diff --git a/src/command/render/defaults.ts b/src/command/render/defaults.ts
index e6ef78d8d16..2cd97b7fcf5 100644
--- a/src/command/render/defaults.ts
+++ b/src/command/render/defaults.ts
@@ -39,9 +39,12 @@ export async function generateDefaults(
   let allDefaults: FormatPandoc | undefined;
 
   if (options.format.pandoc) {
-    allDefaults = (options.format.pandoc
-      ? ld.cloneDeep(options.format.pandoc)
-      : {}) as FormatPandoc;
+    allDefaults = {
+      ...(options.format.pandoc || {}),
+      variables: {
+        ...(options.format.pandoc?.variables || {}),
+      },
+    } as FormatPandoc;
 
     // resolve filters
     const resolvedFilters = await resolveFilters(
diff --git a/src/command/render/filters.ts b/src/command/render/filters.ts
index 5e5eec61c9e..20fd5e97649 100644
--- a/src/command/render/filters.ts
+++ b/src/command/render/filters.ts
@@ -713,6 +713,7 @@ function initFilterParams(dependenciesFile: string) {
 const kQuartoFilterMarker = "quarto";
 const kQuartoCiteProcMarker = "citeproc";
 
+// NB: this mutates `pandoc.citeproc`
 export async function resolveFilters(
   filters: QuartoFilter[],
   options: PandocOptions,
diff --git a/src/command/render/flags.ts b/src/command/render/flags.ts
index a2fa17bfcc7..10be31e5b33 100644
--- a/src/command/render/flags.ts
+++ b/src/command/render/flags.ts
@@ -27,8 +27,6 @@ import {
 import { isQuartoMetadata } from "../../config/metadata.ts";
 import { RenderFlags, RenderOptions } from "./types.ts";
 
-import * as ld from "../../core/lodash.ts";
-
 import { isAbsolute, SEP_PATTERN } from "../../deno_ral/path.ts";
 import { normalizePath } from "../../core/path.ts";
 import { removeFlags } from "../../core/flags.ts";
@@ -471,7 +469,12 @@ export function removePandocToArg(args: string[]) {
 }
 
 export function removePandocTo(renderOptions: RenderOptions) {
-  renderOptions = ld.cloneDeep(renderOptions);
+  renderOptions = {
+    ...renderOptions,
+    flags: {
+      ...(renderOptions.flags || {}),
+    },
+  } as RenderOptions;
   delete renderOptions.flags?.to;
   if (renderOptions.pandocArgs) {
     renderOptions.pandocArgs = removePandocToArg(renderOptions.pandocArgs);
diff --git a/src/command/render/freeze.ts b/src/command/render/freeze.ts
index 240de38cd30..2db57afedda 100644
--- a/src/command/render/freeze.ts
+++ b/src/command/render/freeze.ts
@@ -20,8 +20,6 @@ import {
   LF,
 } from "../../deno_ral/fs.ts";
 
-import { cloneDeep } from "../../core/lodash.ts";
-
 import { inputFilesDir } from "../../core/render.ts";
 import { TempContext } from "../../core/temp.ts";
 import { md5HashSync } from "../../core/hash.ts";
@@ -55,13 +53,15 @@ export function freezeExecuteResult(
   result: ExecuteResult,
 ) {
   // resolve includes within executeResult
-  result = cloneDeep(result) as ExecuteResult;
+  const innerResult = {
+    ...result,
+  } as ExecuteResult;
   const resolveIncludes = (
     name: "include-in-header" | "include-before-body" | "include-after-body",
   ) => {
-    if (result.includes) {
-      if (result.includes[name]) {
-        result.includes[name] = result.includes[name]!.map((file) =>
+    if (innerResult.includes) {
+      if (innerResult.includes[name]) {
+        innerResult.includes[name] = innerResult.includes[name]!.map((file) =>
           // Storing file content using LF line ending
           format(Deno.readTextFileSync(file), LF)
         );
@@ -73,7 +73,7 @@ export function freezeExecuteResult(
   resolveIncludes(kIncludeAfterBody);
 
   // make the supporting dirs relative to the input file dir
-  result.supporting = result.supporting.map((file) => {
+  innerResult.supporting = innerResult.supporting.map((file) => {
     if (isAbsolute(file)) {
       return relative(normalizePath(dirname(input)), file);
     } else {
@@ -88,7 +88,7 @@ export function freezeExecuteResult(
   const freezeJsonFile = freezeResultFile(input, output, true);
   Deno.writeTextFileSync(
     freezeJsonFile,
-    JSON.stringify({ hash, result }, undefined, 2),
+    JSON.stringify({ hash, result: innerResult }, undefined, 2),
   );
 
