Support for post annotation label reassignement.

docs/final_output.md

@@ -256,3 +256,33 @@ ones. Weighting and the final overall mark belong to the separate grading flow.
 - [ODS export](../copienator/commands/update_ods.py)
 - [Final-mark stamping](../copienator/commands/add_final_score.py)
 - [Cleanup retention](../copienator/commands/clean.py)
+
+
+## Manual modifications after annotation reading
+
+`modify-annotations EVALUATION --annotation-dir BGnot` (or `Bnot`) applies
+`annotation_modifications.txt`. The GUI exposes it between annotation reading
+and return preparation. Its `### Source: BGnot`/`Bnot` line must match the mode.
+Instruction operators follow manual resolution syntax but act on reviewed raster
+**bodies**, excluding headers and all supplementary pages. Headers and scores stay
+with their labels. Missing target bodies are allowed; their new header identifies
+the target and its existing score, without inventing feedback or a score.
+
+Both readers record `annotation_baseline.json` and lossless hidden
+`.annotation-base-*.png` images in each copy's annotation directory. The JSON
+stores the exact header height, baseline answer metadata, and filtered membership.
+Older outputs require one full annotation read before body editing. Legacy
+selective redo still works, but cannot infer missing header boundaries.
+
+Each application rebuilds from that baseline and publishes all affected copies
+and the mode's `annotation_modifications_applied.txt` in one rollback-capable
+transaction. Reapplying is idempotent; removing an instruction restores its prior
+content and membership. Annotation rereads refresh the baseline and replay the
+applied snapshot, not the draft. Selective redo preserves unaffected baseline
+layers so previous transfers are never included twice.
+
+The operation rebuilds per-label JPEGs, `info.json`, `Concat.jpg`, and the filtered
+BGnot PDF or Bnot JPEG. Every changed non-empty body is included in the filtered
+output, with its destination label's supplementary material. `score.json` is not
+modified. The GUI marks downstream return preparation stale. Rerun `giving-names`
+without `--update` to refresh both full outputs and individual answer exports.