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I use sourcegraph[0] for most of my searches even on non-entreprise github to work around how broken github search is. Sourcegraph has the ability to search in forks, in a specific commit, or in a set of repos that you define. It's really quite good at doing github-wide searches of arbitrary query. I'm pretty sure its self-hosted solution can be made to work with github entreprise, you might want to check it out :).

Disclaimer: Just a happy sourcegraph user.

[0]: https://sourcegraph.com

1000 repos seems a bit much. Does it mean that when developing a feature you have to change code in tens of repositories And then create separate commits and PRs for each of those? It just seems way too microscopic.

Text search in vscode is done by ripgrep[1].

[1]: https://code.visualstudio.com/updates/v1_11#_text-search-imp...