Enforce exact_match=True when listing JSON file for get_estimated_time for MPH

[alex-l-kong]

What is the purpose of this PR?

Closes #465. The way list_files works is not robust against the new _processing.json files that get written to the CACs. For get_estimated_time, this causes issues when verifying that a FOV exists in the run folder, then loading it in because sometimes it will attempt to verify the _processing.json file and not the main FOV .json file.

How did you implement your changes

Make use of exact_match=True for list_files to enforce hard matching.

Remaining issues

Across several places in toffy and ark, exact_match=True must be used, especially because Bryan's ezSegmenter update makes soft matching the default.

[alex-l-kong]

The current way list_files is implemented for exact_match=True is awkward because it removes file extensions when considering matches: https://github.com/angelolab/alpineer/blob/main/src/alpineer/io_utils.py#L78-L83. Worth thinking if a rewrite is necessary.

[camisowers]

I agree, the logic for dropping the extension when checking for an exact match is probably a good idea. We would just need to check ark and toffy to make sure that isn't in there for a specific reason.

I would add a -processing.json file to all relevant tests in the pipeline, to see if list_files() breaks anywhere else in toffy.