proto: redesign experiment, score set, and publication pages with typed API modules and reusable components

- Refactor ExperimentView, ExperimentSetView, ScoreSetView, and
  PublicationIdentifierView to use MvPageHeader, MvRowActionMenu,
  MvMetadataLine, and other shared Mv* components
- Replace inline axios calls with typed API functions; replace manual
  permission checks with useDatasetPermissions composable
- Delete old component copies from components/ root and common/ that
  were already moved to score-set/, calibration/, collection/, and
  Mv*-prefixed names in prior commits
- Add alerts and metadata slots to MvPageHeader
- Update copilot instructions to reflect new directory structure,
  Mv* prefix convention, and new composables
  - Removes prototype dir as the site is now migrated

Author: bencap

.github/instructions/copilot-instructions.md

@@ -28,9 +28,15 @@ MaveDB UI is the frontend for [MaveDB](https://mavedb.org), a database for Multi
 src/
 ├── assets/          # Global CSS and static images
 ├── components/
-│   ├── common/      # Reusable, generic UI components
+│   ├── calibration/ # Calibration display and editing components
+│   ├── collection/  # Collection management components
+│   ├── common/      # Reusable UI components (all prefixed Mv*)
+│   ├── dashboard/   # Dashboard tab components
+│   ├── forms/       # Form section components for creator/editor pages
 │   ├── layout/      # App shell: MvLayout, MvNavBar, MvFooter
-│   └── screens/     # Top-level route/page components (*View, *Screen, *Creator, *Editor)
+│   ├── score-set/   # Score set visualization and display components
+│   ├── screens/     # Top-level route/page components (*View, *Screen, *Creator, *Editor)
+│   └── variant/     # Variant display components
 ├── composables/     # Vue 3 composables (newer pattern)
 ├── composition/     # Composition functions (older pattern, similar purpose)
 ├── lib/             # Business logic, utilities, API helpers
@@ -43,7 +49,7 @@ src/
 ## Key Conventions
 
 - **Path alias**: Always use `@/` (maps to `src/`) instead of relative imports.
-- **Component naming**: PascalCase `.vue` files. Screens suffixed with `View`, `Screen`, `Creator`, or `Editor`.
+- **Component naming**: PascalCase `.vue` files. Components in `common/` are prefixed `Mv*`. Screens are suffixed with `View`, `Screen`, `Creator`, or `Editor`.
 - **TypeScript**: Prefer `.ts` for new files. Strict mode is enabled (`noUnusedLocals`, `noUnusedParameters`, `noFallthroughCasesInSwitch`).
 - **No test framework**: There is currently no automated test suite in this project.
 - **Node version**: 20.x is required.

