Add commit-by-commit refactor summary since Jan 12 baseline

[SzymonLukasik]

Motivation

• Provide a concise, commit-by-commit summary of the refactor work performed since the Jan 12 baseline "update modules" commit.
• Capture the large architectural changes, module split, logging/config improvements, and new backbone implementations to aid reviewers and future maintenance.

Description

• Add refactor_branch_changes_working.md containing a chronological summary of every commit since the Jan 12 baseline plus a short summary of the baseline itself.
• The document highlights the move from monolithic files to package-based multiplex_model/modules/ and multiplex_model/utils/, the addition of multiple backbone implementations, configuration and logging cleanups, and project packaging updates.
• Note the analysis was performed on the current work branch because no separate refactor branch was present in this clone.
• The new file was created in the repository and persisted as a working summary for reviewers.

Testing

• Ran repository inspection commands to build the report: git fetch --all --prune, git branch -a -vv, and git log --oneline --decorate --date=short which completed successfully.
• Verified per-commit statistics with git show --stat for the baseline and subsequent commits which completed successfully.
• Confirmed the generated file exists and contains the expected content with wc -l refactor_branch_changes_working.md and sed -n '1,220p' refactor_branch_changes_working.md which completed successfully.

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Codex Task