diff --git a/scripts/generate_prism_css.ts b/scripts/generate_prism_css.ts
index d95ea9366..9ac077d33 100755
--- a/scripts/generate_prism_css.ts
+++ b/scripts/generate_prism_css.ts
@@ -25,8 +25,8 @@ for (const [key, value] of Object.entries(vscDarkPlus as Record<string, unknown>
 }
 
 // Convert CSS properties object to CSS string
-function cssPropertiesToString(props: CSSProperties): string {
-  return Object.entries(props)
+function cssPropertiesToString(props: CSSProperties, selector: string): string {
+  const entries = Object.entries(props)
     .filter(([key]) => {
       // Skip font-family and font-size - we want to inherit these
       return key !== "fontFamily" && key !== "fontSize";
@@ -35,8 +35,14 @@ function cssPropertiesToString(props: CSSProperties): string {
       // Convert camelCase to kebab-case
       const cssKey = key.replace(/([A-Z])/g, "-$1").toLowerCase();
       return `  ${cssKey}: ${value};`;
-    })
-    .join("\n");
+    });
+
+  // Add background: transparent to pre/code elements to prevent double backgrounds
+  if (selector.startsWith("pre") || selector.startsWith("code")) {
+    entries.push("  background: transparent;");
+  }
+
+  return entries.join("\n");
 }
 
 // Generate CSS content
@@ -55,7 +61,7 @@ function generateCSS(): string {
   ];
 
   for (const [selector, props] of Object.entries(syntaxStyleNoBackgrounds)) {
-    const cssRules = cssPropertiesToString(props);
+    const cssRules = cssPropertiesToString(props, selector);
     if (cssRules.trim().length > 0) {
       // Handle selectors that need .token prefix
       let cssSelector = selector;
diff --git a/src/components/Messages/AssistantMessage.tsx b/src/components/Messages/AssistantMessage.tsx
index 831f382de..8e3f9af0d 100644
--- a/src/components/Messages/AssistantMessage.tsx
+++ b/src/components/Messages/AssistantMessage.tsx
@@ -21,7 +21,7 @@ const RawContent = styled.pre`
   word-break: break-word;
   margin: 0;
   padding: 8px;
-  background: rgba(0, 0, 0, 0.2);
+  background: var(--color-code-bg);
   border-radius: 3px;
 `;
 
diff --git a/src/components/Messages/MarkdownComponents.tsx b/src/components/Messages/MarkdownComponents.tsx
index e38ab9490..af5079bd2 100644
--- a/src/components/Messages/MarkdownComponents.tsx
+++ b/src/components/Messages/MarkdownComponents.tsx
@@ -38,7 +38,7 @@ export const markdownComponents = {
         padding: "0.25em 0.5em",
         border: "1px solid rgba(255, 255, 255, 0.1)",
         borderRadius: "4px",
-        background: "rgba(0, 0, 0, 0.2)",
+        background: "var(--color-code-bg)",
       }}
     >
       {children}
diff --git a/src/components/Messages/Mermaid.tsx b/src/components/Messages/Mermaid.tsx
index 7b418eb57..39ffc2d19 100644
--- a/src/components/Messages/Mermaid.tsx
+++ b/src/components/Messages/Mermaid.tsx
@@ -165,7 +165,7 @@ export const Mermaid: React.FC<{ chart: string }> = ({ chart }) => {
         <div
           style={{
             color: "var(--color-text-secondary)",
-            background: "rgba(0, 0, 0, 0.2)",
+            background: "var(--color-code-bg)",
             padding: "12px",
             fontStyle: "italic",
           }}
@@ -189,7 +189,7 @@ export const Mermaid: React.FC<{ chart: string }> = ({ chart }) => {
         style={{
           position: "relative",
           margin: "1em 0",
-          background: "rgba(0, 0, 0, 0.2)",
+          background: "var(--color-code-bg)",
           borderRadius: "4px",
           padding: "16px",
         }}
@@ -243,7 +243,7 @@ export const Mermaid: React.FC<{ chart: string }> = ({ chart }) => {
             ref={modalContainerRef}
             className="mermaid-container mermaid-modal"
             style={{
-              background: "rgba(0, 0, 0, 0.2)",
+              background: "var(--color-code-bg)",
               padding: "24px",
               borderRadius: "8px",
               minWidth: "80vw",
diff --git a/src/components/RightSidebar/CodeReview/FileTree.tsx b/src/components/RightSidebar/CodeReview/FileTree.tsx
index 89f07f03c..bec1c2435 100644
--- a/src/components/RightSidebar/CodeReview/FileTree.tsx
+++ b/src/components/RightSidebar/CodeReview/FileTree.tsx
@@ -2,9 +2,11 @@
  * FileTree - Displays file hierarchy with diff statistics
  */
 
