Carry retire-class passthroughs as v1; openminds_element carry-128; species text accepted in the round trip

src/did/+did2/+convert/+migrators_j/Contents.m

@@ -965,8 +965,12 @@
 %         Deferred: stimulus_bath migrates to a formulation-valued manipulation in the
 %         NDI layer / the coarse resolveDeferredBaths pass.
 %     stimulus_parameter
-%         Brainstorm-J migrator: did_v1 stimulus_parameter -- a PASSTHROUGH that
-%         normalises the template's own untypeable placeholder.
+%         Brainstorm-J migrator: did_v1 stimulus_parameter -- carried whole as v1
+%         (since 2026-10-29, [one folder, final classes only]; see the end of the
+%         function). Until then it was a PASSTHROUGH that normalised the template's
+%         own untypeable placeholder; the history below explains that repair, which a
+%         carried document no longer needs (it is not read against V2). A non-empty
+%         char or a non-numeric `value` still errors.
 %     stimulus_presentation
 %         Brainstorm-J migrator: did_v1 stimulus_presentation -- the decomposition is
 %         DONE BY THE NDI SECOND PASS; pass 1 is a GUARDED PASSTHROUGH that carries

src/did/+did2/+convert/+migrators_j/daqmetadatareader.m

@@ -134,6 +134,14 @@
 filePattern = jGetChar(blk, 'tab_separated_file_parameter');
 
 if isempty(implClass) && isempty(filePattern)
+    % [one folder, final classes only] (Jess Haley, 2026-10-29, did-schema
+    % V_eta_go_forward_class_audit.md): a retire class's V2 file is deleted once no
+    % v1 document passes through under it, so this document, left as v1 on purpose,
+    % is carried whole as v1 with a note ([passthrough stays v1], Jess Haley,
+    % 2026-10-24) instead of passing through silently. Register row carry-129 covers it.
+    % carry-register: carry-129
+    did2.convert.reportNote('carried_as_v1', 'daqmetadatareader', jCarryId(src), ...
+        '[carry-129] malformed: no reader class and no file parameter, so nothing to declare ([passthrough stays v1])');
     bodies = {src};         % see THE GUARD above
     return;
 end

src/did/+did2/+convert/+migrators_j/daqreader.m

@@ -151,6 +151,14 @@
 % a body with NEITHER a class name NOR a reader string says nothing at all,
 % and minting entities from it would be the hollow-document defect.
 if isempty(implClass) && isempty(readerString)
+    % [one folder, final classes only] (Jess Haley, 2026-10-29, did-schema
+    % V_eta_go_forward_class_audit.md): a retire class's V2 file is deleted once no
+    % v1 document passes through under it, so this document, left as v1 on purpose,
+    % is carried whole as v1 with a note ([passthrough stays v1], Jess Haley,
+    % 2026-10-24) instead of passing through silently. Register row carry-130 covers it.
+    % carry-register: carry-130
+    did2.convert.reportNote('carried_as_v1', 'daqreader', jCarryId(src), ...
+        '[carry-130] malformed: no reader class and no reader string, so nothing to declare ([passthrough stays v1])');
     bodies = {src};
     return;
 end

