@jbrowse/core 5.0.0-beta.1 → 5.0.0-beta.2

package/esm/ReExports/modules.js

@@ -1,44 +1,20 @@
 // eslint-disable-next-line no-restricted-imports
 import * as React from 'react';
-import * as mst from '@jbrowse/mobx-state-tree';
 import { alpha, createTheme, useTheme } from '@mui/material';
 import SvgIcon, { createSvgIcon } from '@mui/material/SvgIcon';
 import * as MUIUtils from '@mui/material/utils';
-import * as mobx from 'mobx';
 import * as mxreact from 'mobx-react';
 import * as ReactDom from 'react-dom';
 import * as ReactDomClient from 'react-dom/client';
-import * as ReactJSXRuntime from 'react/jsx-runtime';
-import Plugin from '../Plugin.js';
-import * as Configuration from '../configuration/index.js';
-import * as BaseAdapterExports from '../data_adapters/BaseAdapter/index.js';
-import * as dataAdapterCache from '../data_adapters/dataAdapterCache.js';
-import AdapterType from '../pluggableElementTypes/AdapterType.js';
-import DisplayType from '../pluggableElementTypes/DisplayType.js';
-import TrackType from '../pluggableElementTypes/TrackType.js';
-import ViewType from '../pluggableElementTypes/ViewType.js';
-import WidgetType from '../pluggableElementTypes/WidgetType.js';
-import * as pluggableElementTypes from '../pluggableElementTypes/index.js';
-import * as pluggableElementTypeModels from '../pluggableElementTypes/models/index.js';
 import * as coreUi from '../ui/index.js';
-import * as corePalette from '../ui/palette.js';
-import * as coreTheme from '../ui/theme.js';
-import Base1DView from '../util/Base1DViewModel.js';
-import * as coreColor from '../util/color/index.js';
-import * as coreIo from '../util/io/index.js';
-import * as coreLayouts from '../util/layouts/index.js';
-import * as coreMstReflection from '../util/mst-reflection.js';
-import * as rxjs from '../util/rxjs.js';
-import * as trackUtils from '../util/tracks.js';
 import { cx, keyframes, makeStyles } from '../util/tss-react/index.js';
-import * as mstTypes from '../util/types/mst.js';
 import { BaseFeatureDetail } from './BaseFeatureDetails.js';
 import { DataGridEntries } from './MuiDataGridReExports.js';
 import { Entries } from './MuiReExports.js';
 import { MUIStyles } from './MuiStylesReExports.js';
 import { lazyMap } from './lazify.js';
 import reExportsList from './list.js';
-import * as coreUtil from './publicUtil.js';
+import { sharedModules } from './sharedModules.js';
 function makeLegacyMakeStyles() {
     return (args) => {
         const useStyles = makeStyles()(args);
@@ -48,14 +24,10 @@ function makeLegacyMakeStyles() {
 const tssReact = { cx, keyframes, makeStyles };
 const legacyMakeStyles = makeLegacyMakeStyles();
 const libs = {
-    mobx,
-    '@jbrowse/mobx-state-tree': mst,
-    'mobx-state-tree': mst,
-    react: React,
-    'react/jsx-runtime': ReactJSXRuntime,
+    ...sharedModules,
+    'mobx-react': mxreact,
     'react-dom': ReactDom,
     'react-dom/client': ReactDomClient,
-    'mobx-react': mxreact,
     // Only lazy component entries are re-exported. The grid *hooks*
     // (useGridApiContext/useGridApiRef/useGridRootProps) are intentionally left
     // out: statically importing them here pulled the entire ~1.2 MB
@@ -114,12 +86,7 @@ const libs = {
         ToggleButton: Entries.ToggleButton,
         ToggleButtonGroup: Entries.ToggleButtonGroup,
     },
-    '@jbrowse/core/Plugin': Plugin,
-    '@jbrowse/core/configuration': Configuration,
-    '@jbrowse/core/util/types/mst': mstTypes,
     '@jbrowse/core/ui': coreUi,
-    '@jbrowse/core/ui/theme': coreTheme,
-    '@jbrowse/core/ui/palette': corePalette,
     // BaseTooltip is deliberately absent from the '@jbrowse/core/ui' barrel: the
     // re-export alone held @floating-ui (~266KB) on the startup path, since eager
     // plugin entries import that barrel. Serving it as its own module behind
@@ -128,23 +95,7 @@ const libs = {
     // (bundled by tview and msaview) reads it too, so dropping it from the barrel
     // with no ABI home is what broke them.
     ...lazyMap({ BaseTooltip: React.lazy(() => import('../ui/BaseTooltip.js')) }, '@jbrowse/core/ui/'),
-    '@jbrowse/core/util': coreUtil,
-    '@jbrowse/core/util/color': coreColor,
-    '@jbrowse/core/util/layouts': coreLayouts,
-    '@jbrowse/core/util/tracks': trackUtils,
-    '@jbrowse/core/util/Base1DViewModel': Base1DView,
-    '@jbrowse/core/util/io': coreIo,
-    '@jbrowse/core/util/mst-reflection': coreMstReflection,
-    '@jbrowse/core/util/rxjs': rxjs,
-    '@jbrowse/core/pluggableElementTypes': pluggableElementTypes,
-    '@jbrowse/core/pluggableElementTypes/ViewType': ViewType,
-    '@jbrowse/core/pluggableElementTypes/AdapterType': AdapterType,
-    '@jbrowse/core/pluggableElementTypes/DisplayType': DisplayType,
-    '@jbrowse/core/pluggableElementTypes/TrackType': TrackType,
-    '@jbrowse/core/pluggableElementTypes/WidgetType': WidgetType,
-    '@jbrowse/core/pluggableElementTypes/models': pluggableElementTypeModels,
     '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail': BaseFeatureDetail,
-    '@jbrowse/core/data_adapters/BaseAdapter': BaseAdapterExports,
     // `adapterCache` is module-level state, so a plugin that bundles its own copy
     // of this file gets a second cache in the RPC worker — and `freeAdapterResources`,
     // which CoreFreeResources calls on the host's copy when the last track using
@@ -152,7 +103,6 @@ const libs = {
     // reference to an adapter (see the comment on that function), so those
     // adapters and everything they hold live as long as the worker. Serving the
     // module is what makes an external RPC method share the host's cache.
-    '@jbrowse/core/data_adapters/dataAdapterCache': dataAdapterCache,
 };
 const libsList = Object.keys(libs);
 // make sure that all the items in the ReExports/list array (used by build

