fix: preserve core runtime state

[mehalter]

Runtime state

• Preserve rooter, session, Tree-sitter, buffer, and toggle state across reloads and lifecycle transitions.
• Handle stale files, Windows paths, terminal folding, and command variants without changing the public API.

Documentation and types

• Correct configuration docs and align mapping and command annotations with supported values.

Validation

• Passed StyLua, Selene, typos, diff checks, focused runtime tests, and a full tracked-source LuaLS audit.