docs(plan): fix .trodesconf importer store-write path + DIO/type cleanups

Third/fourth-review fixes to phase-4 apply + phase-1 + shared-contracts:
- re-import lands in BOTH the versioned snapshot AND the editable animal.devices
  mirror, via an extended addConfigurationSnapshotToAnimal that also carries the
  off-export siblings; the mirror sync is probe-fields-only (electrode_groups +
  ntrode map) so data_acq_device/device are preserved, not dropped.
- first-config seeds v1 by importing before createAnimal (extended to set v1
  siblings); the sibling-incapable updateAnimal fallback is removed.
- sourceName added to TrodesconfImportPlan; dioInventory typed ParsedDioChannel[];
  phase-1 DIO direction aligned to shared-contracts (input=0 => out, ECU_ ids).

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

Author: edeno

.claude/docs/plans/trodesconf-import/phase-1-parser.md

@@ -27,12 +27,13 @@ is its sole producer.
 - **ntrodes:** select every `<SpikeNTrode>` (in document order); for each, read `id` (Number),
   `refNTrodeID`/`refChan` (Number, optional — `refNTrodeID <= 0` ⇒ omit), and its nested
   `<SpikeChannel>` elements → `channelCount = count`, `hwChans = [Number(hwChan)…]` in order.
-- **dio:** select `<Channel dataType="digital">`; resolve `direction` by the stricter rule in
-  [shared-contracts §1](shared-contracts.md#1-parsedtrodesconfig) — explicit `input="1"`⇒`in` /
-  `output="1"`⇒`out`; else id token (`…Din…`⇒`in`, `…Dout…`⇒`out`); else `'unknown'`. **Do NOT treat a
-  missing `input` as output** — `BlankWorkspace.trodesconf` has `Controller_Din*` with no `input` attr.
-  Preserve board-native ids **verbatim** (`Din1`, `MCU_Din3`, `Controller_Din1`, `Dout2`). De-duplicate
-  by `id`.
+- **dio:** select `<Channel dataType="digital">`; resolve `direction` **exactly per**
+  [shared-contracts §1](shared-contracts.md#1-parsedtrodesconfig): if an `input` attr is present,
+  `input="1"`⇒`in`, **`input="0"` (or any non-`1`)⇒`out`** (matching `convert_dios.py`); **else** (no
+  `input` attr — e.g. `BlankWorkspace.trodesconf`'s `Controller_Din*`) by id token **after stripping a
+  leading `ECU_`/`MCU_`/`Controller_` prefix**: `…Din…`⇒`in`, `…Dout…`⇒`out`; else `'unknown'`. **Never
+  treat a missing `input` as output.** Preserve board-native ids **verbatim** (`Din1`, `ECU_Din1`,
+  `ECU_Dout1`, `MCU_Din3`, `Controller_Din1`, `Dout2`). De-duplicate by `id`.
 - **header metadata:** read `numChannels` + `samplingRate` from `<HardwareConfiguration>` (or
   `<GlobalOptions>` in older configs — check both) as Numbers; absent → omit. (`numChannels` powers the
   Phase 2 integrity check; `samplingRate` is provenance only.)
@@ -80,5 +81,6 @@ Dispatch `code-reviewer` against the diff. Confirm:
 - Parser is total (the malformed/empty/sparse tests prove no throw escapes).
 - Output matches [`ParsedTrodesConfig`](shared-contracts.md#1-parsedtrodesconfig) exactly; `hwChans`/refs
   are parsed but documented as reference-only.
-- Board variants (`Din*` vs `MCU_Din*`) both handled.
+- Direction matches §1 (`input="0"`⇒out; missing `input`⇒id-token); all id variants handled (`Din*`,
+  `ECU_Din*`/`ECU_Dout*`, `MCU_Din*`, `Controller_Din*`), kept verbatim.
 - No app-type coupling; no plan/phase references in code or test names.

