Tidy up some resume functionality

[delucchi-cmu]

Change Description

A few clean-ups that don't change much functionality of resuming catalog, margin cache, or SOAP generation pipelines.

• Moves delete_resume_log_files up to the super class, so all resume plans can use the argument.
• Exposes user options for retaining intermediate files in margin generation and SOAP, as this was requested for catalog import and might be useful here as well.
• Moves margin cache pixel calculation more into the planning stages. Reduces the scope of the variables, and the negative pixel calculation can count toward the "planning" phase time.
• Only create directories for margin cache if the leaf files will be created.

Code Quality

• [x] I have read the Contribution Guide and LINCC Frameworks Code of Conduct
• [x] My code follows the code style of this project
• [x] My code builds (or compiles) cleanly without any errors or warnings
• [x] My code contains relevant comments and necessary documentation

[codecov[bot]]

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 99.56%. Comparing base (d27f650) to head (26596c9).

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #324 +/- ## ======================================= Coverage 99.55% 99.56% ======================================= Files 26 26 Lines 1363 1370 +7 ======================================= + Hits 1357 1364 +7 Misses 6 6 ```

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