Whenever a call to JGit returns a Repository the caller should make sure
to call close() on it if he doesn't need it anymore. Since instances of
Repository contain e.g. open FileOutputStreams (for pack files)
forgetting to close the repository can lead to resource leaks.

This was the reason why dozens of the JUnit tests failed on Windows
with "Can't delete file ...." errors. 

In LocalDiskRepositoryTestCase.tearDown() we tried to delete the
repositories we used during tests which failed because we had open
FileOutputStreams.

Not only the obvious cases during Clone or Init operations returned
Repositories, but also the new SubModule API created repository
instances. In some places we even forgot to close submodule repositories
in our internal coding.

To see the effects of this fix run the JGit JUnit tests under Windows.
On other platforms it's harder to see because either the leaking
resources don't lead to failing JUnit tests (on Unix you can delete
files with open FileOutputStreams) or the java gc runs differently and
cleans up the resources earlier.

Change-Id: I6d4f637b0d4af20ff4d501db091548696373a58a
Signed-off-by: Christian Halstrick <christian.halstrick@sap.com>
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>

Change-Id: I763590a45d75f00a09097ab6f89581a3bbd3c797

This prevents existing entries from being cleared when the
.gitmodules config is saved after the new submodule configuration
is added.

Change-Id: I66841f5e758a7527e2e6e25cf1318e5fea91a909
Signed-off-by: Kevin Sawicki <kevin@github.com>

Interpret submodule URLs that start with './' or '../' as
relative to either the configured remote for the HEAD branch,
or 'origin', or the parent repository working directory if no
remote URL is configured

Bug: 368536
Change-Id: Id4985824023b75cd45cd64a4dd9d421166391e10

Adds the following commands:
    - Add
    - Init
    - Status
    - Sync
    - Update

This also updates AddCommand so that file patterns added that
are submodules can be staged in the index.

Change-Id: Ie5112aa26430e5a2a3acd65a7b0e1d76067dc545
Signed-off-by: Kevin Sawicki <kevin@github.com>
Signed-off-by: Chris Aniszczyk <zx@twitter.com>