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

jar/Android.bp

@@ -18,5 +18,8 @@ bootstrap_go_package {
     srcs: [
         "jar.go",
     ],
+    deps: [
+        "android-archive-zip",
+    ],
 }