Fix broken git prefix detection

If JGit got a cygwin path it would fail to resolve directories
relative to it.

Also add system property to debug problems with the FS utilities.
Enable debug using -Djgit.fs.debug=1

Furthermore use -Djgit.gitprefix=<path> to set the git prefix
manually.

Change-Id: I5a58ee45c2d2ae5322f87fd6972526169b2918c8
Signed-off-by: Robin Rosenberg <robin.rosenberg@dewire.com>

org.eclipse.jgit/src/org/eclipse/jgit/util/FS.java

@@ -286,7 +286,9 @@ public abstract class FS {
 				}
 			}
 		} catch (IOException e) {
-			// ignore
+			if (SystemReader.getInstance().getProperty("jgit.fs.debug") != null)
+				System.err.println(e);
+			// Ignore error (but report)
 		}
 		return null;
 	}
@@ -295,6 +297,11 @@ public abstract class FS {
 	public File gitPrefix() {
 		Holder<File> p = gitPrefix;
 		if (p == null) {
+			String overrideGitPrefix = SystemReader.getInstance().getProperty(
+					"jgit.gitprefix");
+			if (overrideGitPrefix != null)
+				p = new Holder<File>(new File(overrideGitPrefix));
+			else
 				p = new Holder<File>(discoverGitPrefix());
 			gitPrefix = p;
 		}

org.eclipse.jgit/src/org/eclipse/jgit/util/FS_Win32.java

@@ -106,8 +106,12 @@ class FS_Win32 extends FS {
 		String w = readPipe(userHome(), //
 				new String[] { "bash", "--login", "-c", "which git" }, //
 				Charset.defaultCharset().name());
-		if (w != null)
-			return new File(w).getParentFile().getParentFile();
+		if (w != null) {
+			// The path may be in cygwin/msys notation so resolve it right away
+			gitExe = resolve(null, w);
+			if (gitExe != null)
+				return gitExe.getParentFile().getParentFile();
+		}
 		return null;
 	}