• Fix: graphify hook install now embeds the current interpreter (sys.executable) directly into the generated hook scripts. Previously, uv tool and pipx installs silently no-oped on git commit in GUI clients and CI runners where ~/.local/bin is not on PATH — the hook could not find the graphify launcher, fell through all detection probes, and exited 0 without rebuilding. If you already have hooks installed, re-run graphify hook install to pick up the fix (#1127).
• Fix: hook scripts also probe graphify-out/.graphify_python as a fallback interpreter source, covering Windows/Git Bash installs where the launcher is a binary with no parseable shebang, and the case where the pinned path goes stale after a reinstall.
• Security: hook script hardening — _PINNED= uses single quotes to prevent shell injection; nohup "$GRAPHIFY_PYTHON" -c is properly quoted; the fallback emits a loud stderr diagnostic instead of a bare silent exit 0.
• Fix: manifest.json keys, .graphify_root, and cache/ast/*.json source_file fields are now stored as relative paths and re-anchored on load. Teams committing graphify-out/ no longer see forced full rebuilds on every CI checkout or clone (#777, #1125).
• Feat: query logging. Every graphify query, graphify path, graphify explain, and MCP query_graph call is appended to ~/.cache/graphify-queries.log in JSON Lines format (timestamp, question, corpus, nodes returned, duration). Control with GRAPHIFY_QUERY_LOG, GRAPHIFY_QUERY_LOG_DISABLE=1, or GRAPHIFY_QUERY_LOG_RESPONSES=1 (#1128).