fix(reprocess): resolve cocoindex via PATH, not just next-to-python

[HumanBean17]

Problem

java-codebase-rag reprocess (no flags) failed with cocoindex not found next to python on installs where the cocoindex console script lives away from the venv python — e.g. ~/.local/bin from pip install --user — even though cocoindex was installed, importable, and on PATH.

Meanwhile every sibling command worked on the same install:

Command	Resolves cocoindex via
init, increment, reprocess --vectors-only, erase	next-to-python → then shutil.which (PATH)
reprocess (no flags)	next-to-python only

The two code paths disagreed: the sync path (pipeline.cocoindex_bin, pipeline.py:45) falls back to shutil.which; the async path (server.run_refresh_pipeline, server.py:425) checked only Path(sys.executable).parent / "cocoindex".

Fix

server.run_refresh_pipeline now reuses the shared pipeline.cocoindex_bin() helper (imported as resolve_cocoindex_bin) instead of hardcoding the next-to-python path. Both paths now resolve cocoindex identically. The not-found message now names both locations checked.

Tests

• test_cocoindex_bin_falls_back_to_path — unit guard on the helper's PATH fallback (shutil.which).
• test_refresh_pipeline_resolves_cocoindex_via_path_not_next_to_python — regression: with vector_stack_installed=True and cocoindex reachable only via PATH, run_refresh_pipeline spawns cocoindex instead of short-circuiting to the not-found failure.

Verification

• tests/package/test_graph_only_boot.py — 6 passed
• tests/package/ tests/mcp/ — 691 passed, 5 skipped
• Full suite — 1295 passed, 14 skipped (6 warnings are pre-existing: lancedb table_names() deprecation, an unrelated FastMCP coroutine warning)

Workaround for users on existing installs (before this ships)

reprocess --graph-only && reprocess --vectors-only, or reinstall cocoindex into the same venv as java-codebase-rag.

🤖 Generated with Claude Code