fix(git): validate repo_path against current roots on every tool call

[ctonneslan]

Problem

call_tool() validates repo_path only against the CLI --repository argument. When no CLI restriction is set (repository is None), all paths are allowed regardless of the current roots.

If roots change at runtime (client removes a root), a repo that was previously reachable can still be accessed because validate_repo_path returns immediately when allowed_repository is None.

Fix

Validate repo_path against the full list of allowed repos (both roots + CLI) on every tool call by calling list_repos():

allowed_repos = await list_repos()
if allowed_repos:
    resolved_repo = str(repo_path.resolve())
    if not any(
        resolved_repo == r or resolved_repo.startswith(r + "/")
        for r in (str(Path(r).resolve()) for r in allowed_repos)
    ):
        raise ValueError(...)

This ensures:

• Root changes revoke access immediately
• No restart needed when roots are updated
• CLI-only fallback still works when roots aren't available

Fixes #3613