.claude/docs/plans/trodesconf-import/phase-4-apply.md

@@ -17,12 +17,20 @@ byte-identity gate.
 - [src/state/workspaceActions.ts:140-160](../../../../src/state/workspaceActions.ts) — the create-animal
   config-seed path for `isFirstConfig` (seed v1).
 - [src/state/workspaceTransitions.ts:74-80](../../../../src/state/workspaceTransitions.ts) —
-  `ConfigSnapshotInput = {date, description, devices}`. **Extend the type AND the snapshot-building
-  transition** so `dioInventory` reaches the persisted `ConfigurationSnapshot` (smaller-correction #2:
-  type alone is insufficient).
+  `ConfigSnapshotInput = {date, description, devices}` (extend with the two siblings).
+- [src/state/workspaceTransitions.ts:240-258](../../../../src/state/workspaceTransitions.ts) —
+  `addConfigurationSnapshotToAnimal`: builds the snapshot from `{date,description,devices}` only and
+  **does not set `updated.devices`** (the mirror). Extend it to carry the siblings + set the mirror
+  (must-fix #1, see Tasks).
+- [src/state/workspaceTransitions.ts:155-168](../../../../src/state/workspaceTransitions.ts) —
+  `applyAnimalUpdates`' devices-mirror (rewrites only the latest snapshot's `electrode_groups`/`ntrode…`,
+  not the siblings) — why `updateAnimal` can't seed v1's siblings (must-fix #2) and why siblings survive
+  later edits.
+- [src/pages/AnimalEditor/wiring/ElectrodeGroupsContainer.tsx:94](../../../../src/pages/AnimalEditor/wiring/ElectrodeGroupsContainer.tsx)
+  — the editor reads `animal.devices` (the mirror); hence the mirror must match the new snapshot.
 - [src/state/workspaceTypes.ts:299-322](../../../../src/state/workspaceTypes.ts) —
-  `ConfigurationSnapshot` (add optional `dioInventory` as a **sibling** of `devices` so `diffProbeConfigs`
-  is untouched).
+  `ConfigurationSnapshot` (add optional `dioInventory: ParsedDioChannel[]` + `trodesImport` as
+  **siblings** of `devices` so `diffProbeConfigs` is untouched).
 - [src/state/persistence.ts:16-20,188](../../../../src/state/persistence.ts) +
   [src/state/workspaceMigrations.ts:70-103](../../../../src/state/workspaceMigrations.ts) — the
   persistence-invariant decision (overview Rollout).
@@ -35,25 +43,52 @@ byte-identity gate.
 