package/esm/ReExports/publicUtil.d.ts

@@ -1 +1 @@
-export { AuthNeededError, BEZIER_CONNECTOR_MAX_REACH_PX, ENCODED_PREFIX, IUPAC_MOTIF_REGEX, IntervalTree, JSON_PREFIX, MAX_ZOOM_RATE_PER_MS, SCROLL_ZOOM_FACTOR_DIVISOR, SHARE_PREFIX, SimpleFeature, UNKNOWN, UNSUPPORTED, UnknownRefNameError, ZOOM_ACTIVE_WINDOW_MS, accumulateScroll, adapterConfigFromSpec, addAdapterGuesser, addAddTrackComponent, addAndShowTrack, addOrReplaceView, addTrackFromWidget, addTrackTypeGuesser, aesDecrypt, aesEncrypt, animationAllowed, applyOrderWithin, applyZoomAccum, assembleLocString, assembleLocStringRaw, avg, b64PadSuffix, bezierConnectorPath, bpSpanPx, bpToPx, bytesForRegions, calculateRedispatchRange, canReplaceView, capitalizeFirst, checkStopToken, checkStopTokenThrottled, clamp, clearFileFromCache, cmpStr, coarseStripHTML, codonTable, compareLocStrings, compareLocs, complement, complementTable, createProgressReporter, createScrollLatch, createSharedSetup, createStatusChannel, createStatusFanOut, createStatusWindow, createStopToken, createStopTokenChecker, createStopTokenRotation, dedupe, defaultCodonTable, defaultStarts, diagonalizeRegions, diffTrackConfig, doesIntersect2, downloadStatus, drawImageOntoCanvasContext, encodeSessionParam, ensureFileHandleReady, expandLooseTrackConfig, featureSpanPx, fetchAndMaybeUnzip, fetchAndMaybeUnzipText, fetchJson, fileToLocation, findFileHandleIds, findParentThat, findParentThatIs, flattenTrackConfigDelta, formatRelativeTime, fromUrlSafeB64, gatherOverlaps, generateCodonTable, generateUnknownTrackConf, generateUnsupportedTrackConf, getAssemblyHost, getBlob, getBlobMap, getBpDisplayStr, getConfAssemblyNames, getContainingDisplay, getContainingTrack, getContainingView, getDialogHost, getEnv, getFileFromCache, getFileHandle, getFileName, getFillProps, getFrame, getNotificationSink, getNumberGrouping, getPaletteHost, getPluginUpdate, getRenderingServices, getRpcHost, getRpcSessionId, getSession, getSessionServices, getStr, getStrokeProps, getTickDisplayStr, getTrackAssemblyNames, getTrackName, getZoomNormalizer, groupBy, guessAdapter, guessTrackConf, guessTrackType, hasFileHandlesInCache, hasSharedArrayBuffer, hashCode, hideTrackGeneric, installedVersionFromUrl, intersection2, isAbortException, isAbstractMenuManager, isActivelyZooming, isAppRootModel, isAuthNeededException, isBlobLocation, isDataCurrent, isDisplayModel, isElectron, isFeature, isFileHandleLocation, isFileSystemAccessSupported, isGzip, isLocalPathLocation, isLooseTrackConfig, isNode, isObject, isPalindromic, isPluginInstalled, isRootModelWithInternetAccounts, isRpcResult, isSelectionContainer, isSessionModel, isSessionServices, isSessionModelWithConfigEditing, isSessionModelWithConnectionEditing, isSessionModelWithConnections, isSessionModelWithWidgets, isSessionWithAddAssembly, isSessionWithAddSessionTrack, isSessionWithAddTracks, isSessionWithPublishTrackConf, isSessionWithDeleteTrackConf, isSessionWithSessionPlugins, isSessionWithSessionTracks, isSessionWithShareURL, isSessionWithViewReplacement, isStopToken, isStopped, isSupportedIndexingAdapter, isTrackModel, isTrackViewModel, isUriLocation, isValidTag, isViewContainer, isViewModel, iupacToRegex, linkify, locStringsToRegions, localStorageGetBoolean, localStorageGetItem, localStorageGetJSON, localStorageGetNumber, localStorageRemoveItem, localStorageSetBoolean, localStorageSetItem, localStorageSetJSON, localStorageSetNumber, makeAbortError, makeIndex, makeIndexType, makeTrackId, markStopTokenStopped, matchTrackId, max, maxFinite, measureGridWidth, measureText, mergeIntervals, mergeTrackConfig, min, minmax, normalizeWheelDelta, notEmpty, objectHash, openFeatureWidget, openPromotableDisplays, parseLocString, parseLocStringOneBased, parseMotifList, pluralize, polarToCartesian, progressLabel, rIC, radToDeg, readSessionFromDynamo, reducePrecision, registerStopTokenBroadcaster, renameRegionIfNeeded, renameRegionsIfNeeded, renderToStaticMarkup, reorder, reorderWithin, resolvePlugin, resolveSelectedIds, restoreFileHandles, restoreFileHandlesFromSnapshot, revcom, reverse, reverseComplementIupac, revlist, saveAs, saveSvgAsImage, selectNamedRegions, setBlobMap, setFileInCache, setNumberGrouping, sha256, sha256Base64, sha256Base64Url, shareEndpoint, shorten, shorten2, showTrackGeneric, springAnimate, statusFraction, statusMessageText, statusProgressLabel, statusReading, stitch, stopStopToken, stopTokenSignal, storeBlobLocation, storeFileHandle, storeFileHandleLocation, stringify, stripAlpha, stripFileExtension, stripTrackIds, sum, svgHtmlToPngBlob, tagRegex, testAdapter, toBase64, toBase64Url, toLocale, toUrlSafeB64, toggleTrackGeneric, truncateMiddle, updateStatus, useDebounce, useLocalStorage, useWidthSetter, verifyPermission, wheelFrameElapsedMs, wheelZoomAccum, withProgress, withStopTokenCheck, withStopTokenSignal, } from '../util/index.ts';
+export { AuthNeededError, BEZIER_CONNECTOR_MAX_REACH_PX, ENCODED_PREFIX, IUPAC_MOTIF_REGEX, IntervalTree, JSON_PREFIX, MAX_ZOOM_RATE_PER_MS, SCROLL_ZOOM_FACTOR_DIVISOR, SHARE_PREFIX, SimpleFeature, UNKNOWN, UNSUPPORTED, UnknownRefNameError, ZOOM_ACTIVE_WINDOW_MS, accumulateScroll, adapterConfigFromSpec, addAdapterGuesser, addAddTrackComponent, addAndShowTrack, addOrReplaceView, addTrackFromWidget, addTrackTypeGuesser, aesDecrypt, aesEncrypt, animationAllowed, applyOrderWithin, applyZoomAccum, assembleLocString, assembleLocStringRaw, avg, b64PadSuffix, bezierConnectorPath, bpSpanPx, bpToPx, bytesForRegions, calculateRedispatchRange, canReplaceView, capitalizeFirst, checkStopToken, checkStopTokenThrottled, clamp, clearFileFromCache, cmpStr, coarseStripHTML, codonTable, compareLocStrings, compareLocs, complement, complementTable, createProgressReporter, createScrollLatch, createSharedSetup, createStatusChannel, createStatusFanOut, createStatusWindow, createStopToken, createStopTokenChecker, createStopTokenRotation, dedupe, defaultCodonTable, defaultStarts, diagonalizeRegions, diffTrackConfig, doesIntersect2, downloadStatus, drawImageOntoCanvasContext, encodeSessionParam, ensureFileHandleReady, expandLooseTrackConfig, featureSpanPx, fetchAndMaybeUnzip, fetchAndMaybeUnzipText, fetchJson, fileToLocation, findFileHandleIds, findParentThat, findParentThatIs, flattenTrackConfigDelta, formatRelativeTime, fromUrlSafeB64, gatherOverlaps, generateCodonTable, generateUnknownTrackConf, generateUnsupportedTrackConf, getAssemblyHost, getBlob, getBlobMap, getBpDisplayStr, getConfAssemblyNames, getContainingDisplay, getContainingTrack, getContainingView, getDialogHost, getEnv, launchOrReplaceView, getFileFromCache, getFileHandle, getFileName, getFillProps, getFrame, getNotificationSink, getNumberGrouping, getPaletteHost, getPluginUpdate, getRenderingServices, getRpcHost, getRpcSessionId, getSession, getSessionServices, getStr, getStrokeProps, getTickDisplayStr, getTrackAssemblyNames, getTrackName, getZoomNormalizer, groupBy, guessAdapter, guessTrackConf, guessTrackType, hasFileHandlesInCache, hasSharedArrayBuffer, hashCode, hideTrackGeneric, installedVersionFromUrl, intersection2, isAbortException, isAbstractMenuManager, isActivelyZooming, isAppRootModel, isAuthNeededException, isBlobLocation, isDataCurrent, isDisplayModel, isElectron, isFeature, isFileHandleLocation, isFileSystemAccessSupported, isGzip, isLocalPathLocation, isLooseTrackConfig, isNode, isObject, isPalindromic, isPluginInstalled, isRootModelWithInternetAccounts, isRpcResult, isSelectionContainer, isSessionModel, isSessionServices, isSessionModelWithConfigEditing, isSessionModelWithConnectionEditing, isSessionModelWithConnections, isSessionModelWithWidgets, isSessionWithAddAssembly, isSessionWithAddSessionTrack, isSessionWithAddTracks, isSessionWithPublishTrackConf, isSessionWithDeleteTrackConf, isSessionWithSessionPlugins, isSessionWithSessionTracks, isSessionWithShareURL, isSessionWithViewReplacement, isStopToken, isStopped, isSupportedIndexingAdapter, isTrackModel, isTrackViewModel, isUriLocation, isValidTag, isViewContainer, isViewModel, iupacToRegex, linkify, locStringsToRegions, localStorageGetBoolean, localStorageGetItem, localStorageGetJSON, localStorageGetNumber, localStorageRemoveItem, localStorageSetBoolean, localStorageSetItem, localStorageSetJSON, localStorageSetNumber, makeAbortError, makeIndex, makeIndexType, makeTrackId, markStopTokenStopped, matchTrackId, max, maxFinite, measureGridWidth, measureText, mergeIntervals, mergeTrackConfig, min, minmax, normalizeWheelDelta, notEmpty, objectHash, openFeatureWidget, openPromotableDisplays, parseLocString, parseLocStringOneBased, parseMotifList, pluralize, polarToCartesian, progressLabel, rIC, radToDeg, readSessionFromDynamo, reducePrecision, registerStopTokenBroadcaster, renameRegionIfNeeded, renameRegionsIfNeeded, reorder, reorderWithin, resolvePlugin, resolveSelectedIds, restoreFileHandles, restoreFileHandlesFromSnapshot, revcom, reverse, reverseComplementIupac, revlist, saveAs, saveSvgAsImage, selectNamedRegions, setBlobMap, setFileInCache, setNumberGrouping, sha256, sha256Base64, sha256Base64Url, shareEndpoint, shorten, shorten2, showTrackGeneric, springAnimate, statusFraction, statusMessageText, statusProgressLabel, statusReading, stitch, stopStopToken, stopTokenSignal, storeBlobLocation, storeFileHandle, storeFileHandleLocation, stringify, stripAlpha, stripFileExtension, stripTrackIds, sum, svgHtmlToPngBlob, tagRegex, testAdapter, toBase64, toBase64Url, toLocale, toUrlSafeB64, toggleTrackGeneric, truncateMiddle, updateStatus, useDebounce, useLocalStorage, useWidthSetter, verifyPermission, wheelFrameElapsedMs, wheelZoomAccum, withProgress, withStopTokenCheck, withStopTokenSignal, } from '../util/index.ts';

