release: 0.9.0

BREAKING: node IDs now include the full repo-relative path (#1504, #1509) — fixes
silent data loss when same-named files live in different directories, and aligns
the AST and LLM id rules. Existing graphs migrate automatically on next build;
`graphify extract --force` to recover previously-collided nodes; Neo4j persisted
stores need a re-import. Also ships the --timing flag (#1490).

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

CHANGELOG.md

@@ -2,7 +2,7 @@
 
 Full release notes with details on each version: [GitHub Releases](https://github.com/safishamsi/graphify/releases)
 
-## Unreleased
+## 0.9.0 (2026-06-28)
 
 - **Breaking — node IDs now include the full repo-relative path** (#1504, #1509). The node-ID stem was the immediate parent dir + filename, so same-named files in different directories collided into one last-writer-wins node and silently dropped graph content (`docs/v1/api/README.md` and `docs/v2/api/README.md` both → `api_readme`). The stem is now the full repo-relative path (`docs_v1_api_readme` vs `docs_v2_api_readme`); top-level files are unchanged (`setup.py` → `setup`). The AST extractor, the LLM system prompt, the extraction-spec, and the two hand-copied stem helpers are all aligned to this one rule (fixing the #1509 AST↔LLM divergence that produced ghost duplicates), and `build_from_json` deterministically re-keys any cached/older semantic fragment onto the new IDs from its `source_file` so the unversioned semantic cache survives without ghosts or a re-bill. **Existing graphs migrate to the new ID format automatically on the next `build`/`update`** (no re-bill). Note: same-named files in different directories that previously collided into one node are only *recovered as distinct nodes* by a fresh extraction — run `graphify extract --force` to rebuild and gain them (migrating an already-collided graph/cache can't resurrect the nodes that were already dropped). If you push to a persisted **Neo4j** store, re-import after upgrading (re-exported IDs change); saved Gephi/yEd (GraphML) layouts go stale; MCP/cypher consumers should query by label rather than persisting node IDs across rebuilds.
 - Feat: `--timing` flag on `graphify extract` and `graphify cluster-only` prints per-stage wall-clock timings to stderr (#1490). Shows how long each pipeline stage takes — `extract`: detect → AST → semantic → build → cluster → analyze → export; `cluster-only`: load → cluster → analyze → label → report → export — plus a final total, so slow stages are visible on large corpora. Off by default (monotonic `perf_counter`, stderr-only); machine-read stdout / `graph.json` are unchanged.

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "graphifyy"
-version = "0.8.51"
+version = "0.9.0"
 description = "AI coding assistant skill (Claude Code, CodeBuddy, Codex, OpenCode, Kilo Code, Cursor, Gemini CLI, Aider, OpenClaw, Factory Droid, Trae, Hermes, Kiro, Pi, Devin CLI, Google Antigravity) - turn any folder of code, docs, papers, images, or videos into a queryable knowledge graph"
 readme = "README.md"
 license = { file = "LICENSE" }