feat(harness): enforce tool timeout policies

[senamakel]

Summary

• add shared, atomically updateable ToolTimeoutSettings with inherited, explicit, unbounded, clamp, and grace semantics
• let RunPolicy opt into those settings without changing default behavior
• enforce the tighter of the tool deadline and remaining run wall-clock budget in serial and parallel tool execution

This closes the gap where Tool::timeout_policy existed as metadata but the harness loop did not consume it.

Validation

• cargo test timeout
• cargo fmt --all -- --check
• cargo clippy --all-targets --all-features -- -D warnings

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Review details

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Configuration used: Organization UI

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📥 Commits

Reviewing files that changed from the base of the PR and between 2583fcc and bf07893.

📒 Files selected for processing (11)

• README.md
• docs/modules/harness/README.md
• docs/spec/README.md
• src/harness/agent_loop/model_call.rs
• src/harness/agent_loop/test.rs
• src/harness/agent_loop/tools.rs
• src/harness/runtime/mod.rs
• src/harness/runtime/types.rs
• src/harness/tool/mod.rs
• src/harness/tool/timeout.rs
• src/harness/tool/timeout_test.rs

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