-import React, { useState } from "react";
+import React from "react";
 import styled from "@emotion/styled";
 import type { FileTreeNode } from "@/utils/git/numstatParser";
+import { usePersistedState } from "@/hooks/usePersistedState";
+import { getFileTreeExpandStateKey } from "@/constants/storage";
 
 const TreeContainer = styled.div`
   flex: 1;
@@ -194,8 +196,30 @@ const TreeNodeContent: React.FC<{
   onSelectFile: (path: string | null) => void;
   commonPrefix: string | null;
   getFileReadStatus?: (filePath: string) => { total: number; read: number } | null;
-}> = ({ node, depth, selectedPath, onSelectFile, commonPrefix, getFileReadStatus }) => {
-  const [isOpen, setIsOpen] = useState(depth < 2); // Auto-expand first 2 levels
+  expandStateMap: Record<string, boolean>;
+  setExpandStateMap: (
+    value: Record<string, boolean> | ((prev: Record<string, boolean>) => Record<string, boolean>)
+  ) => void;
+}> = ({
+  node,
+  depth,
+  selectedPath,
+  onSelectFile,
+  commonPrefix,
+  getFileReadStatus,
+  expandStateMap,
+  setExpandStateMap,
+}) => {
+  // Check if user has manually set expand state for this directory
+  const hasManualState = node.path in expandStateMap;
+  const isOpen = hasManualState ? expandStateMap[node.path] : depth < 2; // Default: auto-expand first 2 levels
+
+  const setIsOpen = (open: boolean) => {
+    setExpandStateMap((prev) => ({
+      ...prev,
+      [node.path]: open,
+    }));
+  };
 
   const handleClick = (e: React.MouseEvent) => {
     if (node.isDirectory) {
@@ -295,6 +319,8 @@ const TreeNodeContent: React.FC<{
             onSelectFile={onSelectFile}
             commonPrefix={commonPrefix}
             getFileReadStatus={getFileReadStatus}
+            expandStateMap={expandStateMap}
+            setExpandStateMap={setExpandStateMap}
           />
         ))}
     </>
@@ -308,6 +334,7 @@ interface FileTreeExternalProps {
   isLoading?: boolean;
   commonPrefix?: string | null;
   getFileReadStatus?: (filePath: string) => { total: number; read: number } | null;
+  workspaceId: string;
 }
 
 export const FileTree: React.FC<FileTreeExternalProps> = ({
@@ -317,7 +344,15 @@ export const FileTree: React.FC<FileTreeExternalProps> = ({
   isLoading = false,
   commonPrefix = null,
   getFileReadStatus,
+  workspaceId,
 }) => {
+  // Use persisted state for expand/collapse per workspace (lifted to parent to avoid O(n) re-renders)
+  const [expandStateMap, setExpandStateMap] = usePersistedState<Record<string, boolean>>(
+    getFileTreeExpandStateKey(workspaceId),
+    {},
+    { listener: true }
+  );
+
   // Find the node at the common prefix path to start rendering from
   const startNode = React.useMemo(() => {
     if (!commonPrefix || !root) return root;
@@ -355,6 +390,8 @@ export const FileTree: React.FC<FileTreeExternalProps> = ({
               onSelectFile={onSelectFile}
               commonPrefix={commonPrefix}
               getFileReadStatus={getFileReadStatus}
+              expandStateMap={expandStateMap}
+              setExpandStateMap={setExpandStateMap}
             />
           ))
         ) : (
diff --git a/src/components/RightSidebar/CodeReview/HunkViewer.tsx b/src/components/RightSidebar/CodeReview/HunkViewer.tsx
index d1f1c6774..85e48b59c 100644
--- a/src/components/RightSidebar/CodeReview/HunkViewer.tsx
+++ b/src/components/RightSidebar/CodeReview/HunkViewer.tsx
@@ -107,7 +107,7 @@ const HunkContent = styled.div`
   font-size: 11px;
   line-height: 1.4;
   overflow-x: auto;
-  background: rgba(0, 0, 0, 0.2);
+  background: var(--color-code-bg);
 
