Resolve standalone inline-manifest roots in file commands

[akhilles]

Note

Low Risk
Small, mechanical change to how the resolve root is computed for several CLI/MCP entrypoints; main risk is unexpected workspace discovery differences when running commands from unusual directories.

Overview
Fixes dependency resolution for file-based commands when invoked on standalone .zen files (including inline manifests) by passing the actual .zen path into crate::resolve::resolve(...) instead of only the parent directory, across bom, layout, open, route, sim, and MCP run_layout.

Updates the changelog to note the resulting behavior change: Board(..., layout_path=...) now resolves to package://workspace/... rather than leaking absolute paths for standalone inline-manifest .zen files.

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[devin-ai-integration]

✅ Devin Review: No Issues Found

Devin Review analyzed this PR and found no potential bugs to report.

View in Devin Review to see 3 additional findings.