Add per-surface MCP tool exposure controls

[copyberry]

Add per-surface MCP tool exposure controls

Why

MCP tools can be exposed directly, discovered through tool search, or called
from Code Mode. Servers need to be able to opt out of any of these surfaces
without disabling their tools everywhere.

What changed

• Add omit_tools_from to MCP server configuration, accepting any combination
  of direct, deferred, and code_mode.
• Apply the exclusions independently when building direct, deferred, and Code
  Mode tool surfaces while keeping omitted tools registered for permitted uses.
• Remove client-private _meta fields from MCP results returned to Code Mode.
• Include the new setting in the configuration schema and MCP config
  serialization.

Testing

• Cover every exposure combination across Code Mode, Code-Mode-only sessions,
  tool search, direct-only namespaces, and prefixed and unprefixed MCP names.
• Verify direct and nested execution paths, parallel-call support, config
  round-tripping, and _meta filtering.

[github-actions]

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