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refactor modularity-breaking implementations #1530

Description

@rvhonorato

Some modules were implementing following an approach that breaks modularity and adds a dependency between them.

For example for clustrmsd to be executed, ilrmsdmatrix or rmsdmatrix MUST have been executed before.

In the other hand clustfcc does not require anything to be executed before and thus follow proper modular implementation.

List of modules that need to be refactored

  • clustrmsd
  • ilrmsdmatrix
  • rmsdmatrix

This can greatly benefit from the caching implementation at #1529

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planned-long-termIssues that will be eventually done, used to mark issues as TODO itemsrefactoringcode improvements without functionality changes

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