Align project dependencies and cleanup stale branches

docs/project-alignment-cleanup.md

@@ -0,0 +1,16 @@
+# Project Alignment Cleanup
+
+## Dependency decisions
+
+- Updated direct runtime and development dependencies to their current compatible releases as part of the June 2026 alignment pass.
+- Kept `eslint` on `^9.39.4` because `eslint-config-next@16.2.7` still depends on plugins that peer against ESLint 9. ESLint 10 is intentionally deferred until the Next lint stack supports it without peer overrides.
+- Added transitive overrides for `postcss`, `tmp`, and `uuid` to remove audit findings from Next and ExcelJS dependency paths while preserving the existing spreadsheet import/export code.
+- Verified ExcelJS still writes and reads an XLSX buffer with the `uuid` override in place.
+
+## Stale branch audit
+
+- `temporary` and `codex/spark` contain the same four unique commits covering upload workflow notes, Supabase project checks, and database cleanup hardening.
+- `codex/database-local` contains the design-system experiment history and a design-system baseline document.
+- `codex/design-system-baseline-20260524` is the earlier design baseline snapshot from the same design-system line.
+
+No stale branch was merged directly. Current `main` already contains the accepted upload workflow, Supabase project safety guidance, cleanup scripts, RAG hardening, and dashboard/document-viewer design work. The remaining branch diffs are either superseded by current tracked files or predate the accepted design implementation, so no code was ported.

package.json

@@ -31,41 +31,43 @@
     "samples:check": "tsx scripts/check-sample-extraction.ts"
   },
   "dependencies": {
-    "@next/env": "^16.2.6",
-    "@supabase/supabase-js": "^2.106.1",
+    "@next/env": "^16.2.7",
+    "@supabase/supabase-js": "^2.107.0",
     "exceljs": "^4.4.0",
     "jszip": "^3.10.1",
     "lucide-react": "^1.17.0",
     "mammoth": "^1.12.0",
-    "next": "16.2.6",
-    "openai": "^6.38.0",
+    "next": "16.2.7",
+    "openai": "^6.41.0",
     "pdf-parse": "^2.4.5",
-    "pdfjs-dist": "^5.7.284",
+    "pdfjs-dist": "^6.0.227",
     "pdfkit": "^0.18.0",
-    "postcss": "^8.5.10",
+    "postcss": "^8.5.15",
     "react": "19.2.7",
-    "react-dom": "19.2.4",
+    "react-dom": "19.2.7",
     "tesseract.js": "^7.0.0",
     "zod": "^4.4.3"
   },
   "overrides": {
-    "postcss": "^8.5.10"
+    "postcss": "^8.5.15",
+    "tmp": "^0.2.7",
+    "uuid": "^11.1.1"
   },
   "devDependencies": {
-    "@tailwindcss/postcss": "^4",
-    "@types/node": "^25",
+    "@tailwindcss/postcss": "^4.3.0",
+    "@types/node": "^25.9.1",
     "@types/pdf-parse": "^1.1.5",
     "@types/pdfkit": "^0.17.6",
-    "@types/react": "^19",
-    "@types/react-dom": "^19",
-    "@vitest/coverage-v8": "^4.1.6",
-    "eslint": "^9",
-    "eslint-config-next": "16.2.6",
+    "@types/react": "^19.2.16",
+    "@types/react-dom": "^19.2.3",
+    "@vitest/coverage-v8": "^4.1.8",
+    "eslint": "^9.39.4",
+    "eslint-config-next": "16.2.7",
     "playwright": "^1.60.0",
     "prettier": "^3.8.3",
-    "tailwindcss": "^4",
-    "tsx": "^4.22.0",
-    "typescript": "^5",
-    "vitest": "^4.1.7"
+    "tailwindcss": "^4.3.0",
+    "tsx": "^4.22.4",
+    "typescript": "^6.0.3",
+    "vitest": "^4.1.8"
   }
 }

scripts/audit-tables.ts

@@ -13,7 +13,12 @@ type Args = {
 };
 
