docs: add complete MCP tool inventory with scope notes

[strawgate]

Summary

• add a full MCP tool inventory table for the /mcp endpoint
• group tools by capability with concise descriptions
• note that visible tools depend on token scopes
• note that /mcp/codemod exposes exec and help

Testing

• docs-only change

[cubic-dev-ai]

1 issue found across 1 file

Confidence score: 4/5

• This PR is safe to merge with minimal risk since the only finding is a low-severity documentation formatting issue (4/10) with no runtime or user-flow regression risk.
• In docs/how-to-guides/mcp-server.md, the !!! note admonition content should be indented by 4 spaces; otherwise the note block may render incorrectly and reduce guide readability.
• Pay close attention to docs/how-to-guides/mcp-server.md - fix admonition indentation so the !!! note block renders as intended.

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Re-trigger cubic</sub>

[strawgate]

I think we want to not include codemode yet