Move initialization into doInitialize and report progress

[fwcd]

Supersedes #24

Performing our initialization (indexing and compiling all modules) before responding to the initialize request, instead of in the initialized notification, seems to be a cleaner way of handling required initialization, since language features like go-to-definition will be fully disabled instead of hanging. Additionally, the client can provide us with a progress token to report progress with.

Since we cannot report diagnostics before responding to initialize, we leave that in the initialized notification handler.