Fix/exclude file fix

[jny0444]

Summary

pyrefly check already skipped files in project-excludes, but LSP workspace indexing did not. Opening one project file still indexed excluded siblings, which could parse large generated files or crash the language server.
Workspace indexing now uses the resolved config's project-excludes instead of only the hardcoded required excludes (node_modules / __pycache__ / venv). Default includes are unchanged, so files outside project_includes can still be indexed. Opening an excluded file still gets language services.

Fixes #4403

AI assistance: used for the regression test and for locating the indexing path; I reviewed and landed the populate_all_workspaces_files change.

Test Plan

Added test_workspace_indexing_honors_project_excludes, which opens an included file with LazyBlocking indexing and checks workspace/symbol:

• an unopened sibling not in project-excludes is indexed
• an unopened file matching project-excludes is not indexed

Ran:

cargo test test_workspace_indexing_honors_project_excludes
cargo test test_diagnostics_file_in_excludes
cargo test test_client_project_excludes
python3 test.py --no-test --no-tensor-shapes --no-conformance --no-jsonschema

No generated files to commit. Existing exclude tests still pass, so diagnostics for opened excluded files stay suppressed.

Optional manual check: project-excludes = ['**/a.py'] with a crasher in a.py; open b.py in the IDE and confirm the LSP stays up.

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[shahhamdihassan]

Thanks @jny0444! The crash in #4403 turns out to be a separate bug (#3670) that we're fixing directly, so this PR is really about whether workspace indexing should skip project-excludes. That changes find-references and rename for excluded files, so I'd like @connernilsen and @kinto0 to weigh in before going further.

[meta-codesync]

This pull request has been imported. If you are a Meta employee, you can view this in D121631043. (Because this pull request was imported automatically, there will not be any future comments.)