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detect_incremental() uses a single global manifest for all subdirectories — --update on one subfolder reports files from the last-graphed folder as deleted

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Valutazione

Difficoltà
3/5
Tempo stimato
1-2 giorni
Idoneità per principianti
72/100
Tipo di issue
Bug
Chiarezza
Specificata chiaramente
Stato di attività
Attiva
Stack tecnologico
python
Ambito
cli, tooling

Direzione di ricerca

Start in graphify/detect.py by tracing detect_incremental(root), load_manifest(), and save_manifest(), then inspect how the --update flow uses deleted_files. Verify that manifests are separated by subdirectory while preserving the existing root-level behavior, and that deleted_files only includes paths belonging to the current root. Confirm the resulting update report no longer includes unrelated folders.

Scritto dal modello di indicizzazione a partire dal testo della issue.

Descrizione

Bug: detect_incremental() uses a single global manifest for all subdirectories — --update on one subfolder reports every file from the last-graphed folder as deleted

Version: graphifyy 0.3.28

What happened

Running the skill's --update flow on one subdirectory of a large repo (e.g. workflows/) after a previous full run had graphed a different subdirectory (e.g. experts/) causes deleted_files in the incremental-detect result to list hundreds of paths from that unrelated, previously-graphed folder.

Live case: --update on workflows/ (a workspace with ~15 top-level graphed subfolders, each run via /graphify <subfolder>) returned deleted_files containing 230+ paths under experts/rechts-kanzlei/... — none of which are under workflows/ and none of which were actually deleted. The last folder graphed before this run was experts/.

Root cause

In graphify/detect.py, the manifest path is a module-level constant:

_MANIFEST_PATH = "graphify-out/manifest.json"

load_manifest() / save_manifest() both default to this single flat path regardless of which root was passed to detect_incremental(root). Every /graphify <subfolder> --update run in a multi-subfolder workspace reads and writes the same manifest file, so the manifest only ever reflects whichever subfolder was graphed most recently. The comparison in detect_incremental():

current_files = {f for flist in full["files"].values() for f in flist}
deleted_files = [f for f in manifest if f not in current_files]

flags every manifest entry not under the current run's file set as deleted — including entries that were never under root to begin with.

Impact

If the caller (e.g. the skill's --update flow) prunes graph nodes whose source_file is in deleted_files, this can silently remove nodes belonging to an unrelated subfolder's graph, depending on which graph is currently loaded. In our case the prune step happened to target the just-loaded subfolder graph, which contained none of the flagged paths, so the visible symptom was only a wrong "N files deleted" count in the diff report — but the mechanism is a correctness bug regardless of the specific graph layout, and could delete real nodes in a different call pattern (e.g. running --update against the root graph, or against a subfolder whose graph overlaps the previously-graphed one).

Suggested fix

Scope the manifest path to root by default (e.g. graphify-out/<sanitized-root>/manifest.json, falling back to the existing flat path for the root-level . invocation to avoid a migration step for existing single-folder setups). Additionally, filter deleted_files to only include manifest entries that were ever under root, as defense in depth against a stale or manually merged manifest.

Happy to share a patch if useful — we worked around it locally by scoping _MANIFEST_PATH per-root and adding the under-root filter to deleted_files.

Lingua principale
Python
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