Revert "Create util class for work tree updating in both filesystem and index."

Revert "Create util class for work tree updating in both filesystem and index."

This reverts commit 5151b324f4605b1091ac5843dcc1f04b3996f0d1. It is
producing NullPointerExceptions during merges, causing Gerrit's
acceptance tests to fail:

com.google.gerrit.extensions.restapi.RestApiException: Cannot rebase ps
[...]
	at com.google.gerrit.server.api.changes.RevisionApiImpl.rebase(RevisionApiImpl.java:280)
	at com.google.gerrit.acceptance.api.change.ChangeIT.rebaseChangeBase(ChangeIT.java:1584)
Caused by: com.google.gerrit.server.update.UpdateException: java.lang.NullPointerException: repository is required
	at com.google.gerrit.server.update.BatchUpdate.executeUpdateRepo(BatchUpdate.java:588)
[...]
Caused by: java.lang.NullPointerException: repository is required
	at org.eclipse.jgit.merge.Merger.nonNullRepo(Merger.java:128)
	at org.eclipse.jgit.merge.ResolveMerger.addDeletion(ResolveMerger.java:380)
	at org.eclipse.jgit.merge.ResolveMerger.processEntry(ResolveMerger.java:553)
	at org.eclipse.jgit.merge.ResolveMerger.mergeTreeWalk(ResolveMerger.java:1224)
	at org.eclipse.jgit.merge.ResolveMerger.mergeTrees(ResolveMerger.java:1174)
	at org.eclipse.jgit.merge.ResolveMerger.mergeImpl(ResolveMerger.java:299)
	at org.eclipse.jgit.merge.Merger.merge(Merger.java:233)
	at org.eclipse.jgit.merge.Merger.merge(Merger.java:186)
	at org.eclipse.jgit.merge.ThreeWayMerger.merge(ThreeWayMerger.java:96)
	at com.google.gerrit.server.change.RebaseChangeOp.rebaseCommit(RebaseChangeOp.java:360)

Change-Id: Idf63de81666d0df118d2d93c4f6e014e00dc05b8