Make typeshed_path a full replacement for bundled stubs

[avokin2]

Problem

A configured typeshed_path only partially redirected import resolution. A user who pointed Pyrefly at their own typeshed still got results — and the declaration URIs
returned over LSP/TSP — out of Pyrefly's bundled stubs:

• Third-party imports always resolved against the bundled stubs, ignoring typeshed_path entirely.
• The bundled stdlib was used as a fallback whenever a module was missing from <typeshed_path>/stdlib.
• Most importantly, the Stdlib object — which supplies the class definitions for int, str, list, … used throughout type checking — was always loaded from a hardcoded
  bundled-typeshed config. So the builtins were bundled even when every other import resolved to the custom typeshed.
• typeshed_path could only be set from pyrefly.toml, leaving editors no way to point Pyrefly at a typeshed without writing a config file.

Fix

Treat typeshed_path, when set, as a complete replacement for the bundled stubs:

• Third-party stubs resolve only from <typeshed_path>/stubs, with each distribution subdirectory as its own search root (mirroring typeshed's layout). The bundled stdlib
  branch is skipped: a miss falls through to the remaining stages (site-packages, …) and never reaches the bundled stubs.
• The stdlib loader config now carries typeshed_path, so compute_stdlib builds the Stdlib from <typeshed_path>/stdlib as well. invalidate_config drops the cached stdlib
  so a changed typeshed_path is picked up.

Because the setting now suffices on its own, no separate opt-out knob is needed.

Finally, surface typeshed_path over LSP via initializationOptions / workspace/configuration (as typeshedPath), deferring to an explicit value from a user-owned config
file when one is present.

Summary

Makes a configured typeshed_path fully shadow Pyrefly's bundled stubs — for stdlib, third-party stubs, and the Stdlib builtins object — and lets editors set it over LSP
without a config file.

Test Plan

Added unit tests for each layer, and replaced the test that locked in the old bundled-always behavior.

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