fix: make stdio redirection scoped and exception-safe

[Ayoubbelguellaoui]

What Changed

• Replaced process-global stdout/stderr redirection in chipcompiler/utility/log.py with a thread-safe, context-managed _StdioRedirect implementation that safely saves and restores file descriptors even upon exceptions.

Updated chipcompiler/engine/flow.py, chipcompiler/engine/rerun.py, and agent/engine.py to ensure step-level log redirects close cleanly.

Updated chipcompiler/runtime/operations.py to treat event publisher exceptions as non-fatal and wrapped active operation tracking in finally blocks to guarantee cleanup.

Added and updated tests in test/cli/rendering/test_progress.py, test/runtime/test_events.py, and test/runtime/test_operations.py to cover stdio restoration, thread isolation under concurrency, and resilient operation tracking.

Scope

Select the areas touched by this PR:

• CLI - command behavior, Typer command surface, output formats, or workspace commands.
• Flow/runtime - workspace lifecycle, EngineFlow, step execution, logs, metrics, or artifacts.
• EDA integration - Yosys, ECC-Tools, DreamPlace, KLayout, PDKs, or native/runtime wrappers.
• Build/package - Nix, PyInstaller, wheels, uv.lock, or release artifacts.
• CI/release - GitHub Actions, version checks, changelog, or release automation.
• Tests/docs only

Runtime And Packaging Impact

• No runtime or packaging impact
• CLI output or machine-readable contract changed
• Workspace layout, flow state, or artifact paths changed
• Native toolchain or wrapper behavior changed
• ecc-tools or ecc-dreamplace dependency changed
• PyInstaller, Nix, or release artifact changed

Notes:

• Fixed critical bugs where process-global stdio redirection corrupts concurrent flow logs, and where event publisher failures leave active operations permanently uncleaned.

Validation

List the commands you ran. Mark checks that are not applicable as N/A.

• uv run pytest test/
• uv run ruff check chipcompiler test
• uv run ruff format --check chipcompiler test
• PyInstaller smoke: ecc --help, ecc --version, ecc version --json
• Nix smoke: nix run .#cli -- --help
• Manual flow smoke:
• Other: - uv run pytest test/ — 1460 passed, 8 skipped, 4 xfailed, 2 environment-related failures.

Skipped checks and reason:

Checklist

• I kept the change scoped to ECC.
• I updated docs or user-facing CLI text where behavior changed.
• I included lockfile or version metadata updates when dependencies changed.
• I documented any submodule updates and why they are needed.
• I did not include local caches, virtual environments, or generated build outputs.
• I explained skipped validation and remaining risk.

[Emin017]

Thank you for your contribution! However, does this PR have any overlapping parts with #236?

[Ayoubbelguellaoui]

There is some overlap at the step-execution/runtime level, particularly around EngineFlow and failure cleanup, but the two PRs address different issues.

PR #236 focuses on containing tool failures, persisting Incomplete, interrupted-operation recovery, and terminal failure state propagation.

This PR focuses specifically on making process-global stdout/stderr redirection scoped and exception-safe, isolating concurrent redirects, and guaranteeing runtime operation cleanup when event publishing fails.

The overlap is therefore limited to the surrounding execution/cleanup paths; the implementations address separate failure modes.

[Emin017]

This PR focuses specifically on making process-global stdout/stderr redirection scoped and exception-safe, isolating concurrent redirects, and guaranteeing runtime operation cleanup when event publishing fails.

The overlap is therefore limited to the surrounding execution/cleanup paths; the implementations address separate failure modes.

Got it, I just merged #236. Could you rebase and resolve the conflicts?