 function parseArgs(): Args {
-  const args: Args = { ownerEmail: process.env.RAG_EVAL_OWNER_EMAIL, allOwners: !process.env.RAG_EVAL_OWNER_EMAIL, limit: 200, failOnMissed: false };
+  const args: Args = {
+    ownerEmail: process.env.RAG_EVAL_OWNER_EMAIL,
+    allOwners: !process.env.RAG_EVAL_OWNER_EMAIL,
+    limit: 200,
+    failOnMissed: false,
+  };
   const tokens = process.argv.slice(2);
   for (let index = 0; index < tokens.length; index += 1) {
     const token = tokens[index];
@@ -85,7 +90,10 @@ async function main() {
   if (imagesResult.error) throw new Error(imagesResult.error.message);
   if (pagesResult.error) throw new Error(pagesResult.error.message);
 
-  const counts = new Map<string, { tables: number; clinicalTables: number; adminTables: number; searchableAdminTables: number; images: number }>();
+  const counts = new Map<
+    string,
+    { tables: number; clinicalTables: number; adminTables: number; searchableAdminTables: number; images: number }
+  >();
   for (const documentId of documentIds) {
     counts.set(documentId, { tables: 0, clinicalTables: 0, adminTables: 0, searchableAdminTables: 0, images: 0 });
   }
@@ -98,7 +106,8 @@ async function main() {
       searchableAdminTables: 0,
       images: 0,
     };
-    const metadata = image.metadata && typeof image.metadata === "object" ? (image.metadata as Record<string, unknown>) : {};
+    const metadata =
+      image.metadata && typeof image.metadata === "object" ? (image.metadata as Record<string, unknown>) : {};
     const useClass = String(
       metadata.clinical_use_class ??
         assessClinicalImageUse({
@@ -153,7 +162,9 @@ async function main() {
       possibleMisses.push(`${document.file_name}: table-like text on pages ${markerPages.slice(0, 8).join(", ")}`);
     }
     if (documentCounts.searchableAdminTables > 0) {
-      searchableAdminIssues.push(`${document.file_name}: searchable admin/reference tables=${documentCounts.searchableAdminTables}`);
+      searchableAdminIssues.push(
+        `${document.file_name}: searchable admin/reference tables=${documentCounts.searchableAdminTables}`,
+      );
     }
     console.log(
       [

scripts/check-indexing.ts

@@ -39,7 +39,9 @@ function hasCurrentMemoryVersion(metadata: unknown, expectedVersion: string) {
 }
 
 function strictEnrichmentVersionRequired() {
-  return process.argv.includes("--strict-enrichment-version") || process.env.RAG_REQUIRE_CURRENT_ENRICHMENT_VERSION === "1";
+  return (
+    process.argv.includes("--strict-enrichment-version") || process.env.RAG_REQUIRE_CURRENT_ENRICHMENT_VERSION === "1"
+  );
 }
 
 async function loadEnrichmentRows(supabase: SupabaseLike, documentIds: string[]) {
@@ -144,7 +146,10 @@ async function main() {
     labelRowsByDocument.set(label.document_id, [...(labelRowsByDocument.get(label.document_id) ?? []), label]);
   }
   for (const section of deepMemoryRows.sections) {
-    sectionRowsByDocument.set(section.document_id, [...(sectionRowsByDocument.get(section.document_id) ?? []), section]);
+    sectionRowsByDocument.set(section.document_id, [
+      ...(sectionRowsByDocument.get(section.document_id) ?? []),
+      section,
+    ]);
   }
   for (const card of deepMemoryRows.memoryCards) {
     memoryRowsByDocument.set(card.document_id, [...(memoryRowsByDocument.get(card.document_id) ?? []), card]);
@@ -173,7 +178,9 @@ async function main() {
   );
   const documentsWithCurrentEnrichmentVersion = indexedDocuments.filter((document) => {
     const summary = summariesByDocument.get(document.id);
-    const generatedLabels = (labelRowsByDocument.get(document.id) ?? []).filter((label) => label.source === "generated");
+    const generatedLabels = (labelRowsByDocument.get(document.id) ?? []).filter(
+      (label) => label.source === "generated",
+    );
     return (
       hasCurrentEnrichmentVersion(document.metadata, ragEnrichmentVersion) &&
       hasCurrentEnrichmentVersion(summary?.metadata, ragEnrichmentVersion) &&
@@ -257,7 +264,8 @@ async function main() {
     issues.push(`indexed documents missing summaries: ${documentsMissingSummaries.length}`);
   if (documentsMissingGeneratedLabels.length > 0)
     issues.push(`indexed documents missing generated labels: ${documentsMissingGeneratedLabels.length}`);
-  if (documentsMissingSections.length > 0) issues.push(`indexed documents missing sections: ${documentsMissingSections.length}`);
+  if (documentsMissingSections.length > 0)
+    issues.push(`indexed documents missing sections: ${documentsMissingSections.length}`);
   if (documentsMissingMemoryCards.length > 0)
     issues.push(`indexed documents missing memory cards: ${documentsMissingMemoryCards.length}`);
   if (requireCurrentEnrichmentVersion && documentsMissingCurrentEnrichmentVersion > 0) {