   // return the file
diff --git a/src/command/render/pandoc.ts b/src/command/render/pandoc.ts
index 0a8973c0068..a6b6abd3e2a 100644
--- a/src/command/render/pandoc.ts
+++ b/src/command/render/pandoc.ts
@@ -391,9 +391,12 @@ export async function runPandoc(
   // save args and metadata so we can print them (we may subsequently edit them)
   const printArgs = [...args];
   let printMetadata = {
-    ...ld.cloneDeep(options.format.metadata),
+    ...options.format.metadata,
+    crossref: {
+      ...(options.format.metadata.crossref || {}),
+    },
     ...options.flags?.metadata,
-  };
+  } as Metadata;
 
   // remove some metadata that are used as parameters to our lua filters
   const cleanMetadataForPrinting = (metadata: Metadata) => {
@@ -691,7 +694,7 @@ export async function runPandoc(
         ),
         ...extras.metadataOverride || {},
       };
-      printMetadata = mergeConfigs(extras.metadata, printMetadata);
+      printMetadata = mergeConfigs(extras.metadata || {}, printMetadata);
       cleanMetadataForPrinting(printMetadata);
     }
 
@@ -820,7 +823,9 @@ export async function runPandoc(
     }
 
     // more cleanup
-    options.format.metadata = cleanupPandocMetadata(options.format.metadata);
+    options.format.metadata = cleanupPandocMetadata({
+      ...options.format.metadata,
+    });
     printMetadata = cleanupPandocMetadata(printMetadata);
 
     if (extras[kIncludeInHeader]) {
@@ -1370,13 +1375,12 @@ export async function runPandoc(
   }
 }
 
+// this mutates metadata[kClassOption]
 function cleanupPandocMetadata(metadata: Metadata) {
-  const cleaned = ld.cloneDeep(metadata);
-
   // pdf classoption can end up with duplicaed options
-  const classoption = cleaned[kClassOption];
+  const classoption = metadata[kClassOption];
   if (Array.isArray(classoption)) {
-    cleaned[kClassOption] = ld.uniqBy(
+    metadata[kClassOption] = ld.uniqBy(
       classoption.reverse(),
       (option: string) => {
         return option.replace(/=.+$/, "");
@@ -1384,7 +1388,7 @@ function cleanupPandocMetadata(metadata: Metadata) {
     ).reverse();
   }
 
-  return cleaned;
+  return metadata;
 }
 
 async function resolveExtras(
@@ -1687,7 +1691,10 @@ function resolveTextHighlightStyle(
   extras: FormatExtras,
   pandoc: FormatPandoc,
 ): FormatExtras {
-  extras = ld.cloneDeep(extras);
+  extras = {
+    ...extras,
+    pandoc: extras.pandoc ? { ...extras.pandoc } : {},
+  } as FormatExtras;
 
   // Get the user selected theme or choose a default
   const highlightTheme = pandoc[kHighlightStyle] || kDefaultHighlightStyle;
diff --git a/src/command/render/project.ts b/src/command/render/project.ts
index 77050f6e2ea..5ce9f59b96e 100644
--- a/src/command/render/project.ts
+++ b/src/command/render/project.ts
@@ -144,7 +144,7 @@ const computeProjectRenderConfig = async (
 
   // force execution for any incremental files (unless options.useFreezer is set)
   let alwaysExecuteFiles = incremental && !inputs.options.useFreezer
-    ? ld.cloneDeep(inputs.files) as string[]
+    ? [...(inputs.files!)]
     : undefined;
 