   /* CSS Grid ensures all diff lines span the same width (width of longest line) */
   display: grid;
diff --git a/src/components/RightSidebar/CodeReview/ReviewPanel.tsx b/src/components/RightSidebar/CodeReview/ReviewPanel.tsx
index d02bb2f0e..01c62a578 100644
--- a/src/components/RightSidebar/CodeReview/ReviewPanel.tsx
+++ b/src/components/RightSidebar/CodeReview/ReviewPanel.tsx
@@ -735,6 +735,7 @@ export const ReviewPanel: React.FC<ReviewPanelProps> = ({
                 isLoading={isLoadingTree}
                 commonPrefix={commonPrefix}
                 getFileReadStatus={getFileReadStatus}
+                workspaceId={workspaceId}
               />
             </FileTreeSection>
           )}
diff --git a/src/components/shared/DiffRenderer.tsx b/src/components/shared/DiffRenderer.tsx
index db5e89a1f..9f7e0134f 100644
--- a/src/components/shared/DiffRenderer.tsx
+++ b/src/components/shared/DiffRenderer.tsx
@@ -111,7 +111,7 @@ export const DiffIndicator = styled.span<{ type: DiffLineType }>`
 export const DiffContainer = styled.div<{ fontSize?: string; maxHeight?: string }>`
   margin: 0;
   padding: 6px 0;
-  background: rgba(0, 0, 0, 0.2);
+  background: var(--color-code-bg);
   border-radius: 3px;
   font-size: ${({ fontSize }) => fontSize ?? "12px"};
   line-height: 1.4;
diff --git a/src/components/tools/BashToolCall.tsx b/src/components/tools/BashToolCall.tsx
index 265b2c26d..901d0235f 100644
--- a/src/components/tools/BashToolCall.tsx
+++ b/src/components/tools/BashToolCall.tsx
@@ -30,7 +30,7 @@ const ScriptPreview = styled.span`
 const OutputBlock = styled.pre`
   margin: 0;
   padding: 6px 8px;
-  background: rgba(0, 0, 0, 0.2);
+  background: var(--color-code-bg);
   border-radius: 3px;
   border-left: 2px solid #4caf50;
   font-size: 11px;
diff --git a/src/components/tools/FileReadToolCall.tsx b/src/components/tools/FileReadToolCall.tsx
index 53be4ce1e..3e3a99cde 100644
--- a/src/components/tools/FileReadToolCall.tsx
+++ b/src/components/tools/FileReadToolCall.tsx
@@ -35,7 +35,7 @@ const MetadataText = styled.span`
 const ContentBlock = styled.div`
   margin: 0;
   padding: 6px 8px;
-  background: rgba(0, 0, 0, 0.2);
+  background: var(--color-code-bg);
   border-radius: 3px;
   font-size: 11px;
   line-height: 1.4;
@@ -79,7 +79,7 @@ const FileInfoRow = styled.div`
   flex-wrap: wrap;
   gap: 16px;
   padding: 6px 8px;
-  background: rgba(0, 0, 0, 0.2);
+  background: var(--color-code-bg);
   border-radius: 3px;
   font-size: 11px;
   line-height: 1.4;
diff --git a/src/components/tools/ProposePlanToolCall.tsx b/src/components/tools/ProposePlanToolCall.tsx
index 57b3fc89a..c2eb6082f 100644
--- a/src/components/tools/ProposePlanToolCall.tsx
+++ b/src/components/tools/ProposePlanToolCall.tsx
@@ -96,7 +96,7 @@ const RawContent = styled.pre`
   word-break: break-word;
   margin: 0;
   padding: 8px;
-  background: rgba(0, 0, 0, 0.2);
+  background: var(--color-code-bg);
   border-radius: 3px;
 `;
 
