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Resolve the collision between the counters this branch adds and the auto-repair path that develop gained (#12524): - main.clj declares both sets of metrics, one beside the other. - files_update.clj keeps the METRICS helpers from this branch and the repair helpers from develop. `record-repair-outcome` now calls `record-metric!` instead of repeating the metrics lookup. - `process-changes-and-validate` keeps develop's `fdata/with-untracked` and runs both validation passes inside it. The hard referential gate now feeds the auto-repair path, so a file damaged before the save is repaired instead of refused. The test `referential-refusal-reports-the-gate-stage-and-code` therefore starts from a valid file and damages it through the changes, which is the case the gate still refuses. AI-assisted-by: claude-opus-5-5 Signed-off-by: Álvaro Tejero Cantero <alvorithm@teje.ro>