Refactor generate_report.py: extract plotting utilities and clean up duplicated code

[JoseEspinosa]

Description of feature

bin/generate_report.py contains duplicated plotting logic and mixes report generation concerns (HTML templating, structure alignment) with data visualization (pLDDT, PAE, sequence coverage plots). This makes the script hard to maintain and test.

A partial refactor already exists in the Australian-Structural-Biology-Computing fork that splits the code into:

• generate_report.py: orchestration, HTML templating, CLI
• plot_utils.py: reusable plotting and structure manipulation functions

Also, leaving here the original TODO int the code for reference.