fix: detect plain JSON Schema objects in tool() overload resolution

[aayushbaluni]

Problem

The deprecated McpServer.tool() variadic overloads were removed during the v2 migration, but callers still rely on them (see issue #1585). When they passed (name, description, plainJsonSchema, handler), older implementations routed any non-Zod object into the ToolAnnotations branch. Plain JSON Schema objects (with nested properties, etc.) were therefore stored as annotations and inputSchema stayed unset, so tools/list exposed an empty object schema and arguments were not validated or forwarded correctly.

Fix

• Restore legacy tool() on McpServer with positional overloads equivalent to the common v1 shapes (tool(name, schema, cb) and tool(name, description, schema, cb)).
• Resolve the schema/annotations slot in order: Standard Schema / Zod raw shape (normalizeRawShapeSchema) → plain JSON Schema (structural heuristic + fromJsonSchema()) → ToolAnnotations-only objects (title, *Hint booleans).
• Throw a clear TypeError when the object matches none of these shapes (replacing silent data loss).

Note: TypeScript overloads for the rare (name, paramsSchema, annotations, cb) / five-argument forms were omitted because they collide with the description overload; those combinations remain supported at runtime via registerTool.

Testing

• Coverage in packages/server/test/server/mcp.compat.test.ts: plain JSON Schema preserves directory_id (and required) through standardSchemaToJsonSchema, annotations-only registration yields empty wire input schema and preserved annotations on tools/list, unrecognized objects throw, and tools/call validates JSON Schema tools end-to-end.

Fixes #1585

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Latest commit: 1a5fea9

The changes in this PR will be included in the next version bump.

This PR includes changesets to release 5 packages

Name	Type
@modelcontextprotocol/server	Patch
@modelcontextprotocol/express	Patch
@modelcontextprotocol/fastify	Patch
@modelcontextprotocol/hono	Patch
@modelcontextprotocol/node	Patch

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