   // file normaliation
diff --git a/src/core/jupyter/display-data.ts b/src/core/jupyter/display-data.ts
index 97210e71eb3..53296ca3d19 100644
--- a/src/core/jupyter/display-data.ts
+++ b/src/core/jupyter/display-data.ts
@@ -123,8 +123,13 @@ export function displayDataWithMarkdownMath(output: JupyterOutputDisplayData) {
   if (Array.isArray(output.data[kTextLatex]) && !output.data[kTextMarkdown]) {
     const latex = output.data[kTextLatex] as string[];
     if (displayDataLatexIsMath(latex)) {
-      output = ld.cloneDeep(output);
-      output.data[kTextMarkdown] = output.data[kTextLatex];
+      output = {
+        ...output,
+        data: {
+          ...output.data,
+          [kTextMarkdown]: latex,
+        },
+      };
       return output;
     }
   }
diff --git a/src/core/jupyter/jupyter.ts b/src/core/jupyter/jupyter.ts
index 30b4316d014..eb34f0a6f39 100644
--- a/src/core/jupyter/jupyter.ts
+++ b/src/core/jupyter/jupyter.ts
@@ -963,7 +963,9 @@ export function mdFromContentCell(
   const contentCellEnvelope = createCellEnvelope(["cell", "markdown"], options);
 
   // clone source for manipulation
-  const source = ld.cloneDeep(cell.source) as string[];
+  const source = typeof cell.source === "string"
+    ? [cell.source]
+    : [...cell.source];
 
   // handle user expressions (if any)
   if (options && source) {
@@ -1461,7 +1463,9 @@ async function mdFromCodeCell(
       }
     }
     md.push("}\n");
-    let source = ld.cloneDeep(cell.source);
+    let source = typeof cell.source === "string"
+      ? [cell.source]
+      : [...cell.source];
     if (fenced) {
       const optionsSource = cell.optionsSource.filter((line) =>
         line.search(/\|\s+echo:\s+fenced\s*$/) === -1
diff --git a/src/execute/jupyter/jupyter.ts b/src/execute/jupyter/jupyter.ts
index 5bc03c342e1..5bf2e81d15b 100644
--- a/src/execute/jupyter/jupyter.ts
+++ b/src/execute/jupyter/jupyter.ts
@@ -243,7 +243,15 @@ export const jupyterEngine: ExecutionEngine = {
       isServerShinyPython(format, kJupyterEngine) &&
       format.render[kKeepHidden] !== true
     ) {
-      format = ld.cloneDeep(format);
+      format = {
+        ...format,
+        render: {
+          ...format.render,
+        },
+        metadata: {
+          ...format.metadata,
+        },
+      };
       format.render[kKeepHidden] = true;
       format.metadata[kRemoveHidden] = "all";
     }
diff --git a/src/execute/ojs/compile.ts b/src/execute/ojs/compile.ts
index 17303e7d9c3..cc33bc02b39 100644
--- a/src/execute/ojs/compile.ts
+++ b/src/execute/ojs/compile.ts
@@ -892,7 +892,9 @@ export async function ojsExecuteResult(
   executeResult: MappedExecuteResult,
   ojsBlockLineNumbers: number[],
 ) {
-  executeResult = ld.cloneDeep(executeResult);
+  executeResult = {
+    ...executeResult,
+  };
 
   // evaluate ojs chunks
   const { markdown, includes, filters, resourceFiles } = await ojsCompile({
diff --git a/src/project/types/website/listing/website-listing-template.ts b/src/project/types/website/listing/website-listing-template.ts
index 335deeaaa06..4d4136a618a 100644
--- a/src/project/types/website/listing/website-listing-template.ts
+++ b/src/project/types/website/listing/website-listing-template.ts
@@ -318,7 +318,9 @@ export function reshapeListing(
   listing: Listing,
   format: Format,
 ): ReshapedListing {
-  const reshaped = cloneDeep(listing) as Listing;
+  const reshaped = {
+    ...listing,
+  } as Listing;
 
   // Add template utilities
   const utilities = {} as Record<string, unknown>;
diff --git a/src/publish/config.ts b/src/publish/config.ts
index 4033ae111a0..be1a3489052 100644
--- a/src/publish/config.ts
+++ b/src/publish/config.ts
@@ -8,8 +8,6 @@ import { warning } from "../deno_ral/log.ts";
 import { stringify } from "../core/yaml.ts";
 import { basename, dirname, join } from "../deno_ral/path.ts";
 
-import * as ld from "../core/lodash.ts";
-
 import { Metadata } from "../config/types.ts";
 import { readYaml, readYamlFromString } from "../core/yaml.ts";
 import { ProjectContext } from "../project/types.ts";
@@ -69,7 +67,9 @@ export function writePublishDeployment(
   publish: PublishRecord,
 ) {
   // don't write 'code' field if false
-  publish = ld.cloneDeep(publish) as PublishRecord;
+  publish = {
+    ...publish,
+  } as PublishRecord;
   if (publish.code === false) {
     delete (publish as Record<string, unknown>).code;
   }