Remove <base/time.h>, moving all uses to std::chrono

Also update some related things (TTimerFd) to use std::chrono while passing through.

orly/indy/manager_base.h: Changed fairly significantly in order to migrate to chrono. Restructured minimally to try to keep things fairly relatable / readable.
orly/indy/disk/durable_manager.h: I did some moderate refactoring to reduce duplication

@jmlvanre can you look over the manager_base and durable_manager changes in specific / make sure I didn't break change existing logic.