fix(cli): initialize DB for workspace run-step

[Emin017]

Summary

Fixes direct ecc workspace run-step execution so pending or rerun steps initialize the ECC DB wrapper before invoking the step runner, while preserving existing run-flow, unknown-step, and
already-successful skip behavior.

This also keeps workspace --json stdout clean when runtime code redirects process stdio to step logs, and aligns the Nix-packaged thirdparty tool pins with the current alpha.4 sources.

Changes

• Initialize the DB engine for real workspace run-step execution without changing EngineFlow.run_step().
• Avoid DB initialization when a non-rerun step is already Success.
• Keep runtime log output out of JSON stdout for workspace commands.
• Keep programmatic cli_main.run() stdio restoration behavior separate from installed CLI process behavior.
• Update Nix packaging for ecc-dreamplace and ecc-tools alpha.4.

Verification

• ruff passed
• focused CLI/formal tests passed
• full pytest passed: 823 passed, 9 skipped, 1 deselected, 13 xfailed
• nix build .#cli passed
• packaged CLI smoke passed for workspace create, run-step Synthesis, and run-step Floorplan
• codex review --base main reported no introduced bugs