fix(data): preserve workspace paths in home reset

[Emin017]

run_flow_with_progress() calls home.reset() at the start of every progress-mode run, and reset() restored the default template including empty parameters/flow/checklist path fields. STA's rebuild_home_checklist() then picked up the empty checklist path (the .get default only applies to a missing key), built Path("") which resolves to the process cwd, and json_write() failed with IsADirectoryError trying to replace the repository directory. The same empty path also silently dropped every home checklist update during CLI runs.

reset() now clears only per-run state (layout/metrics/monitor) and keeps the workspace-lifetime path fields, matching how both callers use it (prepare_workspace_for_rerun re-sets the same paths immediately after). rebuild_home_checklist() additionally recovers home.json files already corrupted by earlier runs: when the stored checklist path is empty it falls back to the default home/checklist.json location and persists the healed path, so subsequent home checklist updates resolve as well.

What Changed

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:

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:

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.