PR-RS1: selective reprocess (--vectors-only / --graph-only)

[HumanBean17]

Scope

Implements PR-RS1 from plans/PLAN-REPROCESS-SPLIT.md / propose/REPROCESS-SPLIT-PROPOSE.md.

• java-codebase-rag reprocess: mutually exclusive --vectors-only and --graph-only; default path unchanged (cocoindex full reprocess then graph builder via server.run_refresh_pipeline).
• Additive phases_run on RefreshIndexOutput; populated on all run_refresh_pipeline exits.
• Phase-aware CLI exit codes (graph-only build failure exits 1, not 2); setup / nothing-spawned exits 2 with phases_run: [].
• One-line stderr drift warning after successful selective runs (not suppressed by --quiet).
• TTY pretty lines (Rebuilt: / Skipped:) for selective success; piped stdout remains JSON.
• Docs: README.md, docs/JAVA-CODEBASE-RAG-CLI.md (including exit_code vs graph_exit_code asymmetry for graph-only).
• Preflight detection in CLI is documented as tied to stub shapes in java_codebase_rag/pipeline.py.
• RefreshIndexOutput class docstring: manual construction must set phases_run for correct CLI mapping.

Tests

PATH="<venv>/bin:$PATH" python -m pytest tests/test_java_codebase_rag_cli.py -q

41 passed (includes 10 new selective reprocess tests and existing test_cli_reprocess_builds_kuzu_path).

Re-index / ontology

No ontology_version bump; no schema change beyond additive JSON field on refresh output.

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