Add tool-semantics init and doctor commands

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Summary

Add tool-semantics init (scaffold project layout) and tool-semantics doctor (environment/config/MCP/model sanity checks).

Milestone

Cross-cutting DX (supports M8–M10)

Suggested labels

enhancement, priority:p2, area:cli, good first issue

Acceptance criteria

• init creates .tool-semantics/ skeleton (config, probes stub, traces/, README pointer)
• doctor checks Python version, install, config parse, baseline/probe validity, optional MCP reachability, model config presence
• Non-zero exit on hard failures; warnings for optional model runner missing
• Help + docs
• Tests for init filesystem and doctor happy/warning paths

Related

• Behavioral baseline layout issue