fix: replace non-atomic write_text() calls with atomic helpers in map_step_runner

[azalio]

Summary

Fixes #456 — replaces 13 remaining Path.write_text() calls in map_step_runner.py.jinja with the _write_json_file() / _write_text_file() atomic helpers that route through atomic_write_text() (tempfile.mkstemp + os.replace).

Path.write_text() truncates the destination file before writing, so a process crash between those two operations leaves a corrupted or zero-byte file. The atomic helpers write to a PID-unique sibling temp file first, then atomically rename into place — readers always see either the old complete file or the new complete file, never a partial write.

Functions fixed

Function	File written	Criticality
generate_implementer_readiness	implementation-readiness.md	medium
build_verification_summary	verification summary	medium
write_pr_draft	pr-draft.md	medium
write_plan_review	plan review .md	medium
update_review_verdict_ledger	review-verdict-ledger.md	medium
replace_active_issues	active-issues.json	HIGH
stage_pending_review_ordering	pending ordering JSON	HIGH
build_learning_handoff	learning handoff .md	medium
add_known_issue	known-issues.json	HIGH
update_plan_status	task_plan_<branch>.md	HIGH
save_research_artifact	research artifact .md	medium
acknowledge_diagnostic	diagnostics ledger JSON	HIGH
discard_worktree	.patch file	low

Five write_text() calls are intentionally retained:

• Two create-only guards (if path.exists(): continue / if not gitignore.exists())
• Two ensure_*_file create-only helpers
• One snapshot backup inside try/except OSError: pass

Testing

• All 834 existing pytest tests pass
• ruff check clean
• pyright 0 errors / 0 warnings / 0 informations
• make check-render passes (generated trees match templates_src)

🤖 Generated with Claude Code

https://claude.ai/code/session_01UgHmPwdEWm3dhsNK4D4KzY

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Generated by Claude Code

Summary by CodeRabbit

• Refactor
  • Standardized how generated reports, plans, patches, review files, and other text artifacts are saved.
  • Standardized JSON output handling while preserving existing formatting.
  • Existing write-error handling and processing behavior remain unchanged.

[coderabbitai]

Caution

Review failed

The pull request is closed.

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Advanced

Run ID: 2aaa8ebb-d415-4e35-b6c7-e1d657e61497

📥 Commits

Reviewing files that changed from the base of the PR and between 64d2c36 and a84d69c.

📒 Files selected for processing (3)

• .map/scripts/map_step_runner.py
• src/mapify_cli/templates/map/scripts/map_step_runner.py
• src/mapify_cli/templates_src/map/scripts/map_step_runner.py.jinja

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📝 Walkthrough

Walkthrough

The runner and its Jinja template now route text artifacts through _write_text_file and JSON artifacts through _write_json_file. Existing serialization and error handling remain unchanged.

Changes

Atomic artifact writes

Layer / File(s)	Summary
Report and review artifacts .map/scripts/map_step_runner.py, src/mapify_cli/templates/map/scripts/map_step_runner.py, src/mapify_cli/templates_src/map/scripts/map_step_runner.py.jinja	Readiness, summary, pull-request, review, and verdict files now use _write_text_file.
State and plan artifacts .map/scripts/map_step_runner.py, src/mapify_cli/templates/map/scripts/map_step_runner.py, src/mapify_cli/templates_src/map/scripts/map_step_runner.py.jinja	Issue and pending-ordering JSON files use _write_json_file. Learning and plan files use _write_text_file.
Snapshots, ledgers, and patches .map/scripts/map_step_runner.py, src/mapify_cli/templates/map/scripts/map_step_runner.py, src/mapify_cli/templates_src/map/scripts/map_step_runner.py.jinja	Snapshot, ledger, and worktree patch writes use _write_text_file.

Estimated code review effort: 2 (Simple) | ~10 minutes

Change: Bug fix · Severity of issue fixed: High

Suggested reviewers: yvasiyarov

✨ Finishing Touches

📝 Generate docstrings

• Create stacked PR
• Commit on current branch

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch claude/compassionate-cerf-he3i8x

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_{A rabbit sees the writers align,
Text hops safely through one line.
JSON keeps its ordered trail,
No torn files disturb the tale.
The runner thumps a steady beat.
Atomic paws make work complete.}

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