfully
merge more cases than the resolve strategy can. This is also the default
in native Git.

Change-Id: I38fd522edb2791f15d83e99038185edb09fed8e1
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>

Instead of the complicated strange stuff, implement staah
apply as cherry-pick.

Provided there are no conflicts and it is requested that
the index should be applied, perform yet another cherry-pick,
but discard tha results thereof it that would result in conflicts.

Bug: 376035
Change-Id: I553f3a753e0124b102a51f8edbb53ddeff2912e2

A few classes such as Constanrs are marked with @SuppressWarnings, as are
toString() methods with many liternal, but otherwise $NLS-n$ is used for
string containing text that should not be translated. A few literals may
fall into the gray zone, but mostly I've tried to only tag the obvious
ones.

Change-Id: I22e50a77e2bf9e0b842a66bdf674e8fa1692f590

- Translate internal exceptions to corresponding API exception
- Do not catch GitAPI exceptions internally to an internal
exception. Just pass them to caller
- Mention thrown exceptions in javadoc

Change-Id: I9044cf86d2b0bcc8b63b7cc016e1bf0055a62053
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>

All commands should throw a GitAPIException so new exceptions can be
added without breaking the builds of old code, i.e. anyone that calls
a Git API should catch GitAPIException and not just the currently known
exceptions.

Now the only checked exceptions on Git API calls are GitException and
subclasses of it. New checked exceptions that are subclasses of
GitException may be added without breaking the API.

Javadoc for GitAPIException is declared on GitCommand and
inherited to subclasses. JGitInternalException is not explicitly
documented anymore.

Unfortunately this change itself breaks the API. The intention is
that it shall be possible to add new checked subclasses of
GitAPIException without breaking the API.

Bug: 366914
EGit-Change-Id: I50380f13fc82c22d0036f47c7859cc3a77e767c5
Change-Id: I50380f13fc82c22d0036f47c7859cc3a77e767c5
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>

Previously a DirCacheCheckout was done using a merge tree reflecting
the state of the repository when the stash was originally done.
This was wrong since unstashing after making subsequent commits
would undo changes already committed by checking out entries from
an outdated tree.

The new approach is to scan for conflicts initially using a 6-way
tree walk that contains the trees for the stashed HEAD, stashed
index, stashed working directory, current HEAD, current index, and
current working directory.  Then perform a subsequent scan of the
stashed HEAD, index, and working directory trees and apply all
the stashed differences to the current index and working directory.

Bug: 372882
Change-Id: Ica65f162132c00a16964e838de66fc8b5cd0b0aa
Signed-off-by: Chris Aniszczyk <zx@twitter.com>

Change-Id: I763590a45d75f00a09097ab6f89581a3bbd3c797

Applies the changes in a stashed commit to the local working
directory and index

Bug: 309355
Change-Id: I9fd5ede8affc7f0060ffa7c5cec34573b6fa2b1b
Signed-off-by: Chris Aniszczyk <zx@twitter.com>