fix(update): run incremental graph rebuild, drop stale "not implemented" warning

[HumanBean17]

What

java-codebase-rag update ran a Lance-only catch-up and then unconditionally printed:

WARNING: AST graph (LadybugDB) incremental rebuild is not yet implemented.

…even though incremental graph rebuild shipped in #284 (67a76de) and increment already calls run_incremental_graph. The two commands share the word "update" but live in different code paths, and only the increment path (cli.py:_cmd_increment) was rewired — the installer's run_update index step (installer.py) was never updated.

So the warning was a lie of omission on the update path: the feature it claims is missing sits one function call away and update could have used it. The warning is truthful only on increment --vectors-only, where the graph step is deliberately skipped.

Change

installer.run_update now mirrors increment:

1. run_cocoindex_update → Lance catch-up (unchanged)
2. run_incremental_graph(...) → graph rebuild (the call that was missing)
3. No warning on success. If the graph step fails, prints a truthful, actionable message (…failed (exit N). Run java-codebase-rag reprocess) instead of claiming the feature is unimplemented.

_INCREMENT_WARNING_LINES stays in cli.py — still the correct message for increment --vectors-only and pinned by test_cli_quiet_parity.py.

Refs: completed proposal propose/completed/INCREMENTAL-GRAPH-PROPOSE.md, tracking issue #73.

User-visible behaviour changes

• java-codebase-rag update now prints Updating index (Lance + graph)... and no longer emits the "graph incremental rebuild is not yet implemented" warning on success.
• update does slightly more work than before (graph catch-up, not just Lance) — the intended outcome; matches increment.
• update --help, README, and docs/JAVA-CODEBASE-RAG-CLI.md updated to describe update as artifact refresh + incremental Lance/graph catch-up, and drop the false "prints graph staleness warning" line.

No reindex / ontology / env-var impact

None. This only rewires which existing pipeline function update calls. No schema, ontology, or embedding change.

Tests

• tests/test_installer.py::TestRunUpdate — added run_incremental_graph mock to test_install_then_update_cycle (update now invokes that step).
• .venv/bin/ruff check . — clean.
• .venv/bin/python -m pytest tests/test_installer.py::TestRunUpdate tests/test_cli_quiet_parity.py -q → 7 passed, 1 skipped (skip is cocoindex/bank-chat-gated).

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