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Kythe has one schema, whereas with Glean each language has its own schema with arbitrary amounts of language-specific detail. You can get a language-agnostic view by defining an abstraction layer as a schema. Our current (work in progress) language-agnostic layer is called "codemarkup" https://github.com/facebookincubator/Glean/blob/main/glean/s...
For wiring up the indexer, there are various methods, it tends to depend very much on the language and the build system. For Flow for example, Glean output is just built into the typechecker, you just run it with some flags to spit out the Glean data. For C++, you need to get the compiler flags from the build system to pass to the Clang frontend. For Java the indexer is a compiler plugin; for Python it's built on libCST. Some indexers send their data directly to a Glean server, others generate files of JSON that get sent using a separate command-line tool.
References use different methods depending on the language. For Flow for example there is a fact for an import that matches up with a fact for the export in the other file. For C++ there are facts that connect declarations with definitions, and references with declarations.
GitHub's linguist library can be used to identify the programming language of a single file: https://github.com/github/linguist#single-file
If you've not had to deal with a codebase that takes VSCode longer than a few minutes to index, then you're probably outside their initial target market. If you've not had to setup a hosted code search tool (eg livegrep https://github.com/livegrep/livegrep ) because there's just too much code,