Fix missing dependencies #514
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…ate dependencies - Improved `McpServerFactory` logic to handle `ResourceTemplate` and `handler` typings more robustly. - Refined `InitSchema` with better defaults and simplified the schema merging in `InitMCPSchema`. - Updated `zod` dependency to `3.25.76` and synchronized `yarn.lock`. - Removed `YarnManager` in favor of `YarnBerryManager` for better package manager support. - Adjusted tests for refined outputs and schema handling. - Minor cleanup in command logic, package managers, and schema validation flow.
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