Missing Kythe outputs with //... build target?

[Tyler Williams]

Hi Kythe friends,

I'm relatively new to Kythe and am trying to generate annotations + serving tables for an entire project. I'm using a command like this:

```

bazel --bazelrc="$KYTHE_DIR"/extractors.bazelrc build --override_repository kythe_release="$KYTHE_DIR" "$TARGET"

```

When I build and generate annotations for a small target / set of targets, I'm able to view the annotations using the kythe CLI. But if I build my entire project using the //... target, the set of annotations emitted is not at all what I expect, it seems incomplete?

To give a specific example, if I generate annotations for a target like //server/util/..., I'll see 10s of paths under kythe://buildbuddy?path=server/util, one for each go package, like:

```

kythe://buildbuddy?path=server/util/log
kythe://buildbuddy?path=server/util/shlex
kythe://buildbuddy?path=server/util/lockmap
kythe://buildbuddy?path=server/util/flag
kythe://buildbuddy?path=server/util/rpcutil

.... etc ...

```

But if I generate annotations for a target like //..., which includes //server/util, I'll only see

kythe://buildbuddy?path=enterprise
kythe://buildbuddy?path=tools
kythe://buildbuddy?path=cli
kythe://buildbuddy?path=static
....

But kythe://buildbuddy?path=server/util is missing. Is it possible to generate annotations for the entire project?

Thanks in advance for your help,

Tyler

[Tyler Williams]

Haven't had a ton of time to dig into this yet but I noticed that when using `zipmerge` instead of `kzip --merge`, the issue is resolved. (Yeah I've seen https://github.com/kythe/kythe/issues/4219).