Fix detection of "initial checkout"

A checkout done directly after cloning (the "initial
checkout") has a different semantic as a default
checkout. That is defined in the documentation of
"git read-tree" [1]. JGit was detecting that it is
doing an initial checkout differently from native
git: jgit used to check that the index is empty
but native git required that the index file does
not exist [2]. Teach JGit to behave like native
git.

[1] https://github.com/git/git/blob/master/Documentation/git-read-tree.txt#L187
[2] https://marc.info/?t=154150811200001&r=1&w=2

Change-Id: I1dd0f1ede7cd7ea60d28607916d0165269a9f628

org.eclipse.jgit/src/org/eclipse/jgit/dircache/DirCacheCheckout.java

@@ -157,7 +157,7 @@ public class DirCacheCheckout {
 
 	private ArrayList<String> toBeDeleted = new ArrayList<>();
 
-	private boolean emptyDirCache;
+	private boolean initialCheckout;
 
 	private boolean performingCheckout;
 
@@ -230,7 +230,7 @@ public class DirCacheCheckout {
 		this.headCommitTree = headCommitTree;
 		this.mergeCommitTree = mergeCommitTree;
 		this.workingTree = workingTree;
-		this.emptyDirCache = (dc == null) || (dc.getEntryCount() == 0);
+		this.initialCheckout = !repo.isBare() && !repo.getIndexFile().exists();
 	}
 
 	/**
@@ -961,7 +961,7 @@ public class DirCacheCheckout {
 				// called before). Ignore the cached deletion and use what we
 				// find in Merge. Potentially updates the file.
 				if (equalIdAndMode(hId, hMode, mId, mMode)) {
-					if (emptyDirCache)
+					if (initialCheckout)
 						update(name, mId, mMode);
 					else
 						keep(dce);