Write methodology rules to a markdown file under run_dir
Source: R/methodology_rules.R
write_methodology_rules.RdCreates run_dir/rules/methodology_rules.md with the generated
rules. The file is human-readable and serves as the canonical record
of the rules text the model was sent on every call during this run.
Per AC9 + AC4, rules are stamped on every call AND archived alongside
the run output so the methodology paper can attribute observed AI
behavior to the specific rules in force.