fix(rag): close audit gaps in the in-house engine

An adversarial audit of the piragi -> in-house swap surfaced nine confirmed
issues; this fixes all of them.

- Re-ingest now REPLACES a source's chunks instead of appending. Add
  VectorStore.delete_by_source and BaseIndexPlugin.replace_on_reingest (default
  True), called before add_chunks in both ingest paths. Without it every
  startup / periodic / manual reindex appended a fresh copy of each doc's
  chunks, growing the tables unbounded and crowding out distinct results.
  Conversations opt OUT (replace_on_reingest=False): their many messages share
  one source URI, so delete-by-source would wipe history.
- index_* now honor the plugin IngestResult. The explicit record endpoints
  (error / standard / decision / review / learning) raise on failure instead of
  writing a green tracking row for content that never persisted;
  conversation / journal indexing stays best-effort but skips the tracking row
  when the embed fails. index_message / index_entry return IngestResult.
- A deprecated index type (code) now returns 404 instead of a 500 leaked from
  _get_plugin's missing-plugin error: add OptimalService.is_index_registered
  and guard the stats / clear / refresh routes. The panel drops the dead 'Code'
  category, filter, badge, label, and mock data.
- Panel: getContext reads 'results' (matches SearchResponse) instead of a
  non-existent 'context' field; the reindex toast no longer reports phantom
  '0 code files'; the stats 'Updated' label uses the max timestamp across
  indexes rather than indexes[0]; ProactiveContextItem matches the wire shape.
- Drop the always-zero per-document chunk_count from the documents API.
- Remove dead RAG settings (hybrid_search, cross_encoder) the engine never
  consumed, and correct stale piragi / BM25 references in code, README, and
  CLAUDE.md. Delete the unused duplicate roboco/kb embedder package the swap
  shipped.

Adds tests for replace-on-reingest (incl. the conversations carve-out) and the
deprecated-index 404.

panel/src/components/knowledge-base/kb-category-nav.tsx

@@ -1,15 +1,10 @@
 "use client";
 
 import { KBIndexType, KBStats } from "@/types";
-import { Code, FileText, MessageSquare, BookOpen, ChevronRight, AlertTriangle, Scale, GitBranch, ClipboardCheck, Lightbulb } from "lucide-react";
+import { FileText, MessageSquare, BookOpen, ChevronRight, AlertTriangle, Scale, GitBranch, ClipboardCheck, Lightbulb } from "lucide-react";
 import { Skeleton } from "@/components/ui/skeleton";
 
 const categoryConfig: Record<KBIndexType, { label: string; description: string; icon: React.ReactNode }> = {
-  [KBIndexType.CODE]: {
-    label: "Code",
-    description: "Source code, functions, and classes",
-    icon: <Code className="h-5 w-5 text-purple-500" />,
-  },
   [KBIndexType.DOCUMENTATION]: {
     label: "Documentation",
     description: "READMEs, guides, and API docs",

panel/src/components/knowledge-base/kb-filters.tsx

@@ -2,10 +2,9 @@
 
 import { KBIndexType } from "@/types";
 import { Checkbox } from "@/components/ui/checkbox";
-import { Code, FileText, MessageSquare, BookOpen, AlertTriangle, Scale, GitBranch, ClipboardCheck, Lightbulb } from "lucide-react";
+import { FileText, MessageSquare, BookOpen, AlertTriangle, Scale, GitBranch, ClipboardCheck, Lightbulb } from "lucide-react";
 
 const indexTypeConfig: Record<KBIndexType, { label: string; icon: React.ReactNode }> = {
-  [KBIndexType.CODE]: { label: "Code", icon: <Code className="h-4 w-4 text-purple-500" /> },
   [KBIndexType.DOCUMENTATION]: { label: "Documentation", icon: <FileText className="h-4 w-4 text-blue-500" /> },
   [KBIndexType.CONVERSATIONS]: { label: "Conversations", icon: <MessageSquare className="h-4 w-4 text-green-500" /> },
   [KBIndexType.JOURNALS]: { label: "Journals", icon: <BookOpen className="h-4 w-4 text-orange-500" /> },

panel/src/components/knowledge-base/kb-index-type-badge.tsx

@@ -2,14 +2,9 @@
 
 import { Badge } from "@/components/ui/badge";
 import { KBIndexType } from "@/types";
-import { Code, FileText, MessageSquare, BookOpen, AlertTriangle, Scale, GitBranch, ClipboardCheck, Lightbulb } from "lucide-react";
+import { FileText, MessageSquare, BookOpen, AlertTriangle, Scale, GitBranch, ClipboardCheck, Lightbulb } from "lucide-react";
 