src/did/+did2/+convert/+migrators_j/daqsystem.m

@@ -313,7 +313,8 @@
     % preserved. The passthrough rescues nothing.
     %
     % IT IS LEFT AS IT IS, DELIBERATELY, and pinned by
-    % testTheResidualPassthroughIsAQuarantinePathByConstruction. NDI sets
+    % testTheResidualPassthroughIsAQuarantinePathByConstruction (since 2026-10-29
+    % testTheResidualDaqsystemIsCarriedWholeAsV1). NDI sets
     % `ndi_daqsystem_class` on every document it writes and gives every real rig
     % a filenavigator and a daqreader, so this branch is unreachable for real
     % data; relaxing the tombstone to admit a hollow document would trade a live
@@ -325,6 +326,18 @@
     % that can carry a document on its own, via the software_id edge, so it has
     % to be counted as something-to-declare or a class-name-only daqsystem would
     % fall into a passthrough that is no longer warranted.
+    %
+    % CARRIED, NOT PASSED THROUGH, since 2026-10-29: the quarantine described
+    % above came from validating the passthrough against the `daqsystem`
+    % tombstone; a carried document is v1 and is not read against V2.
+    % [one folder, final classes only] (Jess Haley, 2026-10-29, did-schema
+    % V_eta_go_forward_class_audit.md): a retire class's V2 file is deleted once no
+    % v1 document passes through under it, so this document, left as v1 on purpose,
+    % is carried whole as v1 with a note ([passthrough stays v1], Jess Haley,
+    % 2026-10-24) instead of passing through silently. Register row carry-131 covers it.
+    % carry-register: carry-131
+    did2.convert.reportNote('carried_as_v1', 'daqsystem', jCarryId(src), ...
+        '[carry-131] malformed: no daqsystem class, navigator, reader or metadata reader, so nothing to declare ([passthrough stays v1])');
     bodies = {src};
     return;
 end

src/did/+did2/+convert/+migrators_j/electrode_offset_voltage.m

@@ -121,6 +121,14 @@
 
 offset = finiteScalar(blk, 'offset');
 if isempty(offset)
+    % [one folder, final classes only] (Jess Haley, 2026-10-29, did-schema
+    % V_eta_go_forward_class_audit.md): a retire class's V2 file is deleted once no
+    % v1 document passes through under it, so this document, left as v1 on purpose,
+    % is carried whole as v1 with a note ([passthrough stays v1], Jess Haley,
+    % 2026-10-24) instead of passing through silently. Register row carry-133 covers it.
+    % carry-register: carry-133
+    did2.convert.reportNote('carried_as_v1', 'electrode_offset_voltage', jCarryId(src), ...
+        '[carry-133] malformed: electrode_offset_voltage.offset is not one finite number, so nothing to fold ([passthrough stays v1])');
     bodies = {src};   % nothing to fold -> carry unchanged (discovery fallback)
     return;
 end

src/did/+did2/+convert/+migrators_j/filenavigator.m

@@ -162,6 +162,14 @@
 mapList    = jFileMatchList(rawField(blk, 'epochprobemap_fileparameters'));
 
 if isempty(implClass) && isempty(mapFormat) && isempty(dataList) && isempty(mapList)
+    % [one folder, final classes only] (Jess Haley, 2026-10-29, did-schema
+    % V_eta_go_forward_class_audit.md): a retire class's V2 file is deleted once no
+    % v1 document passes through under it, so this document, left as v1 on purpose,
+    % is carried whole as v1 with a note ([passthrough stays v1], Jess Haley,
+    % 2026-10-24) instead of passing through silently. Register row carry-132 covers it.
+    % carry-register: carry-132
+    did2.convert.reportNote('carried_as_v1', 'filenavigator', jCarryId(src), ...
+        '[carry-132] malformed: no navigator class, file patterns or epoch map, so nothing to declare ([passthrough stays v1])');
     bodies = {src};         % nothing to declare -- see THE GUARD above
     return;
 end

