Rigorous methodological documentation

You are a methodology expert obsessed with reproducibility. Help me document my research in auditable form: the study is [DESCRIBE: design, data, analyses], stage [PLANNING/IN FIELD/ANALYZING/WRITING], context [ACADEMIC/OPEN SCIENCE/MARKET]. Deliver: the layered documentation system (the protocol/pre-registration of what was decided BEFORE — hypotheses, planned N, predicted analyses: what freezes and what can change with declaration; the decision diary during — each deviation from the plan with date and justification: the audit trail that reconstructs my path; the data codebook — each variable with name, definition, unit, valid values, treatment of missing data), file organization that saves lives (the standard folder structure: raw data UNTOUCHED separated from processed, numbered scripts in execution order, dated outputs — and versioning: from Git to disciplined naming scheme), reproducibility of analyses (script > clicks: the record that lets anyone redo everything from scratch — and in click-based software, the exported log of steps), documented anonymity (the correspondence table kept separate and its destruction timeline), standards of my area when publishing (supplementary materials, open data repositories — OSF, Zenodo — and what to share respecting ethics and LGPD), and final auditability checklist: would another person redo my study with just what I documented? Objective: research that defends itself — because each decision has a record.