package/esm/ReExports/publicUtil.js

@@ -25,4 +25,4 @@
 // The same split is worth making for '@jbrowse/core/ui' (115 pinned names) and
 // '@jbrowse/core/util/tracks' (36), which have the same shape and the same
 // history: BaseTooltip and getParentRenderProps each left this way.
-export { AuthNeededError, BEZIER_CONNECTOR_MAX_REACH_PX, ENCODED_PREFIX, IUPAC_MOTIF_REGEX, IntervalTree, JSON_PREFIX, MAX_ZOOM_RATE_PER_MS, SCROLL_ZOOM_FACTOR_DIVISOR, SHARE_PREFIX, SimpleFeature, UNKNOWN, UNSUPPORTED, UnknownRefNameError, ZOOM_ACTIVE_WINDOW_MS, accumulateScroll, adapterConfigFromSpec, addAdapterGuesser, addAddTrackComponent, addAndShowTrack, addOrReplaceView, addTrackFromWidget, addTrackTypeGuesser, aesDecrypt, aesEncrypt, animationAllowed, applyOrderWithin, applyZoomAccum, assembleLocString, assembleLocStringRaw, avg, b64PadSuffix, bezierConnectorPath, bpSpanPx, bpToPx, bytesForRegions, calculateRedispatchRange, canReplaceView, capitalizeFirst, checkStopToken, checkStopTokenThrottled, clamp, clearFileFromCache, cmpStr, coarseStripHTML, codonTable, compareLocStrings, compareLocs, complement, complementTable, createProgressReporter, createScrollLatch, createSharedSetup, createStatusChannel, createStatusFanOut, createStatusWindow, createStopToken, createStopTokenChecker, createStopTokenRotation, dedupe, defaultCodonTable, defaultStarts, diagonalizeRegions, diffTrackConfig, doesIntersect2, downloadStatus, drawImageOntoCanvasContext, encodeSessionParam, ensureFileHandleReady, expandLooseTrackConfig, featureSpanPx, fetchAndMaybeUnzip, fetchAndMaybeUnzipText, fetchJson, fileToLocation, findFileHandleIds, findParentThat, findParentThatIs, flattenTrackConfigDelta, formatRelativeTime, fromUrlSafeB64, gatherOverlaps, generateCodonTable, generateUnknownTrackConf, generateUnsupportedTrackConf, getAssemblyHost, getBlob, getBlobMap, getBpDisplayStr, getConfAssemblyNames, getContainingDisplay, getContainingTrack, getContainingView, getDialogHost, getEnv, getFileFromCache, getFileHandle, getFileName, getFillProps, getFrame, getNotificationSink, getNumberGrouping, getPaletteHost, getPluginUpdate, getRenderingServices, getRpcHost, getRpcSessionId, getSession, getSessionServices, getStr, getStrokeProps, getTickDisplayStr, getTrackAssemblyNames, getTrackName, getZoomNormalizer, groupBy, guessAdapter, guessTrackConf, guessTrackType, hasFileHandlesInCache, hasSharedArrayBuffer, hashCode, hideTrackGeneric, installedVersionFromUrl, intersection2, isAbortException, isAbstractMenuManager, isActivelyZooming, isAppRootModel, isAuthNeededException, isBlobLocation, isDataCurrent, isDisplayModel, isElectron, isFeature, isFileHandleLocation, isFileSystemAccessSupported, isGzip, isLocalPathLocation, isLooseTrackConfig, isNode, isObject, isPalindromic, isPluginInstalled, isRootModelWithInternetAccounts, isRpcResult, isSelectionContainer, isSessionModel, isSessionServices, isSessionModelWithConfigEditing, isSessionModelWithConnectionEditing, isSessionModelWithConnections, isSessionModelWithWidgets, isSessionWithAddAssembly, isSessionWithAddSessionTrack, isSessionWithAddTracks, isSessionWithPublishTrackConf, isSessionWithDeleteTrackConf, isSessionWithSessionPlugins, isSessionWithSessionTracks, isSessionWithShareURL, isSessionWithViewReplacement, isStopToken, isStopped, isSupportedIndexingAdapter, isTrackModel, isTrackViewModel, isUriLocation, isValidTag, isViewContainer, isViewModel, iupacToRegex, linkify, locStringsToRegions, localStorageGetBoolean, localStorageGetItem, localStorageGetJSON, localStorageGetNumber, localStorageRemoveItem, localStorageSetBoolean, localStorageSetItem, localStorageSetJSON, localStorageSetNumber, makeAbortError, makeIndex, makeIndexType, makeTrackId, markStopTokenStopped, matchTrackId, max, maxFinite, measureGridWidth, measureText, mergeIntervals, mergeTrackConfig, min, minmax, normalizeWheelDelta, notEmpty, objectHash, openFeatureWidget, openPromotableDisplays, parseLocString, parseLocStringOneBased, parseMotifList, pluralize, polarToCartesian, progressLabel, rIC, radToDeg, readSessionFromDynamo, reducePrecision, registerStopTokenBroadcaster, renameRegionIfNeeded, renameRegionsIfNeeded, renderToStaticMarkup, reorder, reorderWithin, resolvePlugin, resolveSelectedIds, restoreFileHandles, restoreFileHandlesFromSnapshot, revcom, reverse, reverseComplementIupac, revlist, saveAs, saveSvgAsImage, selectNamedRegions, setBlobMap, setFileInCache, setNumberGrouping, sha256, sha256Base64, sha256Base64Url, shareEndpoint, shorten, shorten2, showTrackGeneric, springAnimate, statusFraction, statusMessageText, statusProgressLabel, statusReading, stitch, stopStopToken, stopTokenSignal, storeBlobLocation, storeFileHandle, storeFileHandleLocation, stringify, stripAlpha, stripFileExtension, stripTrackIds, sum, svgHtmlToPngBlob, tagRegex, testAdapter, toBase64, toBase64Url, toLocale, toUrlSafeB64, toggleTrackGeneric, truncateMiddle, updateStatus, useDebounce, useLocalStorage, useWidthSetter, verifyPermission, wheelFrameElapsedMs, wheelZoomAccum, withProgress, withStopTokenCheck, withStopTokenSignal, } from '../util/index.js';
