JGit was not handling certain file/folder conflicts during a checkout
correctly. This was reported by Axel Richard in
http://dev.eclipse.org/mhonarc/lists/jgit-dev/msg02358.html.
This commit fixes this problem.

Still JGit behaves intentionally different than native git.
If HEAD contains a tree, and workingtree, Index and Merge contain a file
with same content ... then JGit allows a conflict free checkout of
Merge. Native git always complains that it doesn't want to overwrite
local changes. But there is no need to update the working tree because
Index and Merge are already equal.

A shell script which shows how native git behaves can be found here.
https://gist.github.com/chalstrick/7694959#file-gistfile1-sh

Change-Id: Ifd6a68974d61cd4fa23bc575f3a40773db66cafc
Signed-off-by: Christian Halstrick <christian.halstrick@sap.com>

Change-Id: Iedb54eb9d8396bc3ae66d8754c1527fd9ca655f9

That is the common style and yields better diagnostics on failure.

Change-Id: I831a55615a812734af0912a5d6bbfd1edc75308e

When a file is not in the index and neither contents nor mode differ
between "head" and "merge", the index state should be kept. If they
differ, a checkout conflict should occur. This is described in Git's
git-read-tree.txt.

JGit used to replace the index state with "merge" in both of the above
cases.

A confusing effect of this was that when one removed a file and then did
a rebase, the file silently reappeared again.

The changes to dir/file conflict handling are a consequence of this
change, as the index handling change made tests in DirCacheCheckoutTest
break. I compared these cases to C Git and the new behavior there also
matches what C Git does.

Bug: 387390
Change-Id: I5beb781f12172a68f98c67d4c8029eb51ceae62d
Signed-off-by: Robin Stocker <robin@nibor.org>

Checkout command should throw o.e.j.api.errors.CheckoutConflictException
which is a GitAPIException not o.e.j.errors.CheckoutConflictException.
PullCommand should rethrow the API exception as a JGitInternalException.

Bug: 356922
Change-Id: I865c4905997d9834c85a97fbe7287604daf99075
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>

Handle more cases for file mode changes. Especially make sure that the
following cases are handled correctly.

Case 1)

  An entry in the working tree, HEAD tree, and merge tree have
  different modes and different content.

  Prior Outcome:
    Dirty working tree content is replaced and file mode
    changes are lost.

  New Outcome:
    Conflict is generated.

Case 2)

  An entry in the index and merge tree have the same content
  but different modes but both modes are file type modes.

  Prior Outcome:
    File mode in working tree is not updated and the working
    directory is dirty.

  New Outcome:
    Index is updated and the working directory is clean.

Bug: 363772
Change-Id: I224602d68228eb419813986807f1eeab77e9c302
Signed-off-by: Christian Halstrick <christian.halstrick@sap.com>
Also-by: Kevin Sawicki <kevin@github.com>
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>

This patch introduces CRLF handling to the DirCacheCheckout and
WorkingTreeIterator supporting the AutoCRLF for add, checkout
reset and status and hopefully some other places that depende
on the underlying logic of the affected API's.

The patch includes test cases for the Status command provided by
Tomasz Zarna for bug 353867.

The core.eol and core.safecrlf options are not yet supported.

Bug: 301775
Bug: 353867
Change-Id: I2280a2dc0698829475de6a662a6c6e80b1df7663

Change-Id: I394fc1ef714c8465cbd5af9c73338b9a324ad9c4
Signed-off-by: Chris Aniszczyk <zx@twitter.com>

Replace it with DirCache, like we did to remove GitIndex.

Change-Id: Ia354770cee5c68f19945279b34aef6de54697435

This includes merging ReadTreeTest into DirCacheCheckoutTest and
converting IndexDiffTest to use DirCache only. The GitIndex specific
T0007GitIndex test remains.

GitIndex is deprecated. Let us speed up its demise by focusing the
DirCacheCheckout tests to using DirCache instead.

This also add explicit deprecation comments to methods that depend
on GitIndex in Repository and TreeEntry. The latter is deprecated in
itself.

