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Wire index_repository auto_index_deps and auto_dep_limit arguments through the MCP indexing path so explicit calls can disable or cap dependency indexing without changing background/session defaults. Keep the existing cbm_dep_auto_index API config-driven for current callers and add an already-effective-limit helper for MCP. Add focused MCP tests for false boolean overrides and per-call dependency caps. Validation: CBM_ONLY_SUITE=mcp build/c/test-runner (134/134), CBM_ONLY_SUITE=depindex build/c/test-runner (35/35), source-safety, production cbm build, and isolated CLI dogfood for auto_index_deps:false and auto_dep_limit:1. Signed-off-by: Andrew Hundt <ATHundt@gmail.com>