+export { AuthNeededError, BEZIER_CONNECTOR_MAX_REACH_PX, ENCODED_PREFIX, IUPAC_MOTIF_REGEX, IntervalTree, JSON_PREFIX, MAX_ZOOM_RATE_PER_MS, SCROLL_ZOOM_FACTOR_DIVISOR, SHARE_PREFIX, SimpleFeature, UNKNOWN, UNSUPPORTED, UnknownRefNameError, ZOOM_ACTIVE_WINDOW_MS, accumulateScroll, adapterConfigFromSpec, addAdapterGuesser, addAddTrackComponent, addAndShowTrack, addOrReplaceView, addTrackFromWidget, addTrackTypeGuesser, aesDecrypt, aesEncrypt, animationAllowed, applyOrderWithin, applyZoomAccum, assembleLocString, assembleLocStringRaw, avg, b64PadSuffix, bezierConnectorPath, bpSpanPx, bpToPx, bytesForRegions, calculateRedispatchRange, canReplaceView, capitalizeFirst, checkStopToken, checkStopTokenThrottled, clamp, clearFileFromCache, cmpStr, coarseStripHTML, codonTable, compareLocStrings, compareLocs, complement, complementTable, createProgressReporter, createScrollLatch, createSharedSetup, createStatusChannel, createStatusFanOut, createStatusWindow, createStopToken, createStopTokenChecker, createStopTokenRotation, dedupe, defaultCodonTable, defaultStarts, diagonalizeRegions, diffTrackConfig, doesIntersect2, downloadStatus, drawImageOntoCanvasContext, encodeSessionParam, ensureFileHandleReady, expandLooseTrackConfig, featureSpanPx, fetchAndMaybeUnzip, fetchAndMaybeUnzipText, fetchJson, fileToLocation, findFileHandleIds, findParentThat, findParentThatIs, flattenTrackConfigDelta, formatRelativeTime, fromUrlSafeB64, gatherOverlaps, generateCodonTable, generateUnknownTrackConf, generateUnsupportedTrackConf, getAssemblyHost, getBlob, getBlobMap, getBpDisplayStr, getConfAssemblyNames, getContainingDisplay, getContainingTrack, getContainingView, getDialogHost, getEnv, launchOrReplaceView, getFileFromCache, getFileHandle, getFileName, getFillProps, getFrame, getNotificationSink, getNumberGrouping, getPaletteHost, getPluginUpdate, getRenderingServices, getRpcHost, getRpcSessionId, getSession, getSessionServices, getStr, getStrokeProps, getTickDisplayStr, getTrackAssemblyNames, getTrackName, getZoomNormalizer, groupBy, guessAdapter, guessTrackConf, guessTrackType, hasFileHandlesInCache, hasSharedArrayBuffer, hashCode, hideTrackGeneric, installedVersionFromUrl, intersection2, isAbortException, isAbstractMenuManager, isActivelyZooming, isAppRootModel, isAuthNeededException, isBlobLocation, isDataCurrent, isDisplayModel, isElectron, isFeature, isFileHandleLocation, isFileSystemAccessSupported, isGzip, isLocalPathLocation, isLooseTrackConfig, isNode, isObject, isPalindromic, isPluginInstalled, isRootModelWithInternetAccounts, isRpcResult, isSelectionContainer, isSessionModel, isSessionServices, isSessionModelWithConfigEditing, isSessionModelWithConnectionEditing, isSessionModelWithConnections, isSessionModelWithWidgets, isSessionWithAddAssembly, isSessionWithAddSessionTrack, isSessionWithAddTracks, isSessionWithPublishTrackConf, isSessionWithDeleteTrackConf, isSessionWithSessionPlugins, isSessionWithSessionTracks, isSessionWithShareURL, isSessionWithViewReplacement, isStopToken, isStopped, isSupportedIndexingAdapter, isTrackModel, isTrackViewModel, isUriLocation, isValidTag, isViewContainer, isViewModel, iupacToRegex, linkify, locStringsToRegions, localStorageGetBoolean, localStorageGetItem, localStorageGetJSON, localStorageGetNumber, localStorageRemoveItem, localStorageSetBoolean, localStorageSetItem, localStorageSetJSON, localStorageSetNumber, makeAbortError, makeIndex, makeIndexType, makeTrackId, markStopTokenStopped, matchTrackId, max, maxFinite, measureGridWidth, measureText, mergeIntervals, mergeTrackConfig, min, minmax, normalizeWheelDelta, notEmpty, objectHash, openFeatureWidget, openPromotableDisplays, parseLocString, parseLocStringOneBased, parseMotifList, pluralize, polarToCartesian, progressLabel, rIC, radToDeg, readSessionFromDynamo, reducePrecision, registerStopTokenBroadcaster, renameRegionIfNeeded, renameRegionsIfNeeded, reorder, reorderWithin, resolvePlugin, resolveSelectedIds, restoreFileHandles, restoreFileHandlesFromSnapshot, revcom, reverse, reverseComplementIupac, revlist, saveAs, saveSvgAsImage, selectNamedRegions, setBlobMap, setFileInCache, setNumberGrouping, sha256, sha256Base64, sha256Base64Url, shareEndpoint, shorten, shorten2, showTrackGeneric, springAnimate, statusFraction, statusMessageText, statusProgressLabel, statusReading, stitch, stopStopToken, stopTokenSignal, storeBlobLocation, storeFileHandle, storeFileHandleLocation, stringify, stripAlpha, stripFileExtension, stripTrackIds, sum, svgHtmlToPngBlob, tagRegex, testAdapter, toBase64, toBase64Url, toLocale, toUrlSafeB64, toggleTrackGeneric, truncateMiddle, updateStatus, useDebounce, useLocalStorage, useWidthSetter, verifyPermission, wheelFrameElapsedMs, wheelZoomAccum, withProgress, withStopTokenCheck, withStopTokenSignal, } from '../util/index.js';

