Pivot to text-first column-stack workspace + merge-with-review across AI artifacts

Workspace
- Pivot from "set of open panes" to a Finder-style miller column stack:
  TopBar / LeftSidebar / [section → entity → entity ...] / pinned text editor.
  openPanesStore is now an ordered Column[] with pushFrom / closeFrom /
  setStack; only one top-level section is rooted at a time.
- New entity column panes: Term, Block, Association, Constraint,
  Requirement, Finding. Click-through navigation truncates deeper
  columns automatically.
- LeftSidebar surfaces a pending-count chip per section (single-glance
  navigation cue) and spins its analyze ↻ via SVG Spinner whenever the
  LLM is working — including server-initiated runs caught by the runs
  poll, not just user-triggered ones.

Analyze pipeline + persistence
- Unified `concepts` pass (taxonomy + glossary in one LLM call) replaces
  the two-pass setup. Server still accepts ?section=taxonomy|glossary
  and normalizes them for back-compat.
- model / requirements / detection (assumptions, risks, inconsistencies)
  + cross-layer validation rules (X1–X4: stale term link, unlinked
  formalism, undefined linked term, prose-only term).
- Persistence: NarrativeDocument, ModelSnapshot, ChangelogEntry,
  TaxonomyTerm, RequirementEntry, Finding, AnalysisRun. Re-runs MERGE
  instead of replace: gentle update on existing items, suggested on new,
  deprecated on missing — same idiom for every artifact kind. User pins
  preserve "kept" decisions across re-analyses.
- Migrations: pivot_text_first, add_requirement_linked_term,
  term_review_state, review_state_for_reqs_and_findings,
  add_term_definition_pinned.

Concept ↔ ontology integration
- linkedTermId on Block / Association / Constraint / Requirement.
  PromoteToolbar lets the user formalize a concept inline: + Block /
  + Association / + Constraint / + Requirement, all routed through
  applyOps so undo/redo and SSE work for free.
- decideElement op for in-canvas keep/discard on review-pending model
  elements.

User-authored definitions
- TermColumn definition is click-to-edit. Save (Cmd-Enter / blur),
  Cancel (Esc), Reset to AI suggestion when pinned.
- definitionPinned flag on TaxonomyTerm: future Analyze runs leave the
  user's text alone. setTermDefinition repo function + POST
  /api/projects/[id]/terms/[termId]/definition endpoint.
- mergeTaxonomySuggestion + applyGlossaryDefinitions both pin-aware.

UX/UI
- StatusChip: single component for all state idioms (suggested,
  deprecated, accepted, dismissed, resolved, severity, validation code,
  confidence, warn). Replaces 5+ ad-hoc badge classes.
- PaneControls (PaneViewTabs + PaneFilterChip): separates view-mode
  toggles from filter chips so toggling Pending no longer flips you off
  the current view.
- PaneEmpty: unified empty-state with title + hint + action.
- PaneDrawer: collapsible groups for Pending / Discarded review; cards
  group as Kept (top) → Pending (bottom drawer) → Discarded (Findings
  only, hidden when empty). Restore action recovers dismissed/resolved
  findings.
- ConceptCard unifies Tree and A–Z views in Concepts; only Tree parents
  carry the chevron (no empty placeholder offset).
- Type + spacing tokens (--text-xs..xl, --space-1..6, --lh-tight/ui/
  prose, --radius-*) replace every ad-hoc value.
- Buttons standardized to body sans 500 (was a mishmash of mono / display).
- Card shells unified across Concepts / Requirements / Findings.

