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]/analyze/route.ts

@@ -0,0 +1,33 @@
+// Analyze endpoint. POST with optional ?section= to run one section, or no
+// query param (or ?section=all) to run the full pipeline.
+//
+// Legacy section names "taxonomy" and "glossary" are accepted and mapped to
+// the unified "concepts" pass (T3 of the integration plan). This keeps older
+// clients and any external scripts working through one release.
+
+import { NextResponse } from "next/server";
+import { runAnalyze, type RunSection } from "../../../../../lib/llm/analyze/runAll";
+import { normalizeAnalysisSection } from "../../../../../lib/db/repo";
+
+interface RouteContext {
+  params: Promise<{ projectId: string }>;
+}
+
+export async function POST(req: Request, ctx: RouteContext) {
+  const { projectId } = await ctx.params;
+  const url = new URL(req.url);
+  const sectionRaw = (url.searchParams.get("section") ?? "all").toLowerCase();
+  let section: RunSection;
+  try {
+    section = normalizeAnalysisSection(sectionRaw) as RunSection;
+  } catch {
+    return NextResponse.json({ error: `Invalid section: ${sectionRaw}` }, { status: 400 });
+  }
+  try {
+    const result = await runAnalyze(projectId, section);
+    return NextResponse.json(result);
+  } catch (err) {
+    console.error("[analyze] route failed:", err);
+    return NextResponse.json({ error: (err as Error).message }, { status: 500 });
+  }
+}

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

@@ -0,0 +1,31 @@
+// Narrative document save endpoint. The TipTap editor PUTs the current
+// ProseMirror JSON here on debounce. Source of truth after the pivot.
+
+import { NextResponse } from "next/server";
+import { loadDocument, saveDocument } from "../../../../../lib/db/repo";
+
+interface RouteContext {
+  params: Promise<{ projectId: string }>;
+}
+
+export async function GET(_req: Request, ctx: RouteContext) {
+  const { projectId } = await ctx.params;
+  const doc = await loadDocument(projectId);
+  if (!doc) return NextResponse.json({ doc: null, version: 0 });
+  return NextResponse.json({ doc: doc.doc, version: doc.version, updatedAt: doc.updatedAt });
+}
+
+export async function PUT(req: Request, ctx: RouteContext) {
+  const { projectId } = await ctx.params;
+  let body: unknown;
+  try {
+    body = await req.json();
+  } catch {
+    return NextResponse.json({ error: "Invalid JSON" }, { status: 400 });
+  }
+  if (!body || typeof body !== "object" || !("doc" in body)) {
+    return NextResponse.json({ error: "Missing `doc` field" }, { status: 400 });
+  }
+  const stored = await saveDocument(projectId, (body as { doc: unknown }).doc);
+  return NextResponse.json({ version: stored.version, updatedAt: stored.updatedAt });
+}

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

@@ -0,0 +1,51 @@
+// Per-finding keep/discard/resolve/restore decision.
+//
+// Body: { decision: "keep" | "discard" | "resolve" | "restore" }
+//   keep    → status="accepted" (visible). If was "deprecated", also pinned.
+//   discard → status="dismissed". Persists; future detections skip it.
+//   resolve → status="resolved". Like discard but signals "I fixed it."
+//   restore → status="accepted", pinned cleared. Recovers a dismissed/
+//             resolved finding from the Discarded drawer.
+
+import { NextResponse } from "next/server";
+import {
+  setFindingDecision,
+  restoreFinding,
+  type FindingDecision,
+} from "../../../../../../../lib/db/repo";
+
+interface RouteContext {
+  params: Promise<{ projectId: string; findingId: string }>;
+}
+
+export async function POST(req: Request, ctx: RouteContext) {
+  const { findingId } = await ctx.params;
+  let body: { decision?: string };
+  try {
+    body = await req.json();
+  } catch {
+    return NextResponse.json({ error: "invalid json body" }, { status: 400 });
+  }
+  const decision = body.decision;
+  if (
+    decision !== "keep" &&
+    decision !== "discard" &&
+    decision !== "resolve" &&
+    decision !== "restore"
+  ) {
+    return NextResponse.json(
+      { error: "decision must be 'keep', 'discard', 'resolve', or 'restore'" },
+      { status: 400 }
+    );
+  }
+  try {
+    const finding =
+      decision === "restore"
+        ? await restoreFinding(findingId)
+        : await setFindingDecision(findingId, decision as FindingDecision);
+    return NextResponse.json({ finding });
+  } catch (err) {
+    console.error("[finding/decision] failed:", err);
+    return NextResponse.json({ error: (err as Error).message }, { status: 500 });
+  }
+}

