fix: deprecate --*.disabled CLI flags, wire up --mcp.disabled#3482

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Usr/sogh/deprecate-disabled-flags

Commits on Apr 29, 2026

fix: deprecate --*.disabled CLI flags, wire up --mcp.disabled (#3376)
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Commits on May 7, 2026

address review: update XML docs and add explicit MCP assertion branch
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Merge branch 'main' into Usr/sogh/deprecate-disabled-flags
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