Make MCP StdioTransport fallible, add tests, and small robustness/docs fixes

[devopsariful]

Motivation

• Avoid panics when spawning MCP subprocesses and propagate errors so callers can handle failure.
• Harden Git status and ahead/behind calculations against unexpected git API results.
• Clean up minor docs/strings and align dependency versions for compatibility.

Description

• Change StdioTransport::new to return Result<Self> and use anyhow::Context for richer error messages instead of panicking on spawn or I/O capture failures.
• Update caller in register_server to propagate the fallible StdioTransport::new with ?.
• Improve git module robustness by using Oid::ZERO_SHA1 and handling potential errors from path() and shorthand() calls more defensively.
• Add a unit test stdio_transport_spawn_failure_returns_error to ensure invalid MCP commands return an error instead of panicking, and make small spelling/documentation changes in test files and comments.
• Bump or adjust a few dependency entries in package.json and Cargo.lock to align versions.

Testing

• Ran cargo test which includes the new unit test stdio_transport_spawn_failure_returns_error, and all unit and integration tests completed successfully.
• Ran integration tests covering vector store and config (test_vector_store*, test_config) which passed as part of the test run.
• No automated failures were observed in the modified test suite.

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Codex Task