Fix public-only coverage for excluded re-export origins

[WilliamK112]

Summary:

• keep project-local origins of public re-exports in coverage check --public-only even when the origin file is matched by --project-excludes
• preserve the inverse case: if the public re-export location itself is excluded, the private origin is not counted as public
• add production-shape coverage tests that exercise file-args mode, where package __init__.py may be loaded as __unknown__

Closes #4034.

Duplicate/ownership checks:

• pyrefly coverage check --public-only: --project-excludes shouldn't exclude public re-exports #4034 is open and unassigned
• gh search prs for pyrefly coverage check --public-only: --project-excludes shouldn't exclude public re-exports #4034 / public re-export / project-excludes / public-only returned no open duplicates
• gh pr list --search 4034 only returned unrelated Fix: Handle decorated methods from stubs (Type::Callable) in is_method() Fixes #3465 #3597

Validation:

• cargo +stable-x86_64-pc-windows-gnu test -p pyrefly --lib commands::coverage::collect::tests::test_public_only -- --nocapture
• cargo +stable-x86_64-pc-windows-gnu test -p pyrefly --lib commands::coverage::collect::tests::test_compute_public_fqns -- --nocapture
• cargo +stable-x86_64-pc-windows-gnu test -p pyrefly --lib coverage -- --nocapture (65 passed)
• real temp-project smoke: pyrefly coverage check foo --public-only --project-excludes foo/_something_private.py now reports foo._something_private.bar as coverage-partial and exits 1 at 50% coverage instead of reporting 100.00% (0 of 0 typable)
• cargo +stable-x86_64-pc-windows-gnu fmt --all --check
• git diff --check

I also ran cargo +stable-x86_64-pc-windows-gnu test -p pyrefly --lib; it reached 6185 passed before 5 existing shape_dsl tests hit their internal > 20s watchdog under the full Windows run. Each of those five tests passed when rerun individually.