diff --git a/apps/web/app/api/workspace/suggest-files/route.ts b/apps/web/app/api/workspace/suggest-files/route.ts
index 8a39e029299..793a29d8eb9 100644
--- a/apps/web/app/api/workspace/suggest-files/route.ts
+++ b/apps/web/app/api/workspace/suggest-files/route.ts
@@ -37,7 +37,6 @@ const SKIP_DIRS = new Set([
 function listDir(
 	absDir: string,
 	filter?: string,
-	workspaceRoot?: string,
 ): SuggestItem[] {
 	let entries: Dirent[];
 	try {
@@ -47,13 +46,8 @@ function listDir(
 	}
 
 	const lowerFilter = filter?.toLowerCase();
-	const hideRootIdentity =
-		typeof workspaceRoot === "string" &&
-		resolve(absDir) === resolve(workspaceRoot);
-
 	const sorted = entries
 		.filter((e) => !e.name.startsWith("."))
-		.filter((e) => !(hideRootIdentity && e.name === "IDENTITY.md"))
 		.filter((e) => !(e.isDirectory() && SKIP_DIRS.has(e.name)))
 		.filter((e) => !lowerFilter || e.name.toLowerCase().includes(lowerFilter))
 		.toSorted((a, b) => {
@@ -90,7 +84,6 @@ function searchFiles(
 	query: string,
 	results: SuggestItem[],
 	maxResults: number,
-	workspaceRoot: string,
 	depth = 0,
 ): void {
 	if (depth > 6 || results.length >= maxResults) {return;}
@@ -103,12 +96,9 @@ function searchFiles(
 	}
 
 	const lowerQuery = query.toLowerCase();
-	const hideRootIdentity = resolve(absDir) === resolve(workspaceRoot);
-
 	for (const entry of entries) {
 		if (results.length >= maxResults) {return;}
 		if (entry.name.startsWith(".")) {continue;}
-		if (hideRootIdentity && entry.name === "IDENTITY.md") {continue;}
 		if (entry.isDirectory() && SKIP_DIRS.has(entry.name)) {continue;}
 
 		const absPath = join(absDir, entry.name);
@@ -131,7 +121,7 @@ function searchFiles(
 		}
 
 		if (entry.isDirectory()) {
-			searchFiles(absPath, query, results, maxResults, workspaceRoot, depth + 1);
+			searchFiles(absPath, query, results, maxResults, depth + 1);
 		}
 	}
 }
@@ -404,7 +394,7 @@ export async function GET(req: Request) {
 	if (searchQuery) {
 		// File search: workspace only (skip expensive home dir traversal)
 		const fileResults: SuggestItem[] = [];
-		searchFiles(workspaceRoot, searchQuery, fileResults, 15, workspaceRoot);
+		searchFiles(workspaceRoot, searchQuery, fileResults, 15);
 
 		// DuckDB search: objects and entries (sequential to avoid lock contention)
 		const objectResults = await searchObjects(searchQuery, workspaceRoot, 10);
@@ -426,15 +416,15 @@ export async function GET(req: Request) {
 		const resolved = resolvePath(pathQuery, workspaceRoot);
 		if (!resolved) {
 			const results: SuggestItem[] = [];
-			searchFiles(workspaceRoot, pathQuery, results, 20, workspaceRoot);
+			searchFiles(workspaceRoot, pathQuery, results, 20);
 			return Response.json({ items: results });
 		}
-		const items = listDir(resolved.dir, resolved.filter, workspaceRoot);
+		const items = listDir(resolved.dir, resolved.filter);
 		return Response.json({ items });
 	}
 
 	// Default: list workspace root + all objects
-	const fileItems = listDir(workspaceRoot, undefined, workspaceRoot);
+	const fileItems = listDir(workspaceRoot);
 	const objectItems = await searchObjects("", workspaceRoot, 20);
 	// Deduplicate: if an object also appears as a folder, keep the object version
 	const objectNames = new Set(objectItems.map((o) => o.name));
diff --git a/apps/web/app/api/workspace/tree/route.ts b/apps/web/app/api/workspace/tree/route.ts
index 3f0d640e984..414247ccb61 100644
--- a/apps/web/app/api/workspace/tree/route.ts
+++ b/apps/web/app/api/workspace/tree/route.ts
@@ -115,9 +115,6 @@ function buildTree(
   for (const entry of sorted) {
     // .object.yaml is consumed for metadata; only show it as a visible node when revealing hidden files
     if (entry.name === ".object.yaml" && !showHidden) {continue;}
-    // Keep the root identity system file out of the workspace sidebar tree.
-    if (!relativeBase && entry.name === "IDENTITY.md") {continue;}
-
     const absPath = join(absDir, entry.name);
     const relPath = relativeBase
       ? `${relativeBase}/${entry.name}`
@@ -203,7 +200,7 @@ function buildSkillsVirtualFolder(): TreeNode | null {
       const entries = readdirSync(dir, { withFileTypes: true });
       for (const entry of entries) {
         if (!entry.isDirectory() || seen.has(entry.name)) {continue;}
-        if (entry.name === "dench") {continue;}
+        if (entry.name === "crm" || entry.name === "browser") {continue;}
         const skillMdPath = join(dir, entry.name, "SKILL.md");
         if (!existsSync(skillMdPath)) {continue;}
 
