SWEEP-PP (B): experiment_design.csv is output only, and the pairing card is rebuilt on the draft (PP-02)

AGENTS.md

@@ -87,9 +87,10 @@ src/morphobricks_preprocessing/
                     is wrong with a malformed one (PhysicalSizes.invalid, issue #94)
   dataset.py        dataset consistency from the folders: biological repeats per condition, balance
                     table, unbalanced_images, repeat_missing_conditions, CONSISTENCY_CODES (P2)
-  design.py         experiment design (P3): ExperimentDesign/DesignRow, default pairing, reconcile with
-                    the folders on reruns, design_issues, read/write experiment_design.csv, load_design;
-                    read_confirmed_design/ConfirmedDesign (the strict reader other bricks use, §16)
+  design.py         the rows of experiment_design.csv (an output only since v0.5.1): DesignTable/
+                    DesignRow (read-only), the run's reconcile_design and design_issues against
+                    the folders, write_experiment_design, parse_design_bytes (the strict parser
+                    of the draft's legacy migration); no reader for other bricks (SWEEP-PP)
   design_derive.py  derive_design/write_derived_design: experiment_design.csv from a published
                     description (Spec experiment-v1 11), written by design.write_experiment_design
   design_values.py  the design file's header check (no column twice or unnamed, #83), booleans,
@@ -657,15 +658,15 @@ functions the tests use.
 - **Confirmation** per group (`design_not_confirmed` until then); all-`single` experiments
   get one whole-experiment question. Controls are recorded only.
 - **`experiment_design.csv`** (schema 1): one row per condition x biological-repeat folder,
-  sorted; counts at confirmation; `confirmed_on` ISO date. Lenient reader (any-case
-  booleans, BOM); `DesignFormatError` otherwise, also for a header naming a column twice
-  or not at all (#83, both readers), a repeat group that is not a
-  D-e identity or a `confirmed_on` that is not `YYYY-MM-DD` (naming line and column).
-  Other bricks read it with the strict `read_confirmed_design` (contract §16,
-  question 40): nothing filled in, every group confirmed, SHA-256 of the bytes parsed;
-  `RunInputs.design()` uses it too (#83).
-- **Reruns:** `reconcile_design` keeps answers for known folders, reopens only groups that
-  gain a folder, drops removed folders.
+  sorted; counts at confirmation; `confirmed_on` ISO date. Written by the run only. No brick
+  reads it back (v0.5.1, SWEEP-PP; Spec ADR 0002 AR11 (3)): the lenient reader,
+  `load_design`, the strict `read_confirmed_design`/`ConfirmedDesign`/`DesignCheckError` and
+  `RunInputs.design()` are removed; bricks take `repeat_group` from the description
+  (`Fov.repeat_group`). `parse_design_bytes` (strict, `DesignFormatError` naming line and
+  column, also for a header naming a column twice or not at all, #83) remains for the draft's
+  experiment-v1 §7 migration of a legacy file.
+- **The run's check:** `reconcile_design` keeps the derived rows of known folders, reopens only
+  groups that gain a folder (`design_not_confirmed`), drops removed folders.
 - **v0.5.1: an output only.** Every run is described (`A_DESCRIPTION_REQUIRED` without a
   published `morphobricks.toml`, contract §0); the run derives `experiment_design.csv` from the
   description and writes it with the table (`experiment_design_sha256` in the manifest). The

CHANGELOG.md

@@ -264,6 +264,34 @@ already removed is not repeated here. **Breaking** where it says so.
   fetch, went in PP-C; `test_schema_v2_equivalence.py` was renamed `test_histogram_goldens.py`
   there.)
 
+- **`experiment_design.csv`: an output only, nothing reads it back; the notebook's pairing card
+  rebuilt on the draft** (inventory PP-02, owner answers 3 and 4; Spec ADR 0002 AR11 (3)).
+  **Breaking.** Removed: `read_confirmed_design`, `ConfirmedDesign`, `DesignCheckError` (its
+  codes `missing_experiment_design`, `unreadable_experiment_design`,
+  `changed_experiment_design`), `RunInputs.design()`, the lenient `read_experiment_design`,
+  `load_design`, `DesignChanges`, `default_design`, the editor model `ExperimentDesign` (its
+  `with_group`, `with_confirmed`, `with_control`, `dated`), `design_edit.py`
+  (`DesignEdit`, `DesignEditError`, `apply_design_edit`, `parse_repeat_group`), and the unused
+  `report.design_summary`/`design_table`. The derived rows are now a read-only `DesignTable`
+  (`design.py`): the run's check against the folders (`reconcile_design`, which returns the
+  rows only; `design_issues`), `write_experiment_design`, `DESIGN_COLUMNS`, `design_derive`
+  and the manifest's `experiment_design_sha256` stay, and `RunInputs.open` still checks the
+  file's SHA-256. `parse_design_bytes` (strict) stays for the draft's experiment-v1 §7
+  migration of a legacy file. A brick takes the repeat groups from the description
+  (`Fov.repeat_group`, `resolve_request`). *Check and save* compares the candidate's derived
+  rows with those of the published description, not with the file in the output folder
+  (`check_candidate` lost its `output` argument). **Notebook:** the pairing card shows one row
+  per folder of the draft's base, with the repeat it is paired with
+  (`PreprocessingNotebook.pairing`, replacing `.design`); a change is a draft answer at once.
+  Removed with the retired card parts: the hidden comparability questions
+  (`group_confirmations`, `groups_box`), the hidden control boxes (`controls_box`,
+  `control_checks`, `_sync_controls`), the *Change the experiment design* button, and the dead
+  `_design_pending`/`_design_items`/`_design_confirmed` gates. The shipped notebook file is
+  unchanged (it installs its `RELEASE_REF`). **Downstream** (pins hold until moved):
+  CellPatcher (`normalization.py`, `config.py`, `setting_checks.py`, `file_runs.py`, CP-1) and
+  MorphoFeature (`experiment_design.py`, `fits.py`, MF-4) must read `repeat_group` from the
+  description before their pin passes this change.
+
 ## 0.5.0 - 2026-11-09
 
 Stage 1 of the experiment description (MorphoBricks-Spec experiment-v1, pinned at `1bed024`):

docs/conformance.md

@@ -143,8 +143,8 @@ GS1: a scenario that names fixtures is shown on those fixtures; further fixtures
   `v13`, `v33`, `v34`;
 - `test_the_derived_file_equals_the_golden_file_byte_for_byte`: `v13`, `v33`, `v34`, byte for byte;
 - `test_the_derived_file_equals_the_oracles_on_every_valid_fixture` and
-  `test_the_derived_file_is_read_back_by_the_strict_reader`: every valid fixture, against
-  `refval.derive_csv` and through `read_confirmed_design`;
+  `test_the_derived_file_is_read_back_by_the_strict_parser`: every valid fixture, against
+  `refval.derive_csv` and through `parse_design_bytes`;
 - `test_the_file_names_folders_never_ids`: `v33` carries the folder label `control`, never `ctrl`.
 
 Legacy parity with the `v0.4.0` tag (`tests/test_parity_v0_4_0.py`, 24 passed, the tag's `src`