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You'll notice a list of modules that are supported for instrumentation on line 13. For each module, the agent loads the patch (see the modules folder containing the patches for each module). Then the agent calls the hook() function. This is where the libraries are actually monkey-patched.
Of course, in the real thing, there's a lot more, like caching, resolving module paths, and handling race conditions. If you'd like to read more about the module system, the Node.js docs are pretty detailed. I've also written a bit about some testing libraries that hook into the Node.js module system. And here's an example of someone else hooking into require.
An even better option is auto-instrumentation, where the APM library automatically identifies the libraries you use and track the operations you do with them. This is how Elastic APM works. Honeycomb's Beeline, DataDog's dd-trace and the OpenTelemetry Node.js client also provide automatic instrumentation. Of course, "operations" don't only happen when you interact with other libraries, so these libraries still let you manually add spans.
A number of instrumentation libraries, such as Jaeger and the OpenTracing JS client work this way.
The manual approach is alright for recording custom operations, but it can get pretty tiring doing it for every database query or API call. For that, there's another approach: having the dev explicitly request instrumented wrappers of their libraries. For instance, to automatically [instrument your PostgreSQL queries with Zipkin, you'd need to wrap the pg module with Zipkin's library and use that for your database queries.