 - **Off-export snapshot siblings + transition.** Add to `ConfigurationSnapshot` (both **siblings** of
   `devices`, so `diffProbeConfigs` and the export — which reads only `devices` — are untouched):
-  `dioInventory?: DioChannel[]` and `trodesImport?: { ntrodeChannelCounts: Record<string, number>;
-  sourceName?: string }` (the off-export counts the [§3](shared-contracts.md#3-invariant) completion
-  needs while `device_type` is blank). Add both to `ConfigSnapshotInput` **and** thread them through the
-  snapshot-building transition (`workspaceTransitions.ts`) — the type alone is insufficient
-  (smaller-correction #2). Read via defensive selectors (`getConfigDioInventory`,
+  `dioInventory?: ParsedDioChannel[]` (the shared §1 type — **not** an undefined `DioChannel`) and
+  `trodesImport?: { ntrodeChannelCounts: Record<string, number>; sourceName?: string }` (the off-export
+  counts the [§3](shared-contracts.md#3-invariant) completion needs while `device_type` is blank). Add
+  both to `ConfigSnapshotInput`. Read via defensive selectors (`getConfigDioInventory`,
   `getConfigImportCounts`; absent → `[]`/`{}`).
-- **Apply — re-import vs first-config (must-fix #2).** `applyTrodesconfImport(actions, animalId, plan,
+- **Extend the snapshot transition `addConfigurationSnapshotToAnimal`
+  ([workspaceTransitions.ts:248-258](../../../../src/state/workspaceTransitions.ts)) — type alone is
+  insufficient (must-fix #1/#2).** Today it builds `newVersion` from only `{date, description, devices}`
+  and **does not touch `updated.devices`** (the editable mirror the editor reads at
+  [ElectrodeGroupsContainer.tsx:94](../../../../src/pages/AnimalEditor/wiring/ElectrodeGroupsContainer.tsx)).
+  Change it to (a) copy `config.dioInventory`/`config.trodesImport` onto `newVersion`, **and** (b) sync
+  the new snapshot's **probe fields** into the mirror, **preserving the rest of `animal.devices`**.
+  `animal.devices` is a `DeviceConfiguration` that also owns `data_acq_device` + `device`
+  ([workspaceTypes.ts:157-166](../../../../src/state/workspaceTypes.ts)) — the snapshot `devices` is a
+  probe-only `ProbeConfiguration` ([:299-322](../../../../src/state/workspaceTypes.ts)), and export reads
+  `data_acq_device`/`device` from the mirror ([workspaceUtils.ts:425,465](../../../../src/state/workspaceUtils.ts)),
+  so a full `updated.devices = newVersion.devices` would **drop the recording-system/device catalog**. Use
+  the same merge `applyAnimalUpdates` uses:
+  ```ts
+  updated.devices = normalizeDevices({
+    ...getAnimalDevices(updated),
+    electrode_groups: structuredClone(newVersion.devices.electrode_groups),
+    ntrode_electrode_group_channel_map: structuredClone(newVersion.devices.ntrode_electrode_group_channel_map),
+  });
+  ```
+  **This is a no-op for the existing `ReconfigWizard` caller** (it passes a *clone of the current* probe
+  devices, so the merged mirror is unchanged) and the fix for import (different probe devices) — add a
+  `ReconfigWizard` regression test proving no behavior change there. Without (b), after a Trodes re-import the editor would still show the
+  stale mirror and a subsequent edit would mirror it back over the imported snapshot (data loss). Note
+  `applyAnimalUpdates`'s devices-mirror only rewrites the latest snapshot's `electrode_groups`/`ntrode…`,
+  not the snapshot siblings ([workspaceTransitions.ts:161-167](../../../../src/state/workspaceTransitions.ts)),
+  so the siblings survive later edits.
+- **Apply — re-import vs first-config (must-fix #1/#2).** `applyTrodesconfImport(actions, animalId, plan,
   dayIds)` (e.g. `src/state/trodesconfImportApply.ts`):
   - *Re-import* (`!isFirstConfig`): build `ConfigSnapshotInput = { date, description: "Imported from
-    <plan.sourceName>", devices, dioInventory, trodesImport }` and call
-    `createConfigurationSnapshotAndApplyForward` (a new version — correct here).
-  - *First config* (`isFirstConfig`): **do NOT** call `createConfigurationSnapshotAndApplyForward` —
-    `createAnimal` already creates `configurationHistory[0]` (v1)
-    ([workspaceActions.ts:154-161](../../../../src/state/workspaceActions.ts)), so that would make **v2**.
-    Instead **seed v1 from the import**: either (preferred) build the parsed config *before* `createAnimal`
-    and pass `devices` + the two siblings into the create path (extend `createAnimal`/its v1-snapshot
-    construction to accept `dioInventory`/`trodesImport`), **or** replace v1 in place via `updateAnimal`
-    immediately after create (overwrite `configurationHistory[0].devices` + set the siblings; no new
-    version). Pick one in the PR; the result is a single v1 == the import.
+    ${plan.sourceName}", devices, dioInventory: plan.dioInventory, trodesImport: { ntrodeChannelCounts:
+    plan.ntrodeChannelCounts, sourceName: plan.sourceName } }` and call
+    `createConfigurationSnapshotAndApplyForward` (a new version — correct here). With the transition fix
+    above, this both appends the snapshot **and** updates the mirror atomically.
+  - *First config* (`isFirstConfig`): **import before `createAnimal`** and seed v1 from it.
+    `createAnimal` already sets **both** `animal.devices` and `configurationHistory[0].devices` from the
+    same `devices` input ([workspaceActions.ts:142,154-161](../../../../src/state/workspaceActions.ts)),
+    so passing the imported `devices` makes mirror == v1 == import. **Extend `createAnimal` to also accept
+    + set v1's `dioInventory`/`trodesImport`.** Do **not** use the `updateAnimal` fallback: `updateAnimal`
+    only mirrors `devices` into the latest snapshot and has **no path** to set the snapshot siblings
+    ([workspaceTransitions.ts:155-168](../../../../src/state/workspaceTransitions.ts)) — must-fix #2.
   - **The written `ntrode_id`s are the plan's preserved ids** ([§3](shared-contracts.md#3-invariant)) —
     never re-derived here.
 - **Persistence decision (from the code).** Determine if the load/shape-ensure path tolerates a snapshot
@@ -75,10 +110,12 @@ byte-identity gate.
 | --- | --- |
 | `applyTrodesconfImport` — first config seeds **v1** | after import-at-create, `configurationHistory.length === 1` and `version === 1` (NOT 2); the snapshot's `devices` = the import, with `dioInventory` + `trodesImport.ntrodeChannelCounts` set. |
 | `applyTrodesconfImport` — re-import | new version via the reconfig action; preserved groups keep `device_type`/`location` + grouping; days re-pin. |
+| re-import updates the **mirror** (must-fix #1) | after re-import, `animal.devices`'s **probe fields** (`electrode_groups`/`ntrode…`) equal the imported snapshot's, while `data_acq_device` + `device` are **preserved** (not dropped); a subsequent `updateAnimal` edit mirrors into the NEW snapshot, not over it. |
+| `addConfigurationSnapshotToAnimal` reconfig regression | the existing reconfig path (config.devices = clone of current) is unchanged — mirror stays equal, no observable behavior change. |
 | `ntrode_id` integrity | the persisted snapshot's `ntrode_id`s equal the plan's (== parsed config's); none renumbered on the way to disk. |
 | bad channels reset | bad channels on the old version don't carry onto the new (inherent to the bump). |
 | persistence | a blob without `dioInventory`/`trodesImport` loads with the defensive selectors → `[]`/`{}`; if bumped, the `vN` fixture hydrates to current. |
-| `baselines` | exported YAML byte-identical; **both `dioInventory` and `trodesImport` are off-export** (export reads only `devices`). |
+| `baselines` | exported YAML byte-identical; **both `dioInventory` and `trodesImport` are off-export** (they sit on the snapshot, outside any `devices`; the export merge never reads them). |
 
