Refactor Cleanup of MDTools Analyses

[andthum]

Refactor Cleanup of MDTools Analyses

Type of Change

• Bug fix.
• New feature.
• Code refactoring.
• Dependency update.
• Documentation update.
• Maintenance.
• Other: Description.

• Non-breaking (backward-compatible) change.
• Breaking (non-backward-compatible) change.

Proposed Changes

• Bash script .cleanup_mdt_analyses.sh: Change how specific analyses are gathered/ordered into sub-directories. This affects axial_hex_dist, discrete-hex, contact_hist_at_pos_change and lig_change_at_pos_change*.

PR Checklist

• I followed the guidelines in the Developer's Guide.
• New/changed code is properly tested.
• New/changed code is properly documented.
• The CI workflow is passing.