Rearrange manifest file handling in merge_zips and soong_zip

Jar always puts default MANIFEST.MF files in if none was specified.
Copying that behavior in soong_zip causes problems with merge_zips,
because it ends up taking the default manifest from the classes.jar
instead of the user's manifest from res.jar.  We don't want the
user's manifest in the classes.jar, otherwise a change to the
manifest will cause all the class files to rebuild.  Instead,
move the manifest insertion to the final merge_zips stage.

Test: m -j checkbuild
Change-Id: Id6376961dbaf743c2fb92843f9bdf2e44b963be0
diff --git a/java/java_test.go b/java/java_test.go
index 4f5c0ec..ab5af0a 100644
--- a/java/java_test.go
+++ b/java/java_test.go
@@ -119,8 +119,8 @@
 		t.Errorf(`foo inputs %v != ["a.java"]`, javac.Inputs)
 	}
 
-	bar := filepath.Join(buildDir, ".intermediates", "bar", "classes.jar")
-	baz := filepath.Join(buildDir, ".intermediates", "baz", "classes.jar")
+	bar := filepath.Join(buildDir, ".intermediates", "bar", "classes-compiled.jar")
+	baz := filepath.Join(buildDir, ".intermediates", "baz", "classes-compiled.jar")
 
 	if !strings.Contains(javac.Args["classpath"], bar) {
 		t.Errorf("foo classpath %v does not contain %q", javac.Args["classpath"], bar)
@@ -182,7 +182,7 @@
 
 	check := func(module string, depType depType, deps ...string) {
 		for i := range deps {
-			deps[i] = filepath.Join(buildDir, ".intermediates", deps[i], "classes.jar")
+			deps[i] = filepath.Join(buildDir, ".intermediates", deps[i], "classes-compiled.jar")
 		}
 		dep := strings.Join(deps, ":")
 
@@ -279,12 +279,12 @@
 		t.Errorf(`foo inputs %v != ["a.java"]`, javac.Inputs)
 	}
 
-	bar := filepath.Join(buildDir, ".intermediates", "bar", "classes.jar")
+	bar := filepath.Join(buildDir, ".intermediates", "bar", "classes-compiled.jar")
 	if !strings.Contains(javac.Args["classpath"], bar) {
 		t.Errorf("foo classpath %v does not contain %q", javac.Args["classpath"], bar)
 	}
 
-	baz := filepath.Join(buildDir, ".intermediates", "baz", "classes.jar")
+	baz := filepath.Join(buildDir, ".intermediates", "baz", "classes-compiled.jar")
 	if len(combineJar.Inputs) != 2 || combineJar.Inputs[1].String() != baz {
 		t.Errorf("foo combineJar inputs %v does not contain %q", combineJar.Inputs, baz)
 	}