jni_zero: Fix and add test for placeholders overwriting each other

There was a bug where if you imported a class which had @NativeMethods
it would overwrite the entry in the placeholders jar. This fixes it
by just keeping a set tracking what we've currently added.

I also had to change the golden tests to support multiple files.

Bug: 330173100
Change-Id: Id7161c5606efde2a1edda67f5124d31ed3941fb3
Reviewed-on: https://chromium-review.googlesource.com/c/chromium/src/+/5420173
Reviewed-by: Mohamed Heikal <mheikal@chromium.org>
Commit-Queue: Mohamed Heikal <mheikal@chromium.org>
Auto-Submit: Sam Maier <smaier@chromium.org>
Cr-Commit-Position: refs/heads/main@{#1282644}