Cleanup
- Removed: LeftRail, FindingsPanel, IssuesPanel, SocratesDock,
  ProposalCard, SlashMenu, SlashExtension, slashSuggestion,
  CanvasHeader, TaxonomyPane, GlossaryPane, TermDetail (popover; now
  TermColumn).
- Section ids in openPanesStore: dropped taxonomy/glossary, added
  concepts. localStorage migration runs on hydrate.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

apps/web/app/api/projects/[projectId]/findings/route.ts

@@ -1,27 +1,51 @@
-// GET  /api/projects/[id]/findings — returns the project's open findings
-// POST /api/projects/[id]/findings — runs detection, persists, returns the new set
+// GET  /api/projects/[id]/findings — returns the project's currently visible
+//                                     findings (suggested + accepted + deprecated)
+// POST /api/projects/[id]/findings — runs detection, MERGES (no wipe), returns
+//                                     the new set. Suggestions and deprecations
+//                                     await user keep/discard via the
+//                                     /findings/[findingId]/decision endpoint.
 
 import { NextResponse } from "next/server";
-import { loadProject, listOpenFindings, replaceFindings } from "../../../../../lib/db/repo";
+import {
+  loadProject,
+  listVisibleFindings,
+  listDiscardedFindings,
+  mergeFindingsSuggestion,
+} from "../../../../../lib/db/repo";
 import { detectFindings } from "../../../../../lib/llm/detect";
 
-export async function GET(_req: Request, { params }: { params: Promise<{ projectId: string }> }) {
+function toApi(f: Awaited<ReturnType<typeof listVisibleFindings>>[number]) {
+  return {
+    id: f.id,
+    kind: f.kind,
+    text: f.text,
+    linkedElementIds: f.linkedElementIds,
+    confidence: f.confidence,
+    severity: f.severity,
+    validationCode: f.validationCode,
+    status: f.status,
+    pinned: f.pinned,
+    modelVersion: f.modelVersion,
+    provider: f.provider,
+    llmModel: f.llmModel,
+  };
+}
+
+export async function GET(req: Request, { params }: { params: Promise<{ projectId: string }> }) {
   const { projectId } = await params;
-  const findings = await listOpenFindings(projectId);
-  return NextResponse.json({
-    findings: findings.map(f => ({
-      id: f.id,
-      kind: f.kind,
-      text: f.text,
-      linkedElementIds: f.linkedElementIds,
-      confidence: f.confidence,
-      severity: f.severity,
-      validationCode: f.validationCode,
-      modelVersion: f.modelVersion,
-      provider: f.provider,
-      llmModel: f.llmModel,
-    })),
-  });
+  // ?include=all merges in dismissed + resolved so the FindingsPane Discarded
+  // drawer can render them. Default stays visible-only for back-compat.
+  const url = new URL(req.url);
+  const include = (url.searchParams.get("include") ?? "").toLowerCase();
+  if (include === "all") {
+    const [visible, discarded] = await Promise.all([
+      listVisibleFindings(projectId),
+      listDiscardedFindings(projectId),
+    ]);
+    return NextResponse.json({ findings: [...visible, ...discarded].map(toApi) });
+  }
+  const findings = await listVisibleFindings(projectId);
+  return NextResponse.json({ findings: findings.map(toApi) });
 }
 
 export async function POST(_req: Request, { params }: { params: Promise<{ projectId: string }> }) {
@@ -29,21 +53,16 @@ export async function POST(_req: Request, { params }: { params: Promise<{ projec
   try {
     const { model, version } = await loadProject(projectId);
     const result = await detectFindings(model);
-    const stored = await replaceFindings(projectId, result.findings, version, result.provider, result.model);
+    const stored = await mergeFindingsSuggestion(
+      projectId,
+      result.findings,
+      version,
+      result.provider,
+      result.model
+    );
 
     return NextResponse.json({
-      findings: stored.map(f => ({
-        id: f.id,
-        kind: f.kind,
-        text: f.text,
-        linkedElementIds: f.linkedElementIds,
-        confidence: f.confidence,
-        severity: f.severity,
-        validationCode: f.validationCode,
-        modelVersion: f.modelVersion,
-        provider: f.provider,
-        llmModel: f.llmModel,
-      })),
+      findings: stored.map(toApi),
       meta: {
         provider: result.provider,
         model: result.model,