scripts/enrich-documents.ts

@@ -25,7 +25,8 @@ function parseArgs(argv: string[]): EnrichArgs {
   const args: EnrichArgs = {
     ownerEmail: process.env.RAG_EVAL_OWNER_EMAIL,
     ownerId: process.env.RAG_EVAL_OWNER_ID ?? process.env.LOCAL_NO_AUTH_OWNER_ID,
-    allOwners: !process.env.RAG_EVAL_OWNER_EMAIL && !process.env.RAG_EVAL_OWNER_ID && !process.env.LOCAL_NO_AUTH_OWNER_ID,
+    allOwners:
+      !process.env.RAG_EVAL_OWNER_EMAIL && !process.env.RAG_EVAL_OWNER_ID && !process.env.LOCAL_NO_AUTH_OWNER_ID,
     mode: "summaries-labels-images",
     limit: 25,
     includeCurrent: false,

scripts/eval-search.ts

@@ -221,8 +221,7 @@ async function main() {
 
     if (!args.json) {
       const failureSuffix = result.failures.length ? ` FAIL=${result.failures.join("; ")}` : "";
-      const expectedCoverage =
-        result.expectedFileCount > 1 ? ` allExpectedTop5=${result.expectedAllHitTop5}` : "";
+      const expectedCoverage = result.expectedFileCount > 1 ? ` allExpectedTop5=${result.expectedAllHitTop5}` : "";
       console.log(
         `SEARCH ${result.latencyMs}ms strategy=${result.retrievalStrategy ?? "none"} skippedEmbedding=${result.embeddingSkipped} expectedHit=${result.expectedHitTop3}${expectedCoverage} topScore=${result.topScore.toFixed(3)}${failureSuffix}`,
       );

scripts/import-documents.ts

@@ -160,7 +160,8 @@ async function main() {
     throw new Error("Provide --owner-id, set LOCAL_NO_AUTH_OWNER_ID, or provide --owner-email for a new import batch.");
   }
 
-  const requestedOwnerId = configuredOwnerId ?? (args.ownerEmail ? await findOwnerIdByEmail(supabase, args.ownerEmail) : undefined);
+  const requestedOwnerId =
+    configuredOwnerId ?? (args.ownerEmail ? await findOwnerIdByEmail(supabase, args.ownerEmail) : undefined);
   const batch = await loadOrCreateBatch({
     supabase,
     ownerId: requestedOwnerId,

src/components/AccessibleTable.tsx

@@ -46,7 +46,9 @@ export function AccessibleTable({
     <div className="overflow-x-auto rounded-lg border border-[color:var(--border)] bg-[color:var(--surface)]">
       <table className="min-w-full border-collapse text-left text-sm">
         {caption ? (
-          <caption className={cn("caption-top px-3 py-2 text-left text-xs font-semibold", textMuted)}>{caption}</caption>
+          <caption className={cn("caption-top px-3 py-2 text-left text-xs font-semibold", textMuted)}>
+            {caption}
+          </caption>
         ) : null}
         <thead>
           <tr className="bg-[color:var(--surface-subtle)]">
@@ -66,7 +68,10 @@ export function AccessibleTable({
             return (
               <tr key={`${rowIndex}:${row.join("|")}`} className="border-t border-[color:var(--border)]/70">
                 {row.map((cell, cellIndex) => (
-                  <td key={`${rowIndex}:${cellIndex}`} className="px-3 py-2 align-top leading-5 text-[color:var(--text)]">
+                  <td
+                    key={`${rowIndex}:${cellIndex}`}
+                    className="px-3 py-2 align-top leading-5 text-[color:var(--text)]"
+                  >
                     {cell || <span className={textMuted}>-</span>}
                   </td>
                 ))}