package/esm/ReExports/sharedModules.d.ts

@@ -0,0 +1,96 @@
+import * as React from 'react';
+import * as mst from '@jbrowse/mobx-state-tree';
+import * as mobx from 'mobx';
+import * as ReactJSXRuntime from 'react/jsx-runtime';
+import Plugin from '../Plugin.ts';
+import * as Configuration from '../configuration/index.ts';
+import * as BaseAdapterExports from '../data_adapters/BaseAdapter/index.ts';
+import * as dataAdapterCache from '../data_adapters/dataAdapterCache.ts';
+import AdapterType from '../pluggableElementTypes/AdapterType.ts';
+import DisplayType from '../pluggableElementTypes/DisplayType.ts';
+import TrackType from '../pluggableElementTypes/TrackType.ts';
+import ViewType from '../pluggableElementTypes/ViewType.ts';
+import WidgetType from '../pluggableElementTypes/WidgetType.ts';
+import * as pluggableElementTypes from '../pluggableElementTypes/index.ts';
+import * as pluggableElementTypeModels from '../pluggableElementTypes/models/index.ts';
+import * as corePalette from '../ui/palette.ts';
+import * as coreTheme from '../ui/theme.ts';
+import * as coreColor from '../util/color/index.ts';
+import * as coreIo from '../util/io/index.ts';
+import * as coreLayouts from '../util/layouts/index.ts';
+import * as coreMstReflection from '../util/mst-reflection.ts';
+import * as rxjs from '../util/rxjs.ts';
+import * as trackUtils from '../util/tracks.ts';
+import * as mstTypes from '../util/types/mst.ts';
+import * as coreUtil from './publicUtil.ts';
+export declare const sharedModules: {
+    mobx: typeof mobx;
+    '@jbrowse/mobx-state-tree': typeof mst;
+    'mobx-state-tree': typeof mst;
+    react: typeof React;
+    'react/jsx-runtime': typeof ReactJSXRuntime;
+    '@jbrowse/core/Plugin': typeof Plugin;
+    '@jbrowse/core/configuration': typeof Configuration;
+    '@jbrowse/core/util/types/mst': typeof mstTypes;
+    '@jbrowse/core/ui/theme': typeof coreTheme;
+    '@jbrowse/core/ui/palette': typeof corePalette;
+    '@jbrowse/core/util': typeof coreUtil;
+    '@jbrowse/core/util/color': typeof coreColor;
+    '@jbrowse/core/util/layouts': typeof coreLayouts;
+    '@jbrowse/core/util/tracks': typeof trackUtils;
+    '@jbrowse/core/util/Base1DViewModel': mst.IModelType<{
+        id: mst.IOptionalIType<mst.ISimpleType<string>, [undefined]>;
+        displayedRegions: mst.IOptionalIType<mst.IType<import("../util/index.ts").Region[], import("../util/index.ts").Region[], import("../util/index.ts").Region[]>, [undefined]>;
+        bpPerPx: mst.IType<number | undefined, number, number>;
+        offsetPx: mst.IType<number | undefined, number, number>;
+        minimumBlockWidth: mst.IOptionalIType<mst.ISimpleType<number>, [undefined]>;
+    }, {
+        volatileWidth: number;
+    } & {
+        setDisplayedRegions(regions: import("../util/index.ts").Region[]): void;
+        setBpPerPx(val: number): void;
+        setVolatileWidth(width: number): void;
+    } & {
+        readonly width: number;
+        readonly minBpPerPx: number;
+        readonly maxBpPerPx: number;
+        readonly assemblyNames: string[];
+        readonly displayedRegionsTotalPx: number;
+        readonly maxOffset: number;
+        readonly minOffset: number;
+        readonly totalBp: number;
+    } & {
+        readonly dynamicBlocks: import("../util/blockTypes.ts").BlockSet;
+        readonly staticBlocks: import("../util/blockTypes.ts").BlockSet;
+        readonly currBp: number;
+    } & {
+        pxToBp(px: number): import("../util/Base1DUtils.ts").PxToBpResult;
+        bpToPx(args: {
+            refName: string;
+            coord: number;
+            displayedRegionIndex?: number;
+        }): number | undefined;
+    } & {
+        showAllRegions(): void;
+        zoomOut(): void;
+        zoomIn(): void;
+        zoomTo(bpPerPx: number, offset?: any): number;
+        scrollTo(offsetPx: number): number;
+        centerAt(coord: number, refName: string | undefined, displayedRegionIndex: number): void;
+        scroll(distance: number): number;
+    } & {
+        moveTo(start?: import("../util/Base1DUtils.ts").BpOffset, end?: import("../util/Base1DUtils.ts").BpOffset): void;
+    }, mst._NotCustomized, mst._NotCustomized>;
+    '@jbrowse/core/util/io': typeof coreIo;
+    '@jbrowse/core/util/mst-reflection': typeof coreMstReflection;
+    '@jbrowse/core/util/rxjs': typeof rxjs;
+    '@jbrowse/core/pluggableElementTypes': typeof pluggableElementTypes;
+    '@jbrowse/core/pluggableElementTypes/ViewType': typeof ViewType;
+    '@jbrowse/core/pluggableElementTypes/AdapterType': typeof AdapterType;
+    '@jbrowse/core/pluggableElementTypes/DisplayType': typeof DisplayType;
+    '@jbrowse/core/pluggableElementTypes/TrackType': typeof TrackType;
+    '@jbrowse/core/pluggableElementTypes/WidgetType': typeof WidgetType;
+    '@jbrowse/core/pluggableElementTypes/models': typeof pluggableElementTypeModels;
+    '@jbrowse/core/data_adapters/BaseAdapter': typeof BaseAdapterExports;
+    '@jbrowse/core/data_adapters/dataAdapterCache': typeof dataAdapterCache;
+};

