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watch: _rebuild_code overwrites semantic nodes instead of merging with existing graph #253
Description
Problem
_rebuild_code() in watch.py does a full AST-only rebuild and writes the
result directly to graph.json, overwriting any semantic nodes previously
extracted from docs/papers by the full /graphify pipeline.
In a mixed repo (code + markdown docs), every code file save destroys the
semantic layer (INFERRED edges, rationale nodes, cross-doc surprises,
hyperedges, community labels).
Reproduction
- Run
/graphify .on a repo with code + markdown docs - Note node/edge count (e.g. 473 nodes, 428 edges, 28 INFERRED)
- Start
python3 -m graphify.watch . --debounce 3 - Edit any code file and save
- Graph is now AST-only (e.g. 345 nodes, 307 edges, 0 INFERRED)
Expected behavior
_rebuild_code should:
- Load the existing
graph.json - Remove only AST-derived nodes/edges
- Re-extract AST from code files
- Merge new AST nodes into the graph alongside existing semantic nodes
- Write the merged result
Workaround
Don't use --watch on mixed repos. Use /graphify . --update instead.
Activity
Joseph94m commentedon Apr 12, 2026
The README describes
--watchas:"The graph updates itself" implies an incremental merge, consistent with how
--updateis described separately:But
--watchdoesn't merge._rebuild_codebuilds a new graph from AST-only data and overwritesgraph.jsonentirely. On a mixed repo (code + docs), this silently destroys all semantic nodes, INFERRED edges, hyperedges, and community labels from the prior/graphifyrun.The distinction between
--update(merge) and--watch(overwrite) is not documented and contradicts the "auto-sync" framing.fix bugs #256, #253, #244, #226, #254 and bump to 0.4.3
safishamsi commentedon Apr 12, 2026
Fixed in v0.4.3.
_rebuild_codenow loads the existinggraph.jsonbefore overwriting — it keeps all non-code nodes (docs, papers, images) and their edges, then merges in fresh AST results. Semantic nodes from a full/graphifyrun survive code file saves.fix bugs Graphify-Labs#256, Graphify-Labs#253, Graphify-Labs#244, Gra…
fix bugs #256, #253, #244, #226, #254 and bump to 0.4.3
fix bugs Graphify-Labs#256, Graphify-Labs#253, Graphify-Labs#244, Gra…