src/did/+did2/+convert/+migrators_j/hartley_calc.m

@@ -397,6 +397,19 @@
 % document whole as v1 (carry-100 outside the template, carry-056 inside it),
 % as it does for an unread calculator field
 dropped = [dropped, unreadFields(preBody)];
+% NO SUBJECT: jCalculation hands such a document back unchanged (a calculation
+% requires its subject). [one folder, final classes only] (Jess Haley,
+% 2026-10-29, did-schema V_eta_go_forward_class_audit.md): a retire class's V2
+% file is deleted once no v1 document passes through under it, so it is carried
+% whole as v1 with a note here ([passthrough stays v1], Jess Haley, 2026-10-24)
+% instead of passing through silently. Register row carry-138 covers it.
+if isempty(jSubjectOf(preBody, {'element_id', 'subject_id'}))
+    % carry-register: carry-138
+    did2.convert.reportNote('carried_as_v1', 'hartley_calc', sourceId(preBody), ...
+        '[carry-138] awaiting_home: no element_id or subject_id, so no calculation subject ([passthrough stays v1])');
+    bodies = {preBody};
+    return;
+end
 bodies = jCalculation(preBody, 'receptive_field_calculation', 'rf', ...
     'hartley_calc', 'receptive field', 'ndi.calc.vis.hartley', ...
     'ExtraParameters', extra, 'ExtraInputs', inputs, 'DataBody', true, ...

src/did/+did2/+convert/+migrators_j/openminds_element.m

@@ -20,7 +20,9 @@
 %   the asserted `variable`; the ontology id + label are the term `value`. It is
 %   a timeless subject_assertion (no interaction, no session anchor). 1 -> 1.
 %
-%   If no openMINDS block is present the document is carried unchanged.
+%   If no openMINDS block is present, or the block states an `openminds_id` or
+%   a `fields.description` (carry-128), the document is carried whole as v1
+%   with a `carried_as_v1` note.
 
 arguments
     preBody (1,1) struct
@@ -33,14 +35,44 @@
     block = preBody.openminds_element;
 end
 if isempty(block)
-    v2Body = {preBody};                        % no openMINDS block: carry unchanged
+    % No openMINDS block: nothing to assert, so the document is carried whole
+    % as v1 ([passthrough stays v1], Jess Haley, 2026-10-24) rather than
+    % passed through silently under the retire class `openminds_element`
+    % ([one folder, final classes only], Jess Haley, 2026-10-29, did-schema
+    % V_eta_go_forward_class_audit.md: a retire class's V2 file is deleted
+    % once no v1 document passes through under it). No register row covers a
+    % missing block yet (a question for the team).
+    % carry-register: carry-146
+    did2.convert.reportNote('carried_as_v1', 'openminds_element', sourceIdOf(preBody), ...
+        '[carry-146] malformed: no openminds block, so no term to assert ([passthrough stays v1])');
+    v2Body = {preBody};
     return;
 end
 
 variable = variableForType(jGetChar(block, 'openminds_type'));
 
 flds = struct();
 if isfield(block, 'fields') && isstruct(block.fields); flds = block.fields; end
+
+% [openMINDS element leftovers carried] (Decided by Jess Haley, 2026-10-29,
+% did-schema V_eta_go_forward_class_audit.md): "a v1 `openminds_element`
+% holding an `openminds_id` or a `fields.description` is carried whole as v1,
+% as for openMINDS subjects ([openMINDS subject leftovers])". The term
+% assertion keeps neither, so a document stating either is carried
+% (register row carry-128).
+omId = strtrim(jGetChar(block, 'openminds_id'));
+omDescription = strtrim(jGetChar(flds, 'description'));
+if ~isempty(omId) || ~isempty(omDescription)
+    held = {};
+    if ~isempty(omId); held{end+1} = sprintf('openminds_id "%s"', omId); end
+    if ~isempty(omDescription); held{end+1} = 'fields.description'; end
+    % carry-register: carry-128
+    did2.convert.reportNote('carried_as_v1', 'openminds_element', sourceIdOf(preBody), ...
+        sprintf(['[carry-128] awaiting_home: %s (the term assertion keeps neither) ' ...
+        '([openMINDS element leftovers carried])'], strjoin(held, ' and ')));
+    v2Body = {preBody};
+    return;
+end
 node = firstNonEmpty( ...
     jGetChar(flds, 'preferredOntologyIdentifier'), ...
     jGetChar(flds, 'ontologyIdentifier'), ...
@@ -90,6 +122,13 @@
 if isempty(out); out = 'openminds entity'; end
 end
 