package/esm/ReExports/sharedModules.js

@@ -0,0 +1,59 @@
+// eslint-disable-next-line no-restricted-imports
+import * as React from 'react';
+import * as mst from '@jbrowse/mobx-state-tree';
+import * as mobx from 'mobx';
+import * as ReactJSXRuntime from 'react/jsx-runtime';
+import Plugin from '../Plugin.js';
+import * as Configuration from '../configuration/index.js';
+import * as BaseAdapterExports from '../data_adapters/BaseAdapter/index.js';
+import * as dataAdapterCache from '../data_adapters/dataAdapterCache.js';
+import AdapterType from '../pluggableElementTypes/AdapterType.js';
+import DisplayType from '../pluggableElementTypes/DisplayType.js';
+import TrackType from '../pluggableElementTypes/TrackType.js';
+import ViewType from '../pluggableElementTypes/ViewType.js';
+import WidgetType from '../pluggableElementTypes/WidgetType.js';
+import * as pluggableElementTypes from '../pluggableElementTypes/index.js';
+import * as pluggableElementTypeModels from '../pluggableElementTypes/models/index.js';
+import * as corePalette from '../ui/palette.js';
+import * as coreTheme from '../ui/theme.js';
+import Base1DView from '../util/Base1DViewModel.js';
+import * as coreColor from '../util/color/index.js';
+import * as coreIo from '../util/io/index.js';
+import * as coreLayouts from '../util/layouts/index.js';
+import * as coreMstReflection from '../util/mst-reflection.js';
+import * as rxjs from '../util/rxjs.js';
+import * as trackUtils from '../util/tracks.js';
+import * as mstTypes from '../util/types/mst.js';
+import * as coreUtil from './publicUtil.js';
+// The part of the runtime plugin ABI that is not UI: what a plugin evaluated in
+// the RPC worker can actually use. modules.ts adds the UI on top of it for the
+// main thread; workerModules.ts fills the same keys with a stub instead.
+export const sharedModules = {
+    mobx,
+    '@jbrowse/mobx-state-tree': mst,
+    'mobx-state-tree': mst,
+    react: React,
+    'react/jsx-runtime': ReactJSXRuntime,
+    '@jbrowse/core/Plugin': Plugin,
+    '@jbrowse/core/configuration': Configuration,
+    '@jbrowse/core/util/types/mst': mstTypes,
+    '@jbrowse/core/ui/theme': coreTheme,
+    '@jbrowse/core/ui/palette': corePalette,
+    '@jbrowse/core/util': coreUtil,
+    '@jbrowse/core/util/color': coreColor,
+    '@jbrowse/core/util/layouts': coreLayouts,
+    '@jbrowse/core/util/tracks': trackUtils,
+    '@jbrowse/core/util/Base1DViewModel': Base1DView,
+    '@jbrowse/core/util/io': coreIo,
+    '@jbrowse/core/util/mst-reflection': coreMstReflection,
+    '@jbrowse/core/util/rxjs': rxjs,
+    '@jbrowse/core/pluggableElementTypes': pluggableElementTypes,
+    '@jbrowse/core/pluggableElementTypes/ViewType': ViewType,
+    '@jbrowse/core/pluggableElementTypes/AdapterType': AdapterType,
+    '@jbrowse/core/pluggableElementTypes/DisplayType': DisplayType,
+    '@jbrowse/core/pluggableElementTypes/TrackType': TrackType,
+    '@jbrowse/core/pluggableElementTypes/WidgetType': WidgetType,
+    '@jbrowse/core/pluggableElementTypes/models': pluggableElementTypeModels,
+    '@jbrowse/core/data_adapters/BaseAdapter': BaseAdapterExports,
+    '@jbrowse/core/data_adapters/dataAdapterCache': dataAdapterCache,
+};

package/esm/ReExports/uiStub.d.ts

@@ -0,0 +1 @@
+export declare const uiStub: unknown;

package/esm/ReExports/uiStub.js

@@ -0,0 +1,13 @@
+// What a UI entry of the plugin ABI resolves to inside the RPC worker. A plugin
+// bundle is one file for both realms, and at module scope it reads and calls
+// these entries — destructures components, `styled(Box)(...)`, `observer(C)`,
+// `createSvgIcon(...)` — so every key must exist and every read and call must
+// succeed. Nothing in a worker renders, so no code path ever reaches a
+// difference. `then` is undefined so an await on it settles.
+function stubTarget() { }
+export const uiStub = new Proxy(stubTarget, {
+    get: (_, key) => key === 'then' ? undefined : key === Symbol.toPrimitive ? () => '' : uiStub,
+    has: () => true,
+    apply: () => uiStub,
+    construct: () => uiStub,
+});

package/esm/ReExports/workerModules.d.ts

@@ -0,0 +1,2 @@
+declare const libs: Record<string, unknown>;
+export default libs;

package/esm/ReExports/workerModules.js

@@ -0,0 +1,10 @@
+import reExportsList from './list.js';
+import { sharedModules } from './sharedModules.js';
+import { uiStub } from './uiStub.js';
+// The same keys as modules.ts, so a plugin finds every name it links against;
+// the UI ones hold the stub rather than react-dom and Material UI.
+const libs = {
+    ...Object.fromEntries(reExportsList.map(name => [name, uiStub])),
+    ...sharedModules,
+};
+export default libs;

