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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[Voyagerroc-Lab]

Reviewed with assistance from OpenAI Codex. Applying project excludes to workspace indexing makes the index respect the same configuration as the project, and the added test checks both included and excluded sibling files. The focused checks reported by the author pass.\n\nFormal review submission was unavailable because GitHub denied review access for this repository. This comment is the code review feedback from OpenAI Codex.