_rebuild_code (post-commit hook) unconditionally overwrites graph.json, destroying semantic nodes

[gq5957]

Bug: _rebuild_code (post-commit/post-checkout hook path) silently discards the semantic graph

Summary

graphify.watch._rebuild_code() — the function the installed post-commit/post-checkout git hooks call — builds a graph from only the currently-detected code files via AST extraction, then unconditionally overwrites graphify-out/graph.json with it. If a full /graphify run has already populated the graph with semantic doc/paper/image nodes (from the LLM extraction path), a subsequent code-only hook rebuild destroys all of that, silently, with no warning.

This makes the hook actively dangerous on any repo that mixes code and docs (e.g. a markdown-heavy knowledge base with a handful of scripts): every commit that touches a code file wipes the semantic graph back down to code-AST-only.

Reproduction

1. Run a full /graphify pass on a mixed corpus (docs + a few code files) — confirm graph.json has both code and semantic (document-type) nodes.
2. Install the git hooks: graphify hook install.
3. Commit a change to any code file (.py, .ts, etc. — anything in CODE_EXTENSIONS).
4. Inspect graphify-out/graph.json — the semantic nodes are gone. Only the AST-extracted code nodes remain.

Root cause

In graphify/watch.py::_rebuild_code:

G = build_from_json(result)   # built from code_files ONLY
communities = cluster(G)
...
to_json(G, communities, str(out / "graph.json"))   # unconditional overwrite

There's no attempt to load the existing graph.json and merge; G is built from scratch every time.

Suggested fix

Load the existing graph (if present) and merge the freshly-extracted code subgraph into it, rather than replacing it wholesale:

G = build_from_json(result)

existing_path = watch_path / "graphify-out" / "graph.json"
if existing_path.exists():
    try:
        from networkx.readwrite import json_graph
        existing_data = json.loads(existing_path.read_text())
        G_existing = json_graph.node_link_graph(existing_data, edges="links")
        G_existing.update(G)
        G = G_existing
    except Exception as merge_exc:
        print(f"[graphify watch] Could not merge into existing graph.json ({merge_exc}); writing code-only graph instead.")

communities = cluster(G)

I've applied and tested this patch locally (verified: a 337-node graph with semantic content survives a simulated hook rebuild with the patch, vs. collapsing to 82 nodes without it). Happy to open a PR with this change if useful — let me know.

Secondary note (not a bug, just a heads-up)

The post-commit hook template in hooks.py only triggers on real code extensions, which is correct. Some users may have manually added .md/.mdx to their local hook's trigger list (I found this in the wild) hoping it would "refresh" the doc graph too — worth noting in docs that this doesn't do anything useful today, since _rebuild_code only ever reads code files regardless of what triggered it. Doc/paper/image extraction requires the LLM-driven /graphify --update path, which the hook correctly doesn't attempt.

[Evin009]

Hey! can I take this issue

[safishamsi]

The load-failure overwrite is fixed in v0.9.29: the hook rebuild now refuses to write when the existing graph.json is unreadable (over the size cap or unparseable) instead of silently replacing it, matching the CLI's fail-closed behavior. Note the wholesale-overwrite behavior quoted in the report is pre-0.4.3 (fixed in #253 by merging fresh AST with existing semantic nodes); if you're still seeing a 337->82 collapse, please upgrade — the installed graphify.watch is what the hook imports. https://github.com/Graphify-Labs/graphify/releases/tag/v0.9.29