src/components/ClinicalDashboard.tsx

@@ -751,15 +751,21 @@ function SectionHeading({
   );
 }
 
-function relevanceChipLabel(relevance: EvidenceRelevance | SourceEvidenceRelevance | null | undefined, grounded = false) {
+function relevanceChipLabel(
+  relevance: EvidenceRelevance | SourceEvidenceRelevance | null | undefined,
+  grounded = false,
+) {
   if (!relevance) return grounded ? "Source-backed" : "No direct support";
   if (relevance.verdict === "direct") return "Source-backed";
   if (relevance.verdict === "partial") return "Partial support";
   if (relevance.verdict === "nearby") return "Nearby only";
   return "No direct support";
 }
 
-function relevanceChipClasses(relevance: EvidenceRelevance | SourceEvidenceRelevance | null | undefined, grounded = false) {
+function relevanceChipClasses(
+  relevance: EvidenceRelevance | SourceEvidenceRelevance | null | undefined,
+  grounded = false,
+) {
   const verdict = relevance?.verdict ?? (grounded ? "direct" : "none");
   if (verdict === "direct") {
     return "border-[color:var(--success)]/20 bg-[color:var(--success-soft)]/45 text-[color:var(--success)]";
@@ -770,7 +776,10 @@ function relevanceChipClasses(relevance: EvidenceRelevance | SourceEvidenceRelev
   return "border-[color:var(--warning)]/25 bg-[color:var(--warning-soft)]/45 text-[color:var(--warning)]";
 }
 