+function id = sourceIdOf(preBody)
+%SOURCEIDOF The v1 document's base.id, or '' (did2.convert.v1read.readBase).
+b = did2.convert.v1read.readBase(preBody);
+id = b.id;
+if ~ischar(id); id = ''; end
+end
+
 function s = firstNonEmpty(varargin)
 s = '';
 for k = 1:numel(varargin)

src/did/+did2/+convert/+migrators_j/private/jCarryId.m

@@ -0,0 +1,15 @@
+function id = jCarryId(body)
+%JCARRYID The v1 document's base.id for a `carried_as_v1` note ('' when it
+%   states none), read with did2.convert.v1read.readBase (a legacy
+%   `ndi_document` identity too).
+%
+%   ID = jCarryId(BODY).
+%
+%   See also did2.convert.reportNote, did2.convert.v1read.readBase.
+
+b = did2.convert.v1read.readBase(body);
+id = b.id;
+if ~ischar(id)
+    id = '';
+end
+end

src/did/+did2/+convert/+migrators_j/private/jModelFit.m

@@ -16,15 +16,29 @@
 %   independent_variables[] / dependent_variable (the names), goodness {sse,
 %   sse_per_point}, input_field / output_field (fit_data).
 %
-%   PASSES THROUGH (returns {PREBODY}, the v1 tombstone validates it) when
-%   the document has no subject (decided: "no subject -> refused"). A missing
+%   CARRIES the document whole as v1 (returns {PREBODY} with a
+%   `carried_as_v1` note; until 2026-10-29 a silent passthrough the v1
+%   tombstone validated) when the document has no subject (decided: "no
+%   subject -> refused"). A missing
 %   operating system no longer passes it through: `operating_system_id` is
 %   OPTIONAL (Jess Haley, 2026-10-21 [calculation-os-optional]), so the edge is
 %   omitted, never invented.
 
 bodies = {preBody};
 subjectId = jSubjectOf(preBody, {'element_id', 'subject_id'});
 if isempty(subjectId)
+    % [one folder, final classes only] (Jess Haley, 2026-10-29, did-schema
+    % V_eta_go_forward_class_audit.md): a retire class's V2 file is deleted once
+    % no v1 document passes through under it, so this document, refused on
+    % purpose, is carried whole as v1 with a note ([passthrough stays v1], Jess
+    % Haley, 2026-10-24) instead of passing through silently. Register rows
+    % carry-136 (fitcurve) and carry-137 (vmspikefit) cover it.
+    stamp = did2.convert.v1read.readStamp(preBody);
+    tag = '[carry-136]';
+    if strcmp(stamp.class_name, 'vmspikefit'); tag = '[carry-137]'; end
+    % carry-register: carry-136 carry-137
+    did2.convert.reportNote('carried_as_v1', stamp.class_name, jCarryId(preBody), ...
+        [tag ' awaiting_home: no element_id or subject_id, so no calculation subject ([passthrough stays v1])']);
     return;
 end
 [software, swId, execEnv] = jSoftwareFromApp(preBody, 'RequireSession', true);

src/did/+did2/+convert/+migrators_j/probe_geometry.m

@@ -201,6 +201,14 @@
 end
 
 if isempty(obsBodies)
+    % [one folder, final classes only] (Jess Haley, 2026-10-29, did-schema
+    % V_eta_go_forward_class_audit.md): a retire class's V2 file is deleted once no
+    % v1 document passes through under it, so this document, left as v1 on purpose,
+    % is carried whole as v1 with a note ([passthrough stays v1], Jess Haley,
+    % 2026-10-24) instead of passing through silently. Register row carry-134 covers it.
+    % carry-register: carry-134
+    did2.convert.reportNote('carried_as_v1', 'probe_geometry', jCarryId(src), ...
+        '[carry-134] malformed: no per-site axis values, so nothing to fold ([passthrough stays v1])');
     bodies = {src};   % nothing to fold -> carry unchanged (discovery fallback)
     return;
 end

