Move the impl of run_tool_with_logging into shell_utils.sh

- This lets other shell scripts use it without being a shell function
- Simplifies run_tool_with_logging which is now in build/soong/bin

Bug: 340648588
Test: atest run_tool_with_logging
Change-Id: I1c1c5c1b115f155929c027c2ea82df5da8b190de