-function hasStrongRelevanceIcon(relevance: EvidenceRelevance | SourceEvidenceRelevance | null | undefined, grounded = false) {
+function hasStrongRelevanceIcon(
+  relevance: EvidenceRelevance | SourceEvidenceRelevance | null | undefined,
+  grounded = false,
+) {
   const verdict = relevance?.verdict ?? (grounded ? "direct" : "none");
   return verdict === "direct" || verdict === "partial";
 }
@@ -905,7 +914,9 @@ function MasterSearchHeader({
   const trimmedQuery = query.trim();
   const canAsk = trimmedQuery.length >= 1 && !loading && realDataReady;
   const compactMobile = hasAnswer;
-  const selectedDocuments = selectedDocumentIds.map((id) => documents.find((document) => document.id === id)).filter(Boolean);
+  const selectedDocuments = selectedDocumentIds
+    .map((id) => documents.find((document) => document.id === id))
+    .filter(Boolean);
   const scopeSummary = selectedDocumentIds.length === 0 ? "All documents" : `${selectedDocumentIds.length} scoped`;
   const scopePreview = selectedDocuments
     .slice(0, 2)
@@ -1066,9 +1077,7 @@ function MasterSearchHeader({
                       : "text-slate-200 hover:bg-white/10 hover:text-white",
                   )}
                   aria-pressed={active}
-                  aria-label={
-                    item.mode === "answer" ? "Switch to answer mode" : "Switch to document search mode"
-                  }
+                  aria-label={item.mode === "answer" ? "Switch to answer mode" : "Switch to document search mode"}
                 >
                   <Icon className="h-4 w-4" />
                   {item.label}
@@ -1167,7 +1176,9 @@ function MasterSearchHeader({
               <Filter className="h-4 w-4 shrink-0" />
               <span className="shrink-0">Scope & prompts</span>
               <span className="rounded-md bg-white/10 px-2 py-0.5 text-[11px] text-slate-300">{scopeSummary}</span>
-              {scopePreview ? <span className="truncate text-xs font-medium text-slate-400">{scopePreview}</span> : null}
+              {scopePreview ? (
+                <span className="truncate text-xs font-medium text-slate-400">{scopePreview}</span>
+              ) : null}
             </span>
             <span className="inline-flex shrink-0 items-center gap-2 text-xs text-slate-400">
               <span>{documents.length} documents</span>
@@ -1635,7 +1646,9 @@ function EvidenceGapPanel({
           <p className={cn("mt-2 text-[15px] leading-6", textMuted)}>{found}</p>
         </article>
         <article className={cn(sourceCard, "p-3")}>
-          <p className="text-xs font-bold uppercase tracking-[0.08em] text-[color:var(--text-soft)]">What was not found</p>
+          <p className="text-xs font-bold uppercase tracking-[0.08em] text-[color:var(--text-soft)]">
+            What was not found
+          </p>
           <p className={cn("mt-2 text-[15px] leading-6", textMuted)}>{missing}</p>
         </article>
         <article className={cn(sourceCard, "p-3 md:col-span-2")}>
@@ -1803,7 +1816,9 @@ function ClinicalOutputPanel({
         icon={ListChecks}
         title="Clinical action view"
         description="Structured from retrieved answer text, exact quotes, citations, and extracted tables."
-        action={<CopyButton label="Copy clinical draft" shortLabel="Draft" copied={copiedWardNote} onClick={onCopyWardNote} />}
+        action={
+          <CopyButton label="Copy clinical draft" shortLabel="Draft" copied={copiedWardNote} onClick={onCopyWardNote} />
+        }
         hideDescriptionOnMobile
         compactMobile
       />
@@ -1823,11 +1838,7 @@ function ClinicalOutputPanel({
           >
             <div className="flex items-start gap-2">
               <span className={cn(iconTilePremium, "h-8 w-8")}>
-                {section.id === "verify-source" ? (
-                  <Target className="h-4 w-4" />
-                ) : (
-                  <CheckCircle2 className="h-4 w-4" />
-                )}
+                {section.id === "verify-source" ? <Target className="h-4 w-4" /> : <CheckCircle2 className="h-4 w-4" />}
               </span>
               <div className="min-w-0">
                 <h3 className="text-sm font-semibold text-[color:var(--text)]">{section.title}</h3>
@@ -4037,7 +4048,9 @@ export function ClinicalDashboard() {
                     <AnswerHeaderActions
                       bestSource={bestSource}
                       grounded={
-                        answer.grounded && answer.confidence !== "unsupported" && currentRelevance?.isSourceBacked !== false
+                        answer.grounded &&
+                        answer.confidence !== "unsupported" &&
+                        currentRelevance?.isSourceBacked !== false
                       }
                       relevance={currentRelevance}
                     />
@@ -4098,7 +4111,9 @@ export function ClinicalDashboard() {
                             <FileText className="h-4 w-4" />
                           </span>
                           <span className="min-w-0">
-                            <span className="block text-sm font-semibold text-[color:var(--text)]">Source narrative</span>
+                            <span className="block text-sm font-semibold text-[color:var(--text)]">
+                              Source narrative
+                            </span>
                             <span className={cn("block truncate text-xs", textMuted)}>
                               Full source-linked answer text and section citations
                             </span>
@@ -4117,7 +4132,9 @@ export function ClinicalDashboard() {
                   <VerificationActionStrip
                     source={bestSource}
                     grounded={
-                      answer.grounded && answer.confidence !== "unsupported" && currentRelevance?.isSourceBacked !== false
+                      answer.grounded &&
+                      answer.confidence !== "unsupported" &&
+                      currentRelevance?.isSourceBacked !== false
                     }
                     citationCount={answer.citations.length}
                     quoteCount={answer.quoteCards?.length ?? 0}
@@ -4177,7 +4194,9 @@ export function ClinicalDashboard() {
               onScopeDocument={scopeOnlyDocument}
             />
           )}
-          {searchMode === "answer" && answer && <VisualEvidenceStrip evidence={visualEvidence} collapsed={weakEvidence} />}
+          {searchMode === "answer" && answer && (
+            <VisualEvidenceStrip evidence={visualEvidence} collapsed={weakEvidence} />
+          )}
           {searchMode === "answer" && answer && (
             <RelatedDocumentsPanel documents={relatedDocuments} onScopeDocument={scopeOnlyDocument} />
           )}