Change-Id: Id89262f7fbfee07871f444378f196ded444f2783
Signed-off-by: Robin Rosenberg <robin.rosenberg@dewire.com>

We deleted the entry if there was a file and an index
entry, but not when there was just an index entry. Now
delete the file in both cases since the missing file
just means our worktree is dirty. This affected the
implementation of reset --hard.

Bug: 347574
Change-Id: Ie66fa61303472422830f5e33614e93ad65094e5d

Duplicates cgit behaviour for merging the case where
OURS is deleted and THEIRS is modified as well as
OURS is modified and THEIRS id deleted.

Change-Id: Ia2ab4f8dc95020f2914ff01c2bf3b1bc62a9d45d
Signed-off-by: Chris Aniszczyk <caniszczyk@gmail.com>

This change moves commonly used methods into the RepositoryTestCase
base class.

Change-Id: I56a46c31ee1661c7ce22eb755ab23da8bc9f5da2
Signed-off-by: Philipp Thun <philipp.thun@sap.com>

This interface has been deprecated for a long time now.
Time to remove it.

Change-Id: I29a938657e4637b2a9d0561940b38d70866613f7
Signed-off-by: Shawn O. Pearce <spearce@spearce.org>

This problem surfaced since EGit Core ResetOperationTest is failing
since change I26806d21. JGit detected checkout conflict for untracked
files which never were tracked by the repository. 

"git reset --hard" in c git also doesn't remove such untracked files.

Change-Id: Icc8e1c548ecf6ed48bd2979c81eeb6f578d347bd
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>

Eclipse has some problem re-running single JUnit tests if
the tests are in Junit 3 format, but the JUnit 4 launcher
is used. This was quite unnecessary and the move was not
completed. We still have no JUnit4 test.

This completes the extermination of JUnit3. Most of the
work was global searce/replace using regular expression,
followed by numerous invocarions of quick-fix and organize
imports and verification that we had the same number of
tests before and after.

- Annotations were introduced.
- All references to JUnit3 classes removed
- Half-good replacement for getting the test name. This was
  needed to make the TestRngs work. The initialization of
  TestRngs was also made lazily since we can not longer find
  out the test name in runtime in the @Before methods.
- Renamed test classes to end with Test, with the exception
  of TestTranslateBundle, which fails from Maven
- Moved JGitTestUtil to the junit support bundle

Change-Id: Iddcd3da6ca927a7be773a9c63ebf8bb2147e2d13
Signed-off-by: Robin Rosenberg <robin.rosenberg@dewire.com>
Signed-off-by: Shawn O. Pearce <spearce@spearce.org>

In the case where DirCacheCheckout was used to checkout a tree
without taking HEAD into account (e.g. during a clone or hard reset)
we didn't handle conflicts correctly. E.g. if there are conflicts
(entries with stage != 0) in the index and we tried to hard reset
we have been processing the conflicting pathes multiple times (once
for every stage). With this fix we will update the index with the
entry from the "merge" state (the state we want checkout) when we
detect existing conflicts.

Change-Id: Iffbddccaa588cf0d1460a5e44dabaf540d996e26
Signed-off-by: Christian Halstrick <christian.halstrick@sap.com>

Implementation of a checkout (or 'git read-tree') operation which
works together with DirCache. This implementation does similar things
as WorkDirCheckout which main problem is that it works with deprecated
GitIndex. Since GitIndex doesn't support multiple stages of a file
which is required in merge situations this new implementation is
required to enable merge support.

Change-Id: I13f0f23ad60d98e5168118a7e7e7308e066ecf9c
Signed-off-by: Christian Halstrick <christian.halstrick@sap.com>
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>
Signed-off-by: Chris Aniszczyk <caniszczyk@gmail.com>

Added a new package org.eclipse.jgit.api and a builder-style API for
jgit. Added also the first implementation for two git commands: Commit
and Log.

This API is intended to be used by external components when
functionalities of the standard git commands are required. It will also
help to ease writing JGit tests.

For internal usages this API may often not be optimal because the git
commands are doing much more than required or they expect parameters of
an unappropriate type.

Change-Id: I71ac4839ab9d2f848307eba9252090c586b4146b
Signed-off-by: Christian Halstrick <christian.halstrick@sap.com>