package/esm/configuration/configurationSchema.d.ts

@@ -85,46 +85,13 @@ export declare function ConfigurationSchema<const DEFINITION extends Configurati
  * it as the plain object it is.
  *
  * Shares `TrackConfigurationReference`'s per-PluginManager cache, so hydrating
- * the same entry twice returns the same node and a track that gets opened later
- * reuses it.
+ * the same entry twice returns the same node — and in admin/embedded sessions a
+ * track opened later resolves to that same node. A non-admin's open track does
+ * not: it resolves to the session's private working copy (ADR-032) and this is
+ * the pristine mirror beside it. The two agree in content, which is what the
+ * caller needs; `CopyConfigEntryPoints.test.ts` pins both halves.
  */
 export declare function hydrateTrackConfig(pluginManager: PluginManager, config: Record<string, unknown>): AnyConfigurationModel | undefined;
-/**
- * Reference to a track configuration. Snapshot output is the trackId string.
- *
- * One load-bearing complication: **`types.union(trackRef, schemaType)` accepts a
- * string id OR a full config.** A view that synthesizes a track nobody else can
- * draw — a read-vs-ref synteny band, an SV inspector row, a circular view's
- * added track — writes the config here rather than registering it in
- * `session.tracks`, and it then lives and dies with the track that holds it.
- * `ReadVsRef.test.tsx` and `SVInspector.test.tsx` are the canaries.
- *
- * NOTE: don't add `as SCHEMATYPE` to the return value. It narrows SnapshotIn
- * to just the object branch, forcing callers to wrap string ids in
- * `@ts-expect-error`. The inferred union SnapshotIn is `string | SnapshotIn<schema>`.
- */
-export declare function TrackConfigurationReference(schemaType: IAnyType): import("@jbrowse/mobx-state-tree").ITypeUnion<any, any, any>;
-/**
- * Reference to a display configuration. Looked up inside the containing track
- * config's `displays` array. Snapshot output is the displayId string.
- *
- * Resolution order:
- *   1. by displayId
- *   2. by `parent.type` — handles old sessions where the saved displayId
- *      no longer matches but a display of the same type exists on the track
- *
- * Step 2 is the safety net because `baseTrackConfig.preProcessSnapshot`
- * already injects a stub display for every registered displayType on the
- * track, so a same-type lookup always succeeds at runtime for properly
- * loaded tracks. An older third step auto-created a *detached* config when
- * neither matched — that produced an orphaned MST node whose edits silently
- * didn't persist. Removed in favor of a clear throw, since
- * preProcessSnapshot's injection makes the path effectively dead.
- *
- * Union-with-schemaType branch is for the same reason as `TrackConfigurationReference`:
- * `CircularView.addTrackConf` passes inline display configs as MST instances.
- */
-export declare function DisplayConfigurationReference(schemaType: IAnyType): import("@jbrowse/mobx-state-tree").ITypeUnion<any, any, any>;
 type ConfigReferenceInstance<SCHEMA extends AnyConfigurationSchemaType> = (SCHEMA extends ConfigurationSchemaType<infer D, any> ? IsAny<D> extends true ? any : SCHEMA['Type'] : SCHEMA['Type']) & {
     [K in GetInheritedIdentifier<SCHEMA>]: string;
 };

package/esm/configuration/configurationSchema.js

@@ -239,34 +239,14 @@ export function ConfigurationSchema(modelName, inputSchemaDefinition, inputOptio
     const { schemaDefinition, options } = preprocessConfigurationSchemaArguments(modelName, inputSchemaDefinition, inputOptions);
     return makeConfigurationSchemaModel(modelName, schemaDefinition, options);
 }
-// The hydration cache lives on the PluginManager instance (see
-// trackConfigHydrationCache's doc comment there and ADR-031), not as a
-// module-level singleton: it must never hand a track resolved on one
-// PluginManager instance a node built with another instance's env, and
-// scoping it to the instance rules that out structurally rather than by
-// convention. Nested a second level by schemaType, since one PluginManager
-// registers a distinct schemaType per track type.
-function frozenTrackHydrationCache(pluginManager, schemaType) {
-    const byType = pluginManager.trackConfigHydrationCache;
-    let cache = byType.get(schemaType);
-    if (!cache) {
-        cache = new WeakMap();
-        byType.set(schemaType, cache);
-    }
-    return cache;
-}
 // The frozen -> live half of TrackConfigurationReference's `get`, shared with
-// hydrateTrackConfig below so there is one hydration and one cache rather than
-// two that can drift on which env or which key they use.
+// hydrateTrackConfig below so there is one hydration rather than two that can
+// drift on which env they build with. The memo it goes through belongs to the
+// PluginManager instance (ADR-031): a node built with one instance's env must
+// never be handed to another, and `pluginManager.hydratedTrackConfig` scopes
+// that structurally rather than by convention.
 function hydrateInto(pluginManager, schemaType, frozen) {
-    const cache = frozenTrackHydrationCache(pluginManager, schemaType);
-    const cached = cache.get(frozen);
-    if (cached) {
-        return cached;
-    }
-    const model = schemaType.create(frozen, { pluginManager });
-    cache.set(frozen, model);
-    return model;
+    return pluginManager.hydratedTrackConfig(schemaType, frozen, () => schemaType.create(frozen, { pluginManager }));
 }
 /**
  * #api core/configuration
@@ -290,8 +270,11 @@ function hydrateInto(pluginManager, schemaType, frozen) {
  * it as the plain object it is.
  *
  * Shares `TrackConfigurationReference`'s per-PluginManager cache, so hydrating
- * the same entry twice returns the same node and a track that gets opened later
- * reuses it.
+ * the same entry twice returns the same node — and in admin/embedded sessions a
+ * track opened later resolves to that same node. A non-admin's open track does
+ * not: it resolves to the session's private working copy (ADR-032) and this is
+ * the pristine mirror beside it. The two agree in content, which is what the
+ * caller needs; `CopyConfigEntryPoints.test.ts` pins both halves.
  */
 export function hydrateTrackConfig(pluginManager, config) {
     const type = config.type;
@@ -315,7 +298,18 @@ export function hydrateTrackConfig(pluginManager, config) {
 // config snapshot (held as a standalone schema instance). Both reference kinds
 // resolve to `schemaType` instances, so MST can't auto-dispatch on the instance
 // side — the explicit snapshot dispatcher (string → ref, object → schema)
-// disambiguates. Shared by TrackConfigurationReference/DisplayConfigurationReference.
+// disambiguates. Shared by TrackConfigurationReference/DisplayConfigurationReference,
+// and by neither accident nor oversight NOT by the plain branch — see the note
+// on it in `ConfigurationReference`.
+//
+// One consequence, because both refs' `set` callbacks read as if it were not
+// true: assigning a config **node** here does not store a reference to it. The
+// dispatcher sees a non-string and picks `schemaType`, so MST tries to adopt the
+// node as an inline child — which throws if it already has a parent. `set` is
+// therefore unreachable on both refs (checked by making it throw: 231 suites
+// stayed green), and exists only because MST rejects a custom reference
+// declaring `get` without it. The plain branch, with no dispatcher, does the
+// opposite and stores the reference.
 function idOrSnapshotUnion(ref, schemaType) {
     return types.union({
         dispatcher: snapshot => (typeof snapshot === 'string' ? ref : schemaType),
@@ -335,7 +329,7 @@ function idOrSnapshotUnion(ref, schemaType) {
  * to just the object branch, forcing callers to wrap string ids in
  * `@ts-expect-error`. The inferred union SnapshotIn is `string | SnapshotIn<schema>`.
  */
-export function TrackConfigurationReference(schemaType) {
+function TrackConfigurationReference(schemaType) {
     const trackRef = types.reference(schemaType, {
         get(id, parent) {
             const session = getSession(parent);
@@ -381,15 +375,26 @@ export function TrackConfigurationReference(schemaType) {
  * Step 2 is the safety net because `baseTrackConfig.preProcessSnapshot`
  * already injects a stub display for every registered displayType on the
  * track, so a same-type lookup always succeeds at runtime for properly
- * loaded tracks. An older third step auto-created a *detached* config when
- * neither matched — that produced an orphaned MST node whose edits silently
- * didn't persist. Removed in favor of a clear throw, since
- * preProcessSnapshot's injection makes the path effectively dead.
+ * loaded tracks. It is what carries a **renamed display type** across for a
+ * catalog track: the injected stub is named for the new type, the display
+ * model's own `preProcessSnapshot` rewrites the state model's, and the saved
+ * `configuration` id still spells the old name, so only the type match
+ * reconnects them. Not every pre-rename session reaches it — a track config
+ * that itself declares the old display entry keeps that entry's `displayId`
+ * through the alias rewrite (`{ ...d, type: canonical }`) and wins the
+ * first-wins dedupe, so its session resolves by id. An older third step
+ * auto-created a *detached* config when neither matched — that produced an
+ * orphaned MST node whose edits silently didn't persist. Removed in favor of a
+ * clear throw.
  *
- * Union-with-schemaType branch is for the same reason as `TrackConfigurationReference`:
- * `CircularView.addTrackConf` passes inline display configs as MST instances.
+ * The union's schemaType branch is symmetry with `TrackConfigurationReference`
+ * rather than a path anything in tree takes: the two production writers,
+ * `showTrackGeneric` and `BaseTrackModel.replaceDisplay`, both write a
+ * displayId string, because a display config belongs in its track config's
+ * `displays` array. It stays because it costs nothing and because dropping it
+ * narrows `SnapshotIn` for every caller.
  */
-export function DisplayConfigurationReference(schemaType) {
+function DisplayConfigurationReference(schemaType) {
     const displayRef = types.reference(schemaType, {
         get(id, parent) {
             // track.configuration is a hydrated MST node (hydrated lazily via
@@ -443,9 +448,17 @@ export function ConfigurationReference(schemaType) {
         ? TrackConfigurationReference(schemaType)
         : id === 'displayId'
             ? DisplayConfigurationReference(schemaType)
-            : // Plain (non-track/display) ref. The union accepts either an id
-                // string (resolved via `types.reference`) or an inline schema
-                // snapshot (held as a standalone schema instance).
+            : // Plain (non-track/display) ref — internet accounts, connections —
+                // resolved by MST's own identifier lookup rather than through the
+                // session. **Deliberately not `idOrSnapshotUnion`**, even though it is
+                // the same two members: this branch is also handed a *live, in-tree*
+                // config node (`initializeInternetAccount` pushes
+                // `jbrowse.internetAccounts[i]` straight through), and an undispatched
+                // union sends that to the reference member because
+                // `BaseReferenceType.isAssignableFrom` defers to its target type. A
+                // `typeof snapshot === 'string'` dispatcher sends it to the schema
+                // member instead, and MST refuses to adopt a node that already has a
+                // parent. `InternetAccounts.test.ts` is the canary.
                 types.union(types.reference(schemaType), schemaType);
     return ref;
 }