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

@@ -0,0 +1,81 @@
+// Per-finding contextual Socrates thread.
+// GET → loads existing messages.
+// POST → sends a user turn; if the thread is empty, primes it with the
+//        finding text so Socrates' opening turn engages with the finding.
+
+import { NextResponse } from "next/server";
+import { prisma } from "../../../../../../../lib/db/client";
+import { loadProject } from "../../../../../../../lib/db/repo";
+import { validate } from "../../../../../../../lib/sysml/validate";
+import {
+  getOrCreateAnchoredThread,
+  listAnchoredThreadMessages,
+  sendUserTurn,
+} from "../../../../../../../lib/llm/socrates";
+
+interface RouteContext {
+  params: Promise<{ projectId: string; findingId: string }>;
+}
+
+export async function GET(_req: Request, ctx: RouteContext) {
+  const { projectId, findingId } = await ctx.params;
+  const finding = await prisma.finding.findUnique({ where: { id: findingId } });
+  if (!finding || finding.projectId !== projectId) {
+    return NextResponse.json({ error: "finding not found" }, { status: 404 });
+  }
+  const threadId = await getOrCreateAnchoredThread(projectId, `finding:${findingId}`, finding.text);
+  const messages = await listAnchoredThreadMessages(threadId);
+  return NextResponse.json({ threadId, finding: { id: finding.id, text: finding.text, kind: finding.kind }, messages });
+}
+
+export async function POST(req: Request, ctx: RouteContext) {
+  const { projectId, findingId } = await ctx.params;
+  let body: { text?: string } = {};
+  try {
+    body = await req.json();
+  } catch {
+    return NextResponse.json({ error: "Invalid JSON" }, { status: 400 });
+  }
+
+  const finding = await prisma.finding.findUnique({ where: { id: findingId } });
+  if (!finding || finding.projectId !== projectId) {
+    return NextResponse.json({ error: "finding not found" }, { status: 404 });
+  }
+
+  const threadId = await getOrCreateAnchoredThread(projectId, `finding:${findingId}`, finding.text);
+
+  // If the thread is empty, prime with the finding text as the opening user
+  // turn so Socrates engages with the right thing.
+  const existing = await listAnchoredThreadMessages(threadId);
+  let userText = (body.text ?? "").trim();
+  if (existing.length === 0 && !userText) {
+    userText = `Discuss this ${finding.kind}: "${finding.text}"`;
+  }
+
+  const { model } = await loadProject(projectId);
+  const issues = validate(model);
+
+  const result = await sendUserTurn({ threadId, model, issues, userText });
+  return NextResponse.json({ threadId, ...result });
+}
+
+export async function PATCH(req: Request, ctx: RouteContext) {
+  // Resolve / dismiss the finding from the contextual thread.
+  const { projectId, findingId } = await ctx.params;
+  let body: { status?: string } = {};
+  try {
+    body = await req.json();
+  } catch {
+    return NextResponse.json({ error: "Invalid JSON" }, { status: 400 });
+  }
+  const status = body.status;
+  if (status !== "resolved" && status !== "dismissed" && status !== "open") {
+    return NextResponse.json({ error: "invalid status" }, { status: 400 });
+  }
+  const finding = await prisma.finding.findUnique({ where: { id: findingId } });
+  if (!finding || finding.projectId !== projectId) {
+    return NextResponse.json({ error: "finding not found" }, { status: 404 });
+  }
+  await prisma.finding.update({ where: { id: findingId }, data: { status } });
+  return NextResponse.json({ ok: true, status });
+}

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,

apps/web/app/api/projects/[projectId]/requirements/[reqId]/decision/route.ts

@@ -0,0 +1,35 @@
+// Per-requirement keep/discard decision. Mirrors the term decision endpoint
+// (see /api/projects/[id]/terms/[termId]/decision).
+//
+// Body: { decision: "keep" | "discard" }
+
+import { NextResponse } from "next/server";
+import { setRequirementDecision, type RequirementDecision } from "../../../../../../../lib/db/repo";
+
+interface RouteContext {
+  params: Promise<{ projectId: string; reqId: string }>;
+}
+
+export async function POST(req: Request, ctx: RouteContext) {
+  const { reqId } = await ctx.params;
+  let body: { decision?: string };
+  try {
+    body = await req.json();
+  } catch {
+    return NextResponse.json({ error: "invalid json body" }, { status: 400 });
+  }
+  const decision = body.decision;
+  if (decision !== "keep" && decision !== "discard") {
+    return NextResponse.json(
+      { error: "decision must be 'keep' or 'discard'" },
+      { status: 400 }
+    );
+  }
+  try {
+    const requirement = await setRequirementDecision(reqId, decision as RequirementDecision);
+    return NextResponse.json({ requirement });
+  } catch (err) {
+    console.error("[requirement/decision] failed:", err);
+    return NextResponse.json({ error: (err as Error).message }, { status: 500 });
+  }
+}