diff --git a/src/components/tools/shared/ToolPrimitives.tsx b/src/components/tools/shared/ToolPrimitives.tsx
index bea2793ea..deda8d39d 100644
--- a/src/components/tools/shared/ToolPrimitives.tsx
+++ b/src/components/tools/shared/ToolPrimitives.tsx
@@ -95,7 +95,7 @@ export const DetailLabel = styled.div`
 export const DetailContent = styled.pre`
   margin: 0;
   padding: 6px 8px;
-  background: rgba(0, 0, 0, 0.2);
+  background: var(--color-code-bg);
   border-radius: 3px;
   font-size: 11px;
   line-height: 1.4;
diff --git a/src/constants/storage.ts b/src/constants/storage.ts
index 7873f7eb7..2173f6b22 100644
--- a/src/constants/storage.ts
+++ b/src/constants/storage.ts
@@ -93,6 +93,15 @@ export function getReviewExpandStateKey(workspaceId: string): string {
   return `reviewExpandState:${workspaceId}`;
 }
 
+/**
+ * Get the localStorage key for FileTree expand/collapse state in Review tab
+ * Stores directory expand/collapse preferences per workspace
+ * Format: "fileTreeExpandState:{workspaceId}"
+ */
+export function getFileTreeExpandStateKey(workspaceId: string): string {
+  return `fileTreeExpandState:${workspaceId}`;
+}
+
 /**
  * List of workspace-scoped key functions that should be copied on fork and deleted on removal
  * Note: Excludes ephemeral keys like getCompactContinueMessageKey
@@ -105,6 +114,7 @@ const PERSISTENT_WORKSPACE_KEY_FUNCTIONS: Array<(workspaceId: string) => string>
   getAutoRetryKey,
   getRetryStateKey,
   getReviewExpandStateKey,
+  getFileTreeExpandStateKey,
 ];
 
 /**
@@ -117,7 +127,7 @@ const EPHEMERAL_WORKSPACE_KEY_FUNCTIONS: Array<(workspaceId: string) => string>
 
 /**
  * Copy all workspace-specific localStorage keys from source to destination workspace
- * This includes: model, input, mode, thinking level, auto-retry, retry state, review expand state
+ * This includes: model, input, mode, thinking level, auto-retry, retry state, review expand state, file tree expand state
  */
 export function copyWorkspaceStorage(sourceWorkspaceId: string, destWorkspaceId: string): void {
   for (const getKey of PERSISTENT_WORKSPACE_KEY_FUNCTIONS) {
diff --git a/src/styles/colors.tsx b/src/styles/colors.tsx
index 5e45bdfba..2951f8cff 100644
--- a/src/styles/colors.tsx
+++ b/src/styles/colors.tsx
@@ -67,6 +67,11 @@ export const GlobalColors = () => (
         --color-text: hsl(0 0% 83%);
         --color-text-secondary: hsl(0 0% 42%);
 
+        /* Code Block Background */
+        --color-code-bg: hsl(
+          0deg 6.43% 8.04%
+        ); /* Slightly darker than main background for code/diff containers */
+
         /* Button Colors */
         --color-button-bg: hsl(0 0% 24%);
         --color-button-text: hsl(0 0% 80%);
diff --git a/src/styles/prism-syntax.css b/src/styles/prism-syntax.css
index ee31f9fbe..a0ebbf57d 100644
--- a/src/styles/prism-syntax.css
+++ b/src/styles/prism-syntax.css
@@ -25,8 +25,9 @@ pre[class*="language-"] {
   ms-hyphens: none;
   hyphens: none;
   padding: 1em;
-  margin: .5em 0;
+  margin: 0.5em 0;
   overflow: auto;
+  background: transparent;
 }
 
 code[class*="language-"] {
@@ -64,17 +65,17 @@ code[class*="language-"] *::selection {
 }
 
 :not(pre) > code[class*="language-"] {
-  padding: .1em .3em;
-  border-radius: .3em;
+  padding: 0.1em 0.3em;
+  border-radius: 0.3em;
   color: #db4c69;
 }
 
 .namespace {
-  -opacity: .7;
+  -opacity: 0.7;
 }
 
 doctype.doctype-tag {
-  color: #569CD6;
+  color: #569cd6;
 }
 
 doctype.name {
@@ -170,7 +171,7 @@ doctype.name {
 }
 
 operator.arrow {
-  color: #569CD6;
+  color: #569cd6;
 }
 
 .token.atrule {
@@ -194,7 +195,7 @@ atrule.url.punctuation {
 }
 
 .token.keyword {
-  color: #569CD6;
+  color: #569cd6;
 }
 
 keyword.module {