[flutter_plugin_tools] Support YAML exception lists (flutter#4183)

Currently the tool accepts `--custom-analysis` to allow a list of packages for which custom `analysis_options.yaml` are allowed, and `--exclude` to exclude a set of packages when running a command against all, or all changed, packages. This results in these exception lists being embedded into CI configuration files (e.g., .cirrus.yaml) or scripts, which makes them harder to maintain, and harder to re-use in other contexts (local runs, new CI systems).

This adds support for both flags to accept paths to YAML files that contain the lists, so that they can be maintained separately, and with inline comments about the reasons things are on the lists.

Also updates the CI to use this new support, eliminating those lists from `.cirrus.yaml` and `tool_runner.sh`

Fixes flutter/flutter#86799