Move towards std::chrono (Remove <base/time>, cleanup in JHM)

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. Unit tests pass, but I konw a lot of the pieces in there aren't unit tested.

Also includes updating JHM to std::chrono (no user-visible functionality change), and misc. low hanging fruit cleanup along the way.
I mention it because I saw that the use of `clock_gettime` in `thread_clock::now()` which was wrapped in `IfLt0`. Let's add it for consistency if nothing else.