src/did/+did2/+convert/+migrators_j/site2channelmap.m

@@ -75,8 +75,17 @@
 end
 [~, collision, unplaced] = jRawAccount(preBody, struct('site2channelmap', {{'map'}}), ...
     {'^probe_id$', '^probe_geometry_id$'});
-jRawCarry('site2channelmap', preBody, collision, unplaced, 'carry-100');
-bodies = {preBody};   % a passthrough, or the carry of the untouched v1 source
+if ~jRawCarry('site2channelmap', preBody, collision, unplaced, 'carry-100')
+    % [one folder, final classes only] (Jess Haley, 2026-10-29, did-schema
+    % V_eta_go_forward_class_audit.md): a retire class's V2 file is deleted once no
+    % v1 document passes through under it, so this document, left as v1 on purpose,
+    % is carried whole as v1 with a note ([passthrough stays v1], Jess Haley,
+    % 2026-10-24) instead of passing through silently. Register row carry-139 covers it.
+    % carry-register: carry-139
+    did2.convert.reportNote('carried_as_v1', 'site2channelmap', jCarryId(preBody), ...
+        '[carry-139] awaiting_home: site2channelmap has no V2 home (its map needs the probe_geometry join) ([passthrough stays v1])');
+end
+bodies = {preBody};   % the carry of the untouched v1 source
 end
 
 % ===================== small helpers =======================================

src/did/+did2/+convert/+migrators_j/stimulus_parameter.m

@@ -1,6 +1,10 @@
 function bodies = stimulus_parameter(preBody)
-%STIMULUS_PARAMETER Brainstorm-J migrator: did_v1 stimulus_parameter -- a
-%   PASSTHROUGH that normalises the template's own untypeable placeholder.
+%STIMULUS_PARAMETER Brainstorm-J migrator: did_v1 stimulus_parameter -- carried
+%   whole as v1 (since 2026-10-29, [one folder, final classes only]; see the
+%   end of the function). Until then it was a PASSTHROUGH that normalised the
+%   template's own untypeable placeholder; the history below explains that
+%   repair, which a carried document no longer needs (it is not read against
+%   V2). A non-empty char or a non-numeric `value` still errors.
 %
 %   Routed from did2.convert.v1_to_v2 only when TargetVersion == 'V_eta'.
 %
@@ -137,9 +141,10 @@
         % empty DOUBLE and validates: `value` is not scalar-constrained).
     elseif ischar(v) || isstring(v)
         if isempty(strtrim(char(v)))
-            % The template's own "unset" placeholder. Absence is the only
-            % spelling of unset that validates.
-            preBody.(BLOCK) = rmfield(preBody.(BLOCK), 'value');
+            % The template's own "unset" placeholder. It used to be removed
+            % here so the passthrough validated against the V_eta tombstone;
+            % the document is now carried whole as v1 (below), which is not
+            % read against V2, so it is kept as v1 wrote it.
         else
             error('did2:convert:stimulusParameterCharValue', ...
                 ['stimulus_parameter.value carries the non-empty char ''%s'' ' ...
@@ -155,5 +160,14 @@
     end
 end
 
+% [one folder, final classes only] (Jess Haley, 2026-10-29, did-schema
+% V_eta_go_forward_class_audit.md): a retire class's V2 file is deleted once no
+% v1 document passes through under it, so this document, held for the stimulus
+% model (#31) and left as v1 on purpose, is carried whole as v1 with a note
+% ([passthrough stays v1], Jess Haley, 2026-10-24) instead of passing through
+% silently. Register row carry-140 covers it.
+% carry-register: carry-140
+did2.convert.reportNote('carried_as_v1', 'stimulus_parameter', jCarryId(preBody), ...
+    '[carry-140] awaiting_home: stimulus_parameter has no V2 home until the stimulus model ([passthrough stays v1])');
 bodies = {preBody};
 end