[manthanut27]

What does this PR do?

Fixes #4562.

This PR ensures that an existing callflow HTML report is preserved if writing a replacement fails.

• Uses write_text_atomic() to write the generated HTML safely.
• Preserves the previous report when staging the replacement fails.
• Adds regression tests for staging write failures, close failures, and successful replacement.

Type of change

• Bug fix
• New feature
• Documentation
• Tests or CI
• Refactor
• Security fix

Verification & Invariants

• Read the CONTRIBUTING.md guide.
• Reproduced the issue and verified the regression test fails without the fix.
• Made the smallest fix necessary.
• Added a regression test for write failure, close failure, and successful replacement.
• Kept the PR description synchronized with the implementation.
• Documented any limitations / unsupported cases explicitly.

Invariant protected: If writing a replacement callflow HTML report fails before replacement completes, the previously generated report must remain unchanged, and temporary files must be cleaned up.

How was this tested?

uv run --frozen python -m pytest tests/test_callflow_html.py -q
# 14 passed

uv run --frozen pytest tests/test_atomic_writes.py -q
# 15 passed, 3 skipped

uv run --frozen ruff check <changed Python files>
# All checks passed

git diff --check
# Passed

Graphify-specific checklist

• Updated generated skill artifacts (not applicable: no skill source fragments changed).
• Confirmed AST/structural extraction remains deterministic (not specifically tested; this change only affects callflow HTML writing).
• Reviewed changes for security implications.
• Confirmed no API keys or local-only graph data are included.
• Disclosed AI authorship in the commit metadata, if required by the repository's convention.

[github-actions]

Thanks for the pull request, @manthanut27. A maintainer will review it soon.

Want to talk it through while it is in review? Come join us on our Discord server. For longer-form discussion there is also GitHub Discussions.

A couple of things that speed up review: make sure the test suite passes on Python 3.10 and 3.13, and that the change keeps extraction deterministic.

[graphify-labs]

Graphify reviewed this change.

No issues found by static checks — no coupling regressions or blocking issues in the code graph. That is not the same as safe to merge: see what was not checked.

Not checked: tests were not run; formal verification proved 0 of 1 changed function(s) (1 not verified).

Formal verification. PR-changed functions: 0/1 verified (0 proven, 0 may-equivalent, 0 distinguished) · 1 not verified (1 vacuous).

Not verified on this run: write\_callflow\_html (vacuous: never exercised).

---

Graphify review — findings

Makes write_callflow_html write the report through write_text_atomic, so a failure while staging or closing the temp file leaves any existing callflow.html untouched and no temp files behind. Adds tests for staging-write failure, staging-close failure, and a successful atomic replace of an existing report.

No blocking issues surfaced.

Analysis details — impact, health, verification

Impact & health

Graphify review

Impact — 583 functions depend on the 168 functions this change touches.

Health — this change adds coupling hotspots:

• worse: write_callflow_html() — 10 callers, 26 callees

Verification — 583 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: 343 function(s) in the blast radius were not formally verified this run

Test selection

Test selection

1 of 432 test file(s) selected (0%) via static blast radius.

• tests/test_callflow_html.py — impact, changed-test

Selection is safe under the controlled-regression assumption; always-run tests + a periodic full run are the backstops. Advisory — it never changes the check verdict.

Docs that may be stale (advisory)

• CHANGELOG.md § 0.9.43 (2026-08-14) (lines 726-734): references changed symbols write
• CHANGELOG.md § 0.9.29 (2026-07-28) (lines 877-887): references changed symbols write
• CHANGELOG.md § 0.9.17 (2026-07-16) (lines 1013-1042): references changed symbols write
• CHANGELOG.md § 0.8.15 (2026-05-22) (lines 1679-1688): references changed symbols write
• docs/superpowers/plans/2026-05-04-incremental-updates-dedup.md § Task 4: Incremental updates — semantic cache + manifest in __main__.py (lines 603-911): references changed symbols write
• docs/superpowers/specs/2026-05-04-incremental-updates-dedup-design.md § Pipeline (every graphify extract run) (lines 17-38): references changed symbols write
• graphify/skill-agents.md § Usage (lines 10-44): references changed symbols write
• graphify/skill-agents.md § Step 1 - Ensure graphify is installed (lines 65-112): references changed symbols write
• graphify/skill-agents.md § Part B - Semantic extraction (parallel subagents) (lines 207-370): references changed symbols write
• graphify/skill-agents.md § Step 4 - Build graph, cluster, analyze, generate outputs (lines 417-479): references changed symbols write

…and 10 more.

Formal verification

Could not verify: Could not verify write\_callflow\_html.

The verifier did not have enough to check write\_callflow\_html, 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: no capturable inputs from the test suite; property tier: not verifiable: all 51 sampled inputs raised on both versions — the function never executed, so 'no divergence' would be vacuous (mostly FileNotFoundError — names the real obstacle, not a sampling gap)

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