 const indexTypeConfig: Record<KBIndexType, { label: string; color: string; icon: React.ReactNode }> = {
-  [KBIndexType.CODE]: {
-    label: "Code",
-    color: "bg-purple-100 text-purple-700 dark:bg-purple-900 dark:text-purple-300",
-    icon: <Code className="h-3 w-3" />,
-  },
   [KBIndexType.DOCUMENTATION]: {
     label: "Docs",
     color: "bg-blue-100 text-blue-700 dark:bg-blue-900 dark:text-blue-300",

panel/src/components/knowledge-base/kb-stats-card.tsx

@@ -3,11 +3,10 @@
 import { Card, CardContent, CardHeader, CardTitle } from "@/components/ui/card";
 import { Skeleton } from "@/components/ui/skeleton";
 import { KBStats, KBIndexType } from "@/types";
-import { Database, Code, FileText, MessageSquare, BookOpen, AlertTriangle, Scale, GitBranch, ClipboardCheck, Lightbulb } from "lucide-react";
+import { Database, FileText, MessageSquare, BookOpen, AlertTriangle, Scale, GitBranch, ClipboardCheck, Lightbulb } from "lucide-react";
 import { formatDistanceToNow } from "date-fns";
 
 const indexIcons: Record<KBIndexType, React.ReactNode> = {
-  [KBIndexType.CODE]: <Code className="h-4 w-4 text-purple-500" />,
   [KBIndexType.DOCUMENTATION]: <FileText className="h-4 w-4 text-blue-500" />,
   [KBIndexType.CONVERSATIONS]: <MessageSquare className="h-4 w-4 text-green-500" />,
   [KBIndexType.JOURNALS]: <BookOpen className="h-4 w-4 text-orange-500" />,
@@ -19,7 +18,6 @@ const indexIcons: Record<KBIndexType, React.ReactNode> = {
 };
 
 const indexLabels: Record<KBIndexType, string> = {
-  [KBIndexType.CODE]: "Code",
   [KBIndexType.DOCUMENTATION]: "Docs",
   [KBIndexType.CONVERSATIONS]: "Convos",
   [KBIndexType.JOURNALS]: "Journals",
@@ -73,6 +71,12 @@ export function KBStatsCard({ stats, isLoading }: KBStatsCardProps) {
     );
   }
 
+  const latestUpdated = stats.indexes.reduce<string | null>(
+    (acc, idx) =>
+      idx.last_updated && (!acc || idx.last_updated > acc) ? idx.last_updated : acc,
+    null,
+  );
+
   return (
     <Card>
       <CardHeader className="pb-2">
@@ -104,9 +108,9 @@ export function KBStatsCard({ stats, isLoading }: KBStatsCardProps) {
             <span>{stats.total_chunks.toLocaleString()}</span>
           </div>
         </div>
-        {stats.indexes[0]?.last_updated && (
+        {latestUpdated && (
           <p className="text-xs text-muted-foreground pt-1">
-            Updated {formatDistanceToNow(new Date(stats.indexes[0].last_updated))} ago
+            Updated {formatDistanceToNow(new Date(latestUpdated))} ago
           </p>
         )}
       </CardContent>

panel/src/components/knowledge-base/knowledge-base-browser.tsx

@@ -64,7 +64,6 @@ import { KBCategoryView } from "./kb-category-view";
 type TabValue = "search" | "ask" | "mentor" | "browse" | "admin";
 
 const INDEX_LABELS: Record<KBIndexType, string> = {
-  [KBIndexType.CODE]: "Codebase",
   [KBIndexType.DOCUMENTATION]: "Documentation",
   [KBIndexType.CONVERSATIONS]: "Conversations",
   [KBIndexType.JOURNALS]: "Agent Journals",
@@ -77,7 +76,6 @@ const INDEX_LABELS: Record<KBIndexType, string> = {
 
 // Valid KB index types for URL param validation
 const VALID_INDEX_TYPES: KBIndexType[] = [
-  KBIndexType.CODE,
   KBIndexType.DOCUMENTATION,
   KBIndexType.CONVERSATIONS,
   KBIndexType.JOURNALS,
@@ -207,12 +205,11 @@ function KnowledgeBaseBrowserContent() {
       const result = await reindexAll.mutateAsync({ force: true });
       // Show detailed results if available
       if (result.overall_success) {
-        const codeCount = result.code?.successful ?? 0;
         const docsCount = result.documentation?.successful ?? 0;
-        toast.success(
-          `Reindexed ${codeCount} code files, ${docsCount} docs. ` +
-            `${result.warnings?.length ? `Warnings: ${result.warnings.length}` : ""}`
-        );
+        const warns = result.warnings?.length
+          ? ` Warnings: ${result.warnings.length}`
+          : "";
+        toast.success(`Reindexed ${docsCount} docs.${warns}`);
       } else {
         toast.warning(
           `Reindex completed with issues: ${result.warnings?.join(", ") ?? "Unknown errors"}`