fix(server): upgrade FastMCP to v3

[trentzeigler]

Description

Upgrades FastMCP from 2.x to 3.x to address the FastMCP CVE floor called out in #1234 and updates the server integration for FastMCP 3 API changes.

Fixes: #1234
Fixes: #1348

Changes

• Raise mcp and fastmcp dependency bounds.
• Migrate FastMCP tool listing from get_tools() dictionary handling to list_tools() list handling.
• Update server mounting to use namespace=.
• Preserve schema compatibility by flattening nested nullable schemas emitted by FastMCP/Pydantic.
• Update unit tests and tool-doc generation for FastMCP 3 behavior.

Testing

• Unit tests added/updated
• Integration tests passed
• Manual checks performed: uv run pytest -q; uv run pre-commit run --all-files

Checklist

• Code follows project style guidelines (linting passes).
• Tests added/updated for changes.
• All tests pass locally.
• Documentation updated (if needed).

[szotrj]

Requesting priority review on this PR. It addresses high-severity security vulnerabilities that are actively blocking development progress. Thanks!

[sarah25ahmed]

@sooperset I am also requesting priority on this PR. Clearly these critical CVEs are blocking multiple users and enterprises and this PR resolves the issue. Thanks!