Reconciliation of the published description with the folder (Stage 1, PR 9)

AGENTS.md

@@ -107,6 +107,11 @@ src/morphobricks_preprocessing/
   description.py        the model (Description, Condition, Channel, Repeat, Member, Unit, Mask)
                     built from a reader-accepted document; description_from_bytes -> DescriptionError
   description_write.py  the canonical writer (Spec experiment-v1 9.1) and section digests (9.3)
+  description_reconcile.py reconcile(published, observed): units unchanged/new/removed by exact folder
+                    labels, N35 reopening (confirmed_on kept), stated renames (FolderRename),
+                    confirm_repeat; description_removal.py candidate (the draft), removal_questions
+                    (one grouped question per condition) and reconfirmations; reconcile_observe.py
+                    observe_folders (image counts of a folder walk)
   description_transition.py the R_* comparison of a candidate with the published file (4.4a, 4.6, 4.9),
                     Reconfirmation (the user's recorded acceptance of a changed ID)
   description_file.py   read_description(path): symlink refusal (R_FILE_SYMLINK), bytes -> Description

CHANGELOG.md

@@ -8,6 +8,26 @@ are in [docs/plan.md](docs/plan.md) §12. Upgrading from v0.3: see the
 
 ## Unreleased
 
+- **Reconciliation of the published description with the folder (Stage 1, PR 9; conformance
+  P07, P08, P15, P33).** New modules `description_reconcile`, `description_removal` and
+  `reconcile_observe`. Each unit is `unchanged`, `new` or `removed`, matched only by its exact
+  source folder labels. A unit that is new beside a confirmed member, a removed unit, channel
+  evidence that no longer fits the declared list and a folder the user stated was renamed
+  (`FolderRename`) reopen the N35 confirmation of that repeat only (`confirmed = false` in the
+  draft, `confirmed_on` copied from the published file, a new date only from the user's
+  `confirm_repeat`). A change of `image_count` alone reopens nothing (it is reported as
+  `CountChange` and the member's count follows the folder). A renamed folder is a removed unit
+  plus a new pending one, never paired by name; a new folder is proposed only for an existing
+  repeat ID equal to its label. A removal needs the user's confirmation, asked once per
+  condition (`removal_questions`: every lost repeat, technical repeat and channel in one
+  question); a removed ID stays in `used_ids`, and a `reference` to a removed condition is never
+  cleared silently. Fix in the merged transition check: `confirmed_on` may now move with the
+  user's new confirmation when a condition ID holds another folder (conformance P33 b); the
+  layout it compares (`repeat_layout`) includes the condition's source folder. Not used by any
+  run, notebook or CLI command yet. Not done here: the pending new units are not in the draft
+  (they need channels and IDs, which are the draft model's), and image-count changes are
+  reported but not appended to `morphobricks.records.jsonl` (the file defines only
+  re-confirmation records).
 - **Discovery and header additions for the experiment description (Stage 1, PR 6).**
   Additive; a run without a description behaves as before. (1) `preflight` and `remasked`
   take `with_description=False`; with it, a condition, repeat or technical-repeat folder that

pyproject.toml

@@ -179,6 +179,9 @@ baseline = "tools/code_rules_baseline.json"
 "morphobricks_preprocessing.description" = "pure"
 "morphobricks_preprocessing.description_write" = "pure"
 "morphobricks_preprocessing.description_transition" = "pure"
+"morphobricks_preprocessing.description_reconcile" = "pure"
+"morphobricks_preprocessing.description_removal" = "pure"
+"morphobricks_preprocessing.reconcile_observe" = "io"
 "morphobricks_preprocessing.description_file" = "io"
 "morphobricks_preprocessing.description_read" = "pure"
 "morphobricks_preprocessing.description_semantics" = "pure"