Release 0.8.45

Path-portability cluster + native-backend hyperedge prompt fix:
- #1417 portable manifest.json from the skill runbooks
- #1418 hyperedge source_file relativization
- #1419 GRAPH_REPORT.md header shows the scan root
- #1423 GRAPHIFY_OUT honoured end-to-end
- native-backend extraction prompt now requests hyperedges (#1430)

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

Author: safishamsi

CHANGELOG.md

@@ -4,6 +4,8 @@ Full release notes with details on each version: [GitHub Releases](https://githu
 
 ## Unreleased
 
+## 0.8.45 (2026-06-22)
+
 - Fix: native-backend semantic extraction now produces hyperedges. The `graphify extract --backend <gemini|claude|claude-cli|openai|kimi|…>` prompt (`llm._EXTRACTION_SYSTEM`) only ever showed `"hyperedges":[]` in its output schema and never explained what a hyperedge is, so every native backend silently emitted zero — while the agent/skill path (whose `extraction-spec.md` fully documents hyperedges) produced them. The two prompts had drifted. The native prompt now carries the same "3 or more nodes participate together" instruction and a populated schema example, so both extraction paths yield the same hyperedge behaviour for a given corpus. Verified end-to-end: a doc that previously produced 0 hyperedges now produces one (correctly relativized, per #1418). Guard tests assert the two prompts can't drift apart again.
 - Fix: `GRAPHIFY_OUT` is now honoured end-to-end. The override (a custom output-dir name or absolute path, for worktrees/shared setups — #686) was only respected by some readers; `graphify extract` and several commands hardcoded `graphify-out/`, so a `GRAPHIFY_OUT=custom-out graphify extract` still wrote to `graphify-out/`, and downstream `query`/`serve`/`update` looked in the wrong place. The output-dir name is now resolved through `graphify.paths` everywhere it matters: the `extract` write dir, `cluster-only`/`label`, `query`/`affected`/`benchmark` defaults, `save-result --memory-dir`, `uninstall --purge`, `cache-check`, the `manifest.json`/`transcripts`/`memory`/`converted` paths in `detect`/`transcribe`, the `build_merge`/`serve`/`benchmark`/`prs` graph-path defaults, and the `detect` scan-exclude (so a renamed output dir is never re-ingested as source). Default behaviour is unchanged — without the env var everything still uses `graphify-out/` (#1423).
 - Fix: the `GRAPH_REPORT.md` header now shows the actual scan root instead of a literal `.`. The split-skill runbook passed `'.'` as the `root` argument to `report.generate` in Steps 4 and 5, so a `/graphify /some/path` run produced a report titled `# Graph Report - .`. It now passes `'INPUT_PATH'` (matching the monoliths, which were already correct). Display-only — no path written to `graph.json`/`manifest.json` was affected (#1419).

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "graphifyy"
-version = "0.8.44"
+version = "0.8.45"
 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" }