.github/instructions/state-management.instructions.md

@@ -29,7 +29,7 @@ The root store holds `routeProps` (Galaxy integration parameters) and registers
 The `item.ts` and `items.js` modules are **not** statically registered. Instead, the `useItem()` and `useItems()` composables in `src/composition/` dynamically register Vuex modules with UUID-based namespaces at the component level:
 
 ```ts
-// src/composition/item.ts.ts (simplified)
+// src/composition/item.ts (simplified)
 export default function useItem({itemTypeName}) {
   const store = useStore()
   const namespace = uuid()
@@ -63,6 +63,35 @@ pubSearch.items // reactive suggestions list
 
 Used across all form pages (ExperimentCreator, ExperimentEditor, ScoreSetCreator, ScoreSetEditor, CalibrationEditor) for: publication search, taxonomy search, target gene search, gene name/assembly lookups, license lists, keyword options, and score set search.
 
+## Dataset Permissions (`src/composables/use-dataset-permissions.ts`)
+
+Wraps the `checkPermissions` API call with reactive state. Auto-fetches when the URN changes. Used by ExperimentSetView, ExperimentView, ScoreSetView, CollectionView, and ScoreSetCalibrationsView.
+
+```ts
+const {permissions} = useDatasetPermissions('score-set', urnRef, ['update', 'delete', 'publish'])
+// permissions.value.update, permissions.value.delete, etc.
+```
+
+## Score Set Downloads (`src/composables/use-score-set-downloads.ts`)
+
+Shared download logic for score set data files. Provides reactive state for the custom data dialog and methods for downloading scores, counts, mapped variants, metadata, custom data, and streaming annotated variants. Used by ScoreSetDownloads and MvVariantPreview.
+
+```ts
+const {downloadFile, downloadMultipleData, customDialogVisible, dataTypeOptions} = useScoreSetDownloads({
+  scoreSet: scoreSetRef
+})
+```
+
+## Variant Coordinates (`src/composables/use-variant-coordinates.ts`)
+
+Stateless utilities for resolving variant HGVS coordinates based on display mode (raw vs mapped). Shared between ScoreSetView (variant search, labels, sequence type detection) and ScoreSetHeatmap.
+
+```ts
+const {getHgvsNt, getHgvsPro, labelForVariant, sequenceTypeOptions} = useVariantCoordinates()
+const nt = getHgvsNt(variant, useMapped) // resolved NT coordinate
+const options = sequenceTypeOptions(variants, useMapped) // [{title: 'DNA', value: 'dna'}, ...]
+```
+
 ## Entity Cache (`src/composables/entity-cache.ts`)
 
 A shared reactive cache for entity lookups (score sets, experiments, experiment sets) with a 5-minute TTL. Deduplicates concurrent requests for the same URN — if a fetch is already in-flight, subsequent callers wait for it rather than starting a duplicate request.

.github/instructions/vue-components.instructions.md

@@ -63,11 +63,11 @@ Top-level route components. Named with suffixes: `*View`, `*Screen`, `*Creator`,
 
 ### Common Components (`src/components/common/`)
 
-Reusable UI primitives: `EntityLink`, `FlexDataTable`, `PageLoading`, `MvSelectList`, `MvCollapsible`, `MvLoader`, `MvScoreSetRow`, `MvSearchFilters`, etc.
+Reusable UI components, all prefixed `Mv*`: `MvEntityLink`, `MvPageLoading`, `MvItemNotFound`, `MvEmailPrompt`, `MvSelectList`, `MvCollapsible`, `MvLoader`, `MvScoreSetRow`, `MvSearchFilters`, `MvTimeSeriesLineChart`, etc.
 
 ### Layout Components (`src/components/layout/`)
 
-App shell components: `MvLayout`, `MvNavBar`, `MvFooter`.
+App shell components: `MvLayout`, `MvNavBar`, `MvFooter`, `MvPageHeader`.
 
 ### Form Section Components (`src/components/forms/`)
 
@@ -91,10 +91,27 @@ Low-level field components:
 - `MvMarkdownField` — Edit/Preview tabs for markdown textarea
 - `MvTagField` — Multi-value chip AutoComplete
 - `MvUploadField` — File upload drop zone
+- `MvFileStatus` — File upload status indicator
 
-### Feature Components (`src/components/`)
+### Score Set Components (`src/components/score-set/`)
 
-Larger feature-specific components in the root components directory: `CalibrationEditor`, `ScoreSetHeatmap`, `ScoreSetHistogram`, `AssayFactSheet`, etc.
+Score set visualization and display components: `ScoreSetHeatmap`, `ScoreSetHistogram`, `ScoreSetVisualizer`, `ScoreSetProcessingStatus`, `ScoreSetDownloads`, `ScoreSetMetadataCard`, `ProteinStructureView`.
+
+### Calibration Components (`src/components/calibration/`)
+
+Calibration display and editing: `CalibrationTable`, `CalibrationEditor`, `CalibrationFields`, `CalibrationClassificationRow`.
+
+### Collection Components (`src/components/collection/`)
+
+Collection management: `CollectionAdder`, `CollectionCreator`, `CollectionDataSetEditor`, `CollectionItemsTable`, `CollectionPermissionsEditor`.
+
+### Dashboard Components (`src/components/dashboard/`)
+
+Dashboard tab panels: `MvDashboardScoreSets`, `MvDashboardExperiments`, `MvDashboardCollections`, `MvDashboardCalibrations`.
+
+### Variant Components (`src/components/variant/`)
+
+Variant display: `MvMeasurementCard`, `VariantInfoSection`.
 
 ## Composables and Composition Functions
 
@@ -150,6 +167,6 @@ Always use the `@/` path alias and always include the file extension (`.vue` for
 
 ```ts
 import MvLayout from '@/components/layout/MvLayout.vue'
-import EntityLink from '@/components/common/EntityLink.vue'
+import MvEntityLink from '@/components/common/MvEntityLink.vue'
 import useItem from '@/composition/item.ts'
 ```