Fix jgit repository not closed

When the close() method is not called on a jgit Repository (or on the wrapping Git object), the process maintains a lock on .pack files (and maybe others).
This causes different problems depending on the underlying OS :

• On Linux, the .pack file is marked as deleted and doesn't prevent the deletion of the repo

  lsof -u ronan |grep "nxruntime.*pack"
  java      24498 ronan  391r      REG               0,43       336   22417108 /home/ronan/dev/sources/nuxeo-connect-priv-MASTER/nuxeo-connect-plugin/target/nxruntime-main-162184526913254447.tmp/data/studio/workspaces/project-0/.git_bare_cache/objects/pack/pack-483c716d2bdd8d81c14eb317a6c97962f93cbf76.pack (deleted)
  

• On Windows, the file is still here and cannot be deleted, causing other commands to fail on a partially deleted repo

  it_should_retrieve_a_branch_snapshot(com.nuxeo.connect.packagerepository.StudioPackageRetrieverTest)  Time elapsed: 0.244 sec  <<< ERROR!
  com.nuxeo.studio.exception.VersioningException: target\nxruntime-main-9072057935275143909.tmp\data\studio\workspaces\project-0\project-0-#1-cloned-2016-08-16-17-20-17\.git: Invalid remote: origin
          at org.eclipse.jgit.transport.TransportLocal$1.open(TransportLocal.java:131)
          at org.eclipse.jgit.transport.TransportBundleFile$1.open(TransportBundleFile.java:106)
          at org.eclipse.jgit.transport.Transport.open(Transport.java:560)
          at org.eclipse.jgit.transport.Transport.open(Transport.java:437)
          at org.eclipse.jgit.transport.Transport.open(Transport.java:318)
          at org.eclipse.jgit.transport.Transport.open(Transport.java:287)
          at org.eclipse.jgit.api.FetchCommand.call(FetchCommand.java:120)
          at com.nuxeo.studio.core.versioning.VersioningGitAbstract$4.call(VersioningGitAbstract.java:224)
          at com.nuxeo.studio.core.versioning.VersioningGitAbstract$4.call(VersioningGitAbstract.java:219)
          at com.nuxeo.studio.core.versioning.VersioningGitAbstract$GitCommandExecutor.execute(VersioningGitAbstract.java:266)
          at com.nuxeo.studio.core.versioning.VersioningGitAbstract.refreshLocal(VersioningGitAbstract.java:219)
          at com.nuxeo.studio.core.versioning.VersioningGitAbstract.resetOnHead(VersioningGitAbstract.java:507)
          at com.nuxeo.studio.core.versioning.VersioningGitAbstract.resetOnBranch(VersioningGitAbstract.java:530)
          at com.nuxeo.studio.core.workspace.WorkspaceProvider.switchToBranch(WorkspaceProvider.java:293)
          at com.nuxeo.studio.core.workspace.DefaultWorkspace.onBranch(DefaultWorkspace.java:139)
          at com.nuxeo.studio.core.workspace.DefaultWorkspacePool.get(DefaultWorkspacePool.java:214)
          at com.nuxeo.studio.core.workspace.WorkspaceServiceImpl.getReadOnlyWorkspace(WorkspaceServiceImpl.java:56)
          at com.nuxeo.studio.core.BranchServiceImpl.getBranches(BranchServiceImpl.java:163)
          at com.nuxeo.studio.core.BranchServiceImpl.getBranchIfExist(BranchServiceImpl.java:150)
          at com.nuxeo.studio.core.BranchServiceImpl.createBranch(BranchServiceImpl.java:117)
          at com.nuxeo.connect.packagerepository.StudioPackageRetrieverTest.it_should_retrieve_a_branch_snapshot(StudioPackageRetrieverTest.java:334)