fix: decorate late tools before registration

[neumie]

Summary

• decorate configured tools registered by later-loaded extensions before Pi snapshots their definitions
• optionally preserve a tool's native call/header renderer while replacing only result rendering
• track decorated tools by object identity, bound pending decorations, and clean interception state across reloads

Why

customToolOverrides can target tools registered after pi-tool-display (for example hypa_shell). The interceptor previously forwarded a tool to Pi before decorating it. If Pi copied the definition during registerTool, the configured renderer never reached the runtime.

The new order decorates first and remains fail-open: if decoration fails, the original tool is still registered.

Scope

• one squashed commit
• no fork branding, package-version change, repository URL change, or CI configuration
• documentation and tests are limited to the affected runtime/API behavior

Validation

• npm run typecheck
• affected API/registration suites: 28/28 passed
• npm pack --dry-run --ignore-scripts
• full local suite: 723/728 passed; the five existing macOS fixture failures reproduce on unmodified upstream main (/var vs /private/var paths and the ignored local config.json fixture)