feat: abort incremental update on failed or empty re-extraction (2/3)

[Const011]

Context

Split from former #1326 (closed) per review feedback — part 2 of 3.

• Part 1: feat: intra-file markdown slicing and adaptive retry (1/3) #1369 (intra-file slicing)
• Part 3: cross-file stitch — stacked on this branch (see follow-up PR)

Reconciled with upstream #1344 (re-extracted files replace prior contribution in build_merge) and #1350 (--no-cluster incremental no-op). This PR does not change the --no-cluster raw-write contract.

Motivation

Incremental extract is the practical way to update a graph file-by-file. We hit a critical data-loss bug: after editing one markdown file and re-running incremental extract, nodes for that file could disappear entirely while exit code stayed 0.

Problem: incremental update silently shrank the graph

Symptom: Changed file’s nodes vanished after incremental re-extract; unrelated files could survive.

Root cause: Incremental merge always pruned changed files before inserting fresh extraction (prune_sources = deleted + changed). If the LLM chunk “completed” but produced zero nodes (invalid JSON, connection blip, truncation), merge still ran: old nodes pruned, nothing replaced.

Upstream #1344 now auto-replaces nodes/edges for source_file values present in the re-extract batch; this PR adds the guardrail that prevents merge when re-extraction itself failed or returned nothing.

Fix

graphify/build.py — path coverage helpers:

• source_path_aliases, source_files_in_extraction
• path_covered_by_extraction, paths_missing_from_extraction

graphify/__main__.py (incremental mode only):

1. After semantic re-extract, abort with exit 1 if any uncached changed file has no nodes/edges in the fresh result, or if any chunk failed.
2. Do not write graph.json or update the manifest on failure — existing graph is preserved.
3. Build prune_sources from deleted files + changed code + successfully re-extracted semantic files only (via path_covered_by_extraction).

Stitch wiring (stitch.py, _stitch_new_ids, etc.) is intentionally not in this PR — see part 3.

Files

File	Change
graphify/build.py	Path coverage helpers for incremental safety
graphify/__main__.py	Abort + _incremental_prune (clustered incremental path)
tests/test_build.py	Import formatting

Test plan

• pytest tests/test_build.py tests/test_extract.py
• Upstream CI on Linux

Made with Cursor

[Const011]

Part 3 (cross-file stitch) is in #1371 — stacked on this branch (feat/incremental-safety). Please merge this before #1371.

[Const011]

Closing this PR as the proposed mechanics has proven to be inefficient in the longer run.