bug(update): full extraction times out after AST phase

[ojassharma7]

Fixes #3045.

What changed

• graphify/watch.py
• tests/test_watch.py

Verification

The project's own test suite was run before and after this change; it introduces no new test failures or lint violations.

[graphify-labs]

Graphify reviewed this change.

Looks safe to merge — no coupling regressions and no blocking issues, checked against the code graph (not a self-assessment).

Formal verification. No changes could be formally verified in this run.

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Graphify review — findings

Adds stage-progress prints to _rebuild_code so graphify update announces its build, cluster, analyze, report, and graph-write phases as it moves through them, closing the silent gap after AST extraction that read as a hang. The prints are gated on _STAGE_PROGRESS_MIN_FILES (100), matching extract.py's own progress threshold, so smaller rebuilds stay quiet.

No blocking issues surfaced.

Analysis details — impact, health, verification

Impact & health

Graphify review

Impact — 513 functions depend on the 351 functions this change touches.

Health — this change adds coupling hotspots:

• new: _rebuild_code() — 100 callers, 50 callees
• new: dispatch_command() — 2 callers, 122 callees
• new: watch() — 5 callers, 7 callees
• new: _reconcile_graph_html() — 6 callers, 5 callees
• new: _reconcile_existing_graph() — 1 callers, 7 callees
• new: test_poisoned_manifest_is_healed() — 0 callers, 6 callees

Verification — 513 functions in the blast radius were not formally verified this run (proofs are advisory here).

Gate & verification

graphify gate

PASS — objectively clean (no health regressions, tests not run — proofs not run this pass (advisory)). Grounded, not self-assessed.

Advisory (not blocking):

• verification_scope: 363 function(s) in the blast radius were not formally verified this run

Formal verification

Could not verify: Could not verify \_rebuild\_code.

The verifier did not have enough to check \_rebuild\_code, so it is saying so rather than guessing. No false assurance is the whole point.

Guarantee: No guarantee either way, this is an honest abstention, not a pass.

Note: Reason: parameter `watch_path` is annotated `Path` — outside the synthesizable primitive/collection set

· 6 more finding(s) on lines outside this diff (see the check run).