[Bug]: graphify update skips or partially rebuilds a missing graph when the manifest survives

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@azizur100389 is already working on this.

Since Nov 5, 2026.

  • #5021 by @azizur100389 — open

Assessment

Difficulty
2/5
Estimated time
1-3 hours
Newbie friendliness
77/100
Issue type
Bug
Clarity
Clearly specified
Activity status
Active
Tech stack
python
Domain
data

Research direction

Start by tracing graphify update and its manifest-derived update path, introduced in #4801, then find the full rebuild path used to create the AST graph. Reproduce by deleting graphify-out/graph.json while keeping graphify-out/manifest.json, then run graphify update . --no-cluster. Done when the update recreates the complete graph both with and without source changes.

Written by the indexing model from the issue text.

Description

Reproduction

Confirmed on v8 at 59b5ab11 (0.9.102), Python 3.12 on Windows. No LLM or API credentials are needed.

  1. Put def first(): return 1 in first.py and def second(): return 2 in second.py in a clean directory.
  2. Run graphify update . --no-cluster.
  3. Delete only graphify-out/graph.json. Leave graphify-out/manifest.json in place.
  4. Run the same update again. Repeat after changing just first.py.
Actual behavior

With no source changes, update exits successfully without recreating the file. With one changed source, it creates a graph containing only that source. The manifest identifies changed bytes but cannot supply unchanged nodes and edges.

Expected behavior

Recreate the complete AST graph using the existing full rebuild path whenever the output graph is absent.

This is a follow-up to the manifest-derived update path in #4801.

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