Tool 0.3.1: add on-demand coding-agent decision gate

[Kinirin]

Summary

Implements the approved Tool 0.3.1 architecture-decision workflow without changing the bound PTSIP Specification snapshot.

• adds ptsip gate for coding-agent polling only when an active task actually needs an unresolved decision;
• adds explicit user-authorized ptsip resolve for chat-originated decisions;
• adds a GitHub App/Webhook reference control plane with persistent decision state and no timer/scheduler reminders;
• enforces first-valid-resolution-wins compare-and-set semantics across chat and Issue responses;
• ignores late Issue replies after a decision has already been resolved;
• validates structured ptsip-clarification-answer/v1 Issue responses from authorized repository writers;
• projects accepted decisions into ptsip.yaml with validation and exact-revision/stale safeguards;
• updates the coding-agent contract and Tool-level reference documentation;
• bumps the Reference Tool to 0.3.1 while retaining Specification 0.2.0-draft revision a877b2f66a7f94c1b844c979e1b08fb08a9a8e45.

A temporary pre-merge workflow verifies Python 3.11/3.14, the complete pytest suite, new CLI entry points, and package build. It will be removed after successful verification.