This PR ports more of the post-initialization C++ shell code to Lean.
All that remains is the initialization of the profiler and task manager.
As initialization tasks rather than main shell code, they were left in
C++ (where the rest of the initialization code currently is).
The `max_memory` and `timeout` Lean options used by the the `--memory`
and `--timeout` command-line options are now properly registered. The
server defaults for max memory and max heartbeats (timeout) were removed
as they were not actually used (because the `server` option that was
checked was neither set nor exists).
This PR also makes better use of the module system in `Shell.lean` and
fixes a minor bug in a previous port where the file name check was
dependent on building the `.ilean` rather than the `.c` file (as was
originally the case).
Fixes#9879.
@kha The runtime folder includes what is needed to link a
standalone Lean program. It is still contains some unnecessary files.
We will be able to remove them after we release Lean4.
