feat(cli): PR-2 stream subprocess I/O and cocoindex [lance] wrap

[HumanBean17]

Scope

Implements PR-2 from plans/PLAN-CLI-PROGRESS-OUTPUT.md: live relay of child stdout/stderr to the parent stderr (non-quiet), full capture for RefreshIndexOutput / CLI failure tails, quiet path unchanged (communicate / capture_output), and Appendix A [lance] bracket lines around cocoindex only.

Changes

• New java_codebase_rag/cli_progress.py: emit_lance_cocoindex_start / emit_lance_cocoindex_finish, accumulate_and_relay_subprocess_streams.
• server.py run_refresh_pipeline: async dual-stream relay; [lance] around cocoindex when quiet=False.
• java_codebase_rag/pipeline.py: threaded relay for run_cocoindex_update (optional lance_project_root) and run_build_ast_graph when verbose.
• java_codebase_rag/cli.py: pass lance_project_root for init/increment when not --quiet.

Tests

New module tests/test_cli_progress_stdout_invariant.py (4 tests) + stdout baselines under tests/fixtures/cli_progress_stdout/.

Manual evidence

.venv/bin/ruff check .
.venv/bin/python -m pytest tests -v

(386 passed, 7 skipped in last full run.)

Notes

• No ontology bump or re-index requirement.
• PR-3 will add pass starts, heartbeats, pipeline header/footer, and docs.

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