Elastic APM .net agent is not instrumenting methods

so that means if not http calls, we have to go for manual instrumentation

Correct.

When will the complete flow is instrumented.., I mean all the method calls, irrespective of http calls or sql client calls?

We don't really aim for that - that would mean an overhead that would be very likely unacceptable for most of the users in production. Also including app and framework methods would lead to a UI that is very hard to understand even with a simple application.

What we already do is that for each span that is created we capture a callstack depending on the duration of the span. Here is the setting to change the duration limit for call stack capturing.

With that you'll see the callstack on every span like this (this is the same for every span - not matter what it captures):

If you set SpanFramesMinDuration to negative value you'll have the callstack for every single span - keep in mind this will still cause some overhead.

With that hopefully you'll get what you aim for - so you could strategically place some code and manually capture spans and for those spans you can get the callstack - but instrumenting every single method is not a recommended way.