docs: clarify v1 and v2 tool schema shapes

[uuzzrm]

Summary

• Document the v1 positional server.tool() raw-shape contract alongside the v2 registerTool() Standard Schema contract.
• Add troubleshooting guidance for the empty inputSchema and the _def crash reported on older v1 releases.
• Add a concise reminder to the troubleshooting checklist.

Fixes #2627

Validation

• git diff --check
• Attempted pnpm run docs:check; this checkout is missing the generated docs/api/typedoc-sidebar.json, and VitePress then reported dead links in the unchanged clients/machine-auth.md and index.md pages.
• The pre-push hook also attempted the repository-wide pnpm checks, but the local dependency setup aborted while installing ignored build scripts; no source or lockfile changes are included in this PR.

This is a docs-only change with no runtime code changes.

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commit: b75abb3