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

@@ -0,0 +1,12 @@
+import { NextResponse } from "next/server";
+import { listRequirements } from "../../../../../lib/db/repo";
+
+interface RouteContext {
+  params: Promise<{ projectId: string }>;
+}
+
+export async function GET(_req: Request, ctx: RouteContext) {
+  const { projectId } = await ctx.params;
+  const reqs = await listRequirements(projectId);
+  return NextResponse.json({ requirements: reqs });
+}

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

@@ -0,0 +1,12 @@
+import { NextResponse } from "next/server";
+import { listLatestAnalysisRuns } from "../../../../../lib/db/repo";
+
+interface RouteContext {
+  params: Promise<{ projectId: string }>;
+}
+
+export async function GET(_req: Request, ctx: RouteContext) {
+  const { projectId } = await ctx.params;
+  const runs = await listLatestAnalysisRuns(projectId);
+  return NextResponse.json({ runs });
+}

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

@@ -0,0 +1,12 @@
+import { NextResponse } from "next/server";
+import { listTerms } from "../../../../../lib/db/repo";
+
+interface RouteContext {
+  params: Promise<{ projectId: string }>;
+}
+
+export async function GET(_req: Request, ctx: RouteContext) {
+  const { projectId } = await ctx.params;
+  const terms = await listTerms(projectId);
+  return NextResponse.json({ terms });
+}

apps/web/app/api/projects/[projectId]/term-link/route.ts

@@ -0,0 +1,20 @@
+import { NextResponse } from "next/server";
+import { linkTermToBlock } from "../../../../../lib/db/repo";
+
+interface RouteContext {
+  params: Promise<{ projectId: string }>;
+}
+
+export async function POST(req: Request, _ctx: RouteContext) {
+  let body: { termId?: string; blockId?: string | null } = {};
+  try {
+    body = await req.json();
+  } catch {
+    return NextResponse.json({ error: "Invalid JSON" }, { status: 400 });
+  }
+  if (!body.termId) {
+    return NextResponse.json({ error: "Missing termId" }, { status: 400 });
+  }
+  await linkTermToBlock(body.termId, body.blockId ?? null);
+  return NextResponse.json({ ok: true });
+}

apps/web/app/api/projects/[projectId]/terms/[termId]/decision/route.ts

@@ -0,0 +1,39 @@
+// Per-term keep/discard decision. Drives the merge-with-review flow:
+// `mergeTaxonomySuggestion` marks pending changes; this endpoint confirms or
+// rejects them.
+//
+// Body: { decision: "keep" | "discard" }
+//   keep    → status="accepted"; if previously "deprecated", also pinned=true
+//             so the next merge doesn't re-deprecate it.
+//   discard → row deleted.
+
+import { NextResponse } from "next/server";
+import { setTermDecision, type TermDecision } from "../../../../../../../lib/db/repo";
+
+interface RouteContext {
+  params: Promise<{ projectId: string; termId: string }>;
+}
+
+export async function POST(req: Request, ctx: RouteContext) {
+  const { termId } = await ctx.params;
+  let body: { decision?: string };
+  try {
+    body = await req.json();
+  } catch {
+    return NextResponse.json({ error: "invalid json body" }, { status: 400 });
+  }
+  const decision = body.decision;
+  if (decision !== "keep" && decision !== "discard") {
+    return NextResponse.json(
+      { error: "decision must be 'keep' or 'discard'" },
+      { status: 400 }
+    );
+  }
+  try {
+    const term = await setTermDecision(termId, decision as TermDecision);
+    return NextResponse.json({ term });
+  } catch (err) {
+    console.error("[term/decision] failed:", err);
+    return NextResponse.json({ error: (err as Error).message }, { status: 500 });
+  }
+}

apps/web/app/api/projects/[projectId]/terms/[termId]/definition/route.ts

@@ -0,0 +1,35 @@
+// User-authored definition for a concept term.
+//
+// Body: { definition: string | null }
+//   non-empty trimmed → set definition + pin (future Analyze leaves it alone)
+//   empty / null      → clear definition + clear pin ("Reset to AI suggestion")
+
+import { NextResponse } from "next/server";
+import { setTermDefinition } from "../../../../../../../lib/db/repo";
+
+interface RouteContext {
+  params: Promise<{ projectId: string; termId: string }>;
+}
+
+export async function POST(req: Request, ctx: RouteContext) {
+  const { termId } = await ctx.params;
+  let body: { definition?: string | null };
+  try {
+    body = await req.json();
+  } catch {
+    return NextResponse.json({ error: "invalid json body" }, { status: 400 });
+  }
+  if (body.definition !== null && typeof body.definition !== "string" && typeof body.definition !== "undefined") {
+    return NextResponse.json(
+      { error: "definition must be a string or null" },
+      { status: 400 }
+    );
+  }
+  try {
+    const term = await setTermDefinition(termId, body.definition ?? null);
+    return NextResponse.json({ term });
+  } catch (err) {
+    console.error("[term/definition] failed:", err);
+    return NextResponse.json({ error: (err as Error).message }, { status: 500 });
+  }
+}