fix(reprocess): build graph on graph-only installs (macOS Intel)

[HumanBean17]

Problem

On Intel Macs (darwin + x86_64), cocoindex[lancedb] / lancedb / sentence-transformers are intentionally gated off by PEP 508 markers in pyproject.toml (torch/lancedb dropped macOS x86_64 wheels), so the install is graph-only by design.

The default java-codebase-rag reprocess went through server.run_refresh_pipeline, which only checked for the cocoindex binary and hard-failed:

{"message": "cocoindex not found next to Python: …/.venv/bin/cocoindex", "success": false, …}
✗ java-codebase-rag reprocess · finished in 1.80s (exit=2)

It never built the graph — inconsistent with init / increment, which already skip vectors and build the graph on graph-only installs.

Fix

run_refresh_pipeline now detects graph-only installs via pipeline.vector_stack_installed() and skips the vectors phase, builds the graph, and returns success with a clear message — mirroring init / increment.

• Extracted the graph-build block into a shared _run_graph_phase() helper (no duplication between the normal vectors→graph path and the new graph-only path). Normal-path semantics are preserved exactly (phases_run, success, exit-code mapping).
• Centralized the operator-facing skip line as VECTORS_SKIPPED_GRAPH_ONLY in pipeline.py (single source of truth; cli.py now imports it as an alias).
• No vectors progress event is emitted on graph-only, so the renderer's vectors task stays invisible (its "never spawned" invariant) rather than hanging at running.

Before → after (Intel Mac)

	before	after
message	cocoindex not found next to Python: …	vectors skipped — … (graph-only mode) + reprocess completed (graph-only; …)
graph built	❌ no	✅ yes
exit code	2	0

Verification

• New regression test test_refresh_pipeline_skips_vectors_and_builds_graph_on_graph_only in tests/test_graph_only_boot.py (the cross-platform graph-only home; the macos-13 CI leg is temporarily disabled, so this in-process coverage is what guards the path on the gate).
• Patched vector_stack_installed in the existing vectors-path baseline test (test_refresh_pipeline_quiet_stderr_baseline) since it fakes a full install.
• Ran the user's exact command on this Intel Mac: now builds the graph and exits 0.
• Full suite: 1112 passed, 0 new failures. The 16 failures observed locally are all pre-existing graph-only/vector-stack-absent tests (Lance/search/tables/increment-Lance-message) — they require lancedb/cocoindex, absent on Intel Mac by design; none touch the code changed here, and they pass on the Ubuntu CI gate where the vector stack is installed.

Out of scope

reprocess --vectors-only still surfaces "cocoindex not found" on graph-only (different sync code path in cli.py). Since --vectors-only is an explicit opt-in where vectors are genuinely impossible, failing there is honest — left as-is here; can extend the clear messaging in a follow-up if desired.

🤖 Generated with Claude Code