refactor!: remove all process-wide globals

[abc8747]

Following #19 (comment), I was working on #24 but noticed that minisky relies on mutable process-wide state everywhere, for example:

minisky/docs/guides/python-api.md

Lines 10 to 15 in 142da23

	import minisky
	minisky.init()
	minisky.sim.reset()
	minisky.traf.cre("KL315", lat=52.0, lon=4.0, hdg=45, alt=5000, spd=250)

Here, minisky.init() mutates module-level variables such as traf, sim, scr, runner, and navdb, which are then accessed throughout the project by importing minisky. Similar global state exists in Command.cmddict, varexplorer.varlist, simulation hooks, and settings loaded at import time, resulting in implicit dependencies.

These objects have no explicit owner or lifetime, and so tests/downstream applications must reset shared state manually. Initialisation depends on import order, and multiple independent simulators cannot safely exist in one process.

This is particularly problematic for plugins, which need a specific runtime to own their configuration, commands, hooks, resources, and teardown.
This PR fully migrates toward an explicit ownership root, removing virtually all singletons and process-global mutables. While it is a significant breaking change, this change is necessary for long-term health and paves the way for proper plugin development.

To migrate:

module level global mutables removed	replacement
minisky.init(...)	with MiniSky(settings, scenario=...) as runtime
minisky.load_plugins()	runtime.load_plugins()
minisky.traf	runtime.traffic
minisky.sim	runtime.simulation
minisky.scr	runtime.console
minisky.runner	runtime.runner
minisky.navdb	runtime.navigation
minisky.stack.{stack(...),cmddict}	runtime.commands.{stack(...),cmddict}
global plugin state	runtime.plugins
varexplorer.varlist	runtime.variables.varlist
global area definitions	runtime.areas
global replacement definitions	runtime.replaceables
INIT, HOLD, OP, END	SimulationState.{INIT,HOLD,OP,END enums
prefer_compiled setting	removed (see issue #27)

Before:

import minisky

minisky.init("scenario.scn")  # settings are hardcoded to root settings.toml
minisky.load_plugins()

After:

from minisky import MiniSky, MiniSkySettings

settings = MiniSkySettings.from_file("settings.toml")  # explicit

# multiple instances of MiniSky() can now be spawned independently without affecting the other!
with MiniSky(settings, scenario="scenario.scn") as runtime:
    # NOTE: load_plugins() may be absorbed into __enter__ in the future once issue #24 is implemented
    runtime.load_plugins()

Note that multiple outstanding issues, such as sys.path mutation during plugin loading (see issue #24), command-list concurrency bugs, stream event wakeups are inherited and remain unfixed.