package/esm/configuration/promotableDefaults.js

@@ -195,14 +195,20 @@ export function applySlotToOpenTracks(displays, slot, value) {
  * track is the same write as filling in a follower, and the distinction the two
  * actions drew is not one the user has any reason to see.
  *
- * The snackbar outlives the click that raised it, so the promotion re-derives
- * `self`'s liveness inside `onClick` rather than closing over a decision —
- * ADR-048 has the ways that goes wrong.
+ * The snackbar outlives the click that raised it, so the promotion closes over
+ * the display TYPE — a string — rather than reaching back through `self`. A
+ * promoted default is keyed by display type and governs tracks opened later, so
+ * it has nothing to do with the clicked display still being open; guarding on
+ * `self` instead meant a user who applied a value, closed the track, then took
+ * the offer got a silent no-op. What is still guarded is the session, which owns
+ * the map the write lands in. ADR-048 has the decisions this does not change:
+ * no track set and no apply/promote decision may be closed over.
  */
 function applyPinClick(self, slot, value, isDefault) {
     const session = getSession(self);
+    const displayType = self.type;
     if (isDefault) {
-        session.setDisplayTypeDefault(self.type, slot, undefined);
+        session.setDisplayTypeDefault(displayType, slot, undefined);
         session.notify('Cleared the default', 'info');
     }
     else {
@@ -211,8 +217,8 @@ function applyPinClick(self, slot, value, isDefault) {
         session.notify(`Applied to ${open.length} open ${pluralize(open.length, 'track')}`, 'info', {
             name: 'Set as the default',
             onClick: () => {
-                if (isAlive(self)) {
-                    session.setDisplayTypeDefault(self.type, slot, value);
+                if (isAlive(session)) {
+                    session.setDisplayTypeDefault(displayType, slot, value);
                 }
             },
         });

package/esm/configuration/promotableResolve.d.ts

@@ -69,7 +69,7 @@ export declare function storedSlotValue(config: AnyConfigurationModel, slot: str
  * about a value a caller is about to offer as a pin's on-value.
  *
  * Exists because a pin built over a value the gate refuses is inert in a way
- * nothing reports: `applyDefaultToggle` writes it to the session store happily,
+ * nothing reports: `applyPinClick` writes it to the session store happily,
  * `resolveSlotIn` then drops it and every track keeps resolving to the tier
  * below, and `isPromotableDefault` compares the *raw* stored value, so the pin
  * draws outline forever while a dead key sits in the user's localStorage. See

package/esm/configuration/promotableResolve.js

@@ -51,7 +51,7 @@ export function storedSlotValue(config, slot) {
  * about a value a caller is about to offer as a pin's on-value.
  *
  * Exists because a pin built over a value the gate refuses is inert in a way
- * nothing reports: `applyDefaultToggle` writes it to the session store happily,
+ * nothing reports: `applyPinClick` writes it to the session store happily,
  * `resolveSlotIn` then drops it and every track keeps resolving to the tier
  * below, and `isPromotableDefault` compares the *raw* stored value, so the pin
  * draws outline forever while a dead key sits in the user's localStorage. See

package/esm/data_adapters/BaseAdapter/BaseFeatureDataAdapter.d.ts

@@ -2,6 +2,7 @@ import { BaseAdapter } from './BaseAdapter.ts';
 import type { AnyConfigurationModel } from '../../configuration/index.ts';
 import type { Feature } from '../../util/simpleFeature.ts';
 import type { AugmentedRegion as Region } from '../../util/types/index.ts';
+import type { FeatureDensity } from './featureDensity.ts';
 import type { BaseOptions } from './types.ts';
 import type { Observable } from 'rxjs';
 /**
@@ -117,6 +118,17 @@ export declare abstract class BaseFeatureDataAdapter<CONF extends AnyConfigurati
      * agent-docs/reference/REGION_TOO_LARGE.md.
      */
     getRegionByteSize(_regions: Region[], _opts?: BaseOptions): Promise<number | undefined>;
+    /**
+     * Features per bin over each region, at the view's `bpPerPx`, for the density
+     * tier the display draws where the region-too-large gate refused the
+     * features. The default reads the `densityAdapter` sidecar slot
+     * (`densityAdapterConfigSchemaFields`) through `getSubAdapter`; `undefined`
+     * means no tier, and the banner stands. ADR-102 records why no index
+     * estimate stands in for a missing sidecar.
+     */
+    getFeatureDensity(regions: Region[], opts: BaseOptions & {
+        bpPerPx: number;
+    }): Promise<FeatureDensity[] | undefined>;
     getSources(regions: Region[], opts?: BaseOptions): Promise<{
         name: string;
         color?: string;