Upgrade to beta.4 from previous version produces double definitions

Created by: ryan-blunden

To reproduce:

Run 3.0 beta

• Clear previous state (~/.sourcegraph)
• Run container using sourcegraph/server:3.0.0-beta
• Create external GitHub service
• Add github.com/sourcegraph-demo/buildkit repository
• Enable basic code intel
• Go to /github.com/sourcegraph-demo/buildkit/-/blob/cache/blobs/blobs.go#L52:22
• Observe definition with a single result.
• Terminate docker container

Upgrade to beta 4

• Run container using sourcegraph/server:3.0.0-beta.4
• Go to /extensions. Observe basic code intel is enabled, as well as lang specific extensions

• Go to /github.com/sourcegraph-demo/buildkit/-/blob/cache/blobs/blobs.go#L52:22
• Observe two definitions provided.