diff --git a/apps/web/app/components/workspace/create-workspace-dialog.tsx b/apps/web/app/components/workspace/create-workspace-dialog.tsx
index e8f61ae32e5..ac19aa1a75a 100644
--- a/apps/web/app/components/workspace/create-workspace-dialog.tsx
+++ b/apps/web/app/components/workspace/create-workspace-dialog.tsx
@@ -204,7 +204,7 @@ export function CreateWorkspaceDialog({ isOpen, onClose, onCreated }: CreateWork
               </div>
 
               {/* Bootstrap toggle */}
-              <label className="flex items-center gap-2 cursor-pointer">
+              <label className="flex items-center gap-2 cursor-pointer hidden">
                 <input
                   type="checkbox"
                   checked={seedBootstrap}
diff --git a/apps/web/app/components/workspace/file-manager-tree.tsx b/apps/web/app/components/workspace/file-manager-tree.tsx
index b5b68385d63..a01694d0dc5 100644
--- a/apps/web/app/components/workspace/file-manager-tree.tsx
+++ b/apps/web/app/components/workspace/file-manager-tree.tsx
@@ -71,7 +71,6 @@ const ALWAYS_SYSTEM_PATTERNS = [
 const ROOT_ONLY_SYSTEM_PATTERNS = [
   /^workspace\.duckdb/,
   /^workspace_context\.yaml$/,
-  /^IDENTITY\.md$/,
 ];
 
 function isSystemFile(path: string): boolean {
diff --git a/apps/web/app/components/workspace/workspace-sidebar.tsx b/apps/web/app/components/workspace/workspace-sidebar.tsx
index 37d1bf17c5e..552d1384951 100644
--- a/apps/web/app/components/workspace/workspace-sidebar.tsx
+++ b/apps/web/app/components/workspace/workspace-sidebar.tsx
@@ -1,6 +1,6 @@
 "use client";
 
-import { useEffect, useState, useRef, useCallback, useMemo } from "react";
+import { useEffect, useState, useRef, useCallback } from "react";
 import { FileManagerTree, type TreeNode } from "./file-manager-tree";
 import { ProfileSwitcher } from "./profile-switcher";
 import { CreateWorkspaceDialog } from "./create-workspace-dialog";
@@ -389,27 +389,6 @@ function dirDisplayName(dir: string): string {
 	return dir.split("/").pop() || dir;
 }
 
-function filterSidebarTree(nodes: TreeNode[]): TreeNode[] {
-	const filtered: TreeNode[] = [];
-	for (const node of nodes) {
-		// Root identity file is system-managed and hidden in Ironclaw UI.
-		if (node.path === "IDENTITY.md") {
-			continue;
-		}
-		// Dench is an always-on managed skill; hide it from the sidebar list.
-		if (node.path === "~skills/dench/SKILL.md") {
-			continue;
-		}
-
-		const children = node.children ? filterSidebarTree(node.children) : undefined;
-		if (node.path === "~skills" && (!children || children.length === 0)) {
-			continue;
-		}
-		filtered.push(children ? { ...node, children } : node);
-	}
-	return filtered;
-}
-
 export function WorkspaceSidebar({
 	tree,
 	activePath,
@@ -436,7 +415,6 @@ export function WorkspaceSidebar({
 }: WorkspaceSidebarProps) {
 	const isBrowsing = browseDir != null;
 	const width = mobile ? "280px" : (widthProp ?? 260);
-	const visibleTree = useMemo(() => filterSidebarTree(tree), [tree]);
 	const [createWorkspaceOpen, setCreateWorkspaceOpen] = useState(false);
 
 	const sidebar = (
@@ -594,7 +572,7 @@ export function WorkspaceSidebar({
 					</div>
 				) : (
 			<FileManagerTree
-				tree={visibleTree}
+				tree={tree}
 				activePath={activePath}
 				onSelect={onSelect}
 				onRefresh={onRefresh}