 ## Fixtures
 
@@ -87,6 +124,9 @@ Phase 2/3 plan + completed-config fixtures; a persistence blob if a bump is take
 ## Review
 
 Dispatch `code-reviewer`. Confirm: reuses the reconfig/seed actions (no duplicated version logic);
-`dioInventory` threaded through the transition (not just typed) + defensively read; persisted
-`ntrode_id`s preserved; `baselines` byte-identical + `dioInventory` off-export; CHANGELOG updated; no
-plan/phase refs in code.
+re-import sets **both** the new snapshot **and** the editable `animal.devices` mirror (must-fix #1), with
+a passing `ReconfigWizard` no-op regression; first-config seeds **v1** via the extended `createAnimal`
+(not a v2, not the sibling-incapable `updateAnimal` fallback — must-fix #2); both siblings (`ParsedDioChannel[]`
+`dioInventory` + `trodesImport`) threaded through `addConfigurationSnapshotToAnimal` + defensively read;
+persisted `ntrode_id`s preserved; `baselines` byte-identical + both siblings off-export; CHANGELOG
+updated; no plan/phase refs in code.

.claude/docs/plans/trodesconf-import/shared-contracts.md

@@ -135,6 +135,7 @@ export interface TrodesconfImportPlan {
     message: string;
   }>;
   isFirstConfig: boolean;
+  sourceName: string;             // carried from ParsedTrodesConfig.sourceName — used for the snapshot description + trodesImport.sourceName
 }
 ```
 - `ntrodeShells` carry **`ntrode_id` verbatim** ([§3](#3-invariant)) with `map: {}`. Expected channel