Revalidate git roots on each request

[davidahmann]

Closes #3613

Problem

The git server resolves the repository allowlist once and can keep accepting paths from roots that were later removed at runtime.

What changed

• rebuild the allowed repository list from the current runtime roots on every tool call
• validate the requested repo path against that live allowlist before dispatching the tool
• add regression tests for exact matches, removed roots, and empty-root handling

Validation

• uv run --python 3.11 pytest tests/test_server.py in src/git

[davidahmann]

This closes the stale-root gap in the git server, so repo paths removed from the live roots set stop being accepted on later tool calls.

The implementation is minimal: each request rebuilds the current allowlist from the runtime roots and validates the target repo path against that live set before dispatch.

Validation:

• uv run --python 3.11 pytest tests/test_server.py (pass)

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