graphify-out/ written to corpus/CWD despite --out / --graph pointing elsewhere

[bbqboogiedwonsen]

Summary

Output artifacts land in the corpus root / CWD even when --out <dir> (or --graph <path>) points elsewhere. Two distinct cases observed on 0.9.7:

Case 1 — extract --out still creates graphify-out/ inside the corpus

cd <repoA>
graphify extract . --out /tmp/scratch/tenant --no-cluster

The requested output is written to /tmp/scratch/tenant/graphify-out/ ✔ — but a stray graphify-out/ also appears in the corpus root (observed containing cache/ and partial content; also reproduced on a run that aborted at the no-LLM-key gate, which left <corpus>/graphify-out/ behind despite --out pointing elsewhere).

Case 2 — cluster-only --graph <elsewhere> writes results to CWD instead

cd <repoA>
graphify cluster-only . --no-label --graph /tmp/scratch/opexone/graphify-out/graph.json

GRAPH_REPORT.md, .graphify_analysis.json, .graphify_labels.json and the clustered graph.json were all written to ./graphify-out/ (CWD); the --graph target file remained un-clustered (community count 0). I.e. the flag selects the input, but outputs ignore its location.

Environment

• graphifyy 0.9.7 (pipx), Python 3.14.5, macOS (arm64)

Expected

All outputs follow --out / live next to --graph. Impact: repo pollution and accidental commits — we had to gitignore graphify-out/ in every corpus repo as a workaround.