fix(runtime): persist tool failures and recover interrupted steps

[KoEkko]

What Changed

• Contain tool exceptions and SystemExit inside the step execution boundary, persist Imcomplete, and preserve the original failure message in runtime events.
• Persist schema-1 runtime operation markers and add an idempotent workspace.recover_interrupted RPC for interrupted steps.
• Finalize subflow/checklist/observer state on terminal failures and update the ecc-dreamplace gitlink for catchable utilization failures.

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:

• Ongoing steps now store info.runtime_operation in workspace.flow.json; the marker is cleared on normal terminal completion.
• workspace.recover_interrupted only transitions matching schema-1 interrupted steps to Imcomplete and does not rerun them.

Validation

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

• uv run pytest test/ --ignore=test/examples/test_soc.py -q
• 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: verified DreamPlace failure persistence and rerun state through the GUI.
• Other: bash .github/scripts/check-version.sh; git diff --check origin/main...HEAD

Skipped checks and reason:

• PyInstaller bundle build was skipped because packaging files are unchanged; CI will run the bundle job.
• Nix smoke was skipped because Nix files are unchanged.

Checklist

• I kept the change scoped to ECC.
• I updated docs or user-facing CLI text where behavior changed. (N/A: no public CLI text or documentation contract 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.