diff --git a/news/changelog-1.6.md b/news/changelog-1.6.md
index cf8faec07f3..2f06dfc868e 100644
--- a/news/changelog-1.6.md
+++ b/news/changelog-1.6.md
@@ -91,6 +91,7 @@ All changes included in 1.6:
 
 ## Projects
 
+- ([#7988](https://github.com/quarto-dev/quarto-cli/issues/7988)): Do not allow `lib-dir` to cause an accidental cleanup of the project directory when its value points to a parent of the project directory.
 - ([#10125](https://github.com/quarto-dev/quarto-cli/issues/10125)): Show path to the project when project YAML validation fails.
 - ([#10268](https://github.com/quarto-dev/quarto-cli/issues/10268)): `quarto create` supports opening project in Positron, in addition to VS Code and RStudio IDE.
 - ([#10285](https://github.com/quarto-dev/quarto-cli/issues/10285)): Include text from before the first chapter sections in search indices. In addition, include text of every element with `.quarto-include-in-search-index` class in search indices.
diff --git a/src/command/render/cleanup.ts b/src/command/render/cleanup.ts
index f7667345a0c..d2fdc1c8547 100644
--- a/src/command/render/cleanup.ts
+++ b/src/command/render/cleanup.ts
@@ -4,7 +4,7 @@
  * Copyright (C) 2020-2022 Posit Software, PBC
  */
 
-import { existsSync } from "../../deno_ral/fs.ts";
+import { existsSync, safeRemoveDirSync } from "../../deno_ral/fs.ts";
 import { dirname, extname, isAbsolute, join } from "../../deno_ral/path.ts";
 
 import * as ld from "../../core/lodash.ts";
@@ -22,11 +22,13 @@ import { isHtmlFileOutput, isLatexOutput } from "../../config/format.ts";
 import { kKeepMd, kKeepTex, kKeepTyp } from "../../config/constants.ts";
 
 import { filesDirLibDir, filesDirMediabagDir } from "./render-paths.ts";
+import { ProjectContext } from "../../project/types.ts";
 
 export function renderCleanup(
   input: string,
   output: string,
   format: Format,
+  project: ProjectContext,
   supporting?: string[],
   keepMd?: string,
 ) {
@@ -90,7 +92,7 @@ export function renderCleanup(
     // clean supporting
     ld.uniq(supporting).forEach((path) => {
       if (existsSync(path)) {
-        safeRemoveSync(path, { recursive: true });
+        safeRemoveDirSync(path, project.dir);
       }
     });
   }
diff --git a/src/command/render/latexmk/latex.ts b/src/command/render/latexmk/latex.ts
index 77cb9ffdd33..13a248961d9 100644
--- a/src/command/render/latexmk/latex.ts
+++ b/src/command/render/latexmk/latex.ts
@@ -5,7 +5,7 @@
  */
 
 import { basename, join } from "../../../deno_ral/path.ts";
-import { existsSync } from "../../../deno_ral/fs.ts";
+import { existsSync, safeRemoveSync } from "../../../deno_ral/fs.ts";
 import { error, info } from "../../../deno_ral/log.ts";
 
 import { PdfEngine } from "../../../config/types.ts";
@@ -67,7 +67,7 @@ export async function runPdfEngine(
   // Clean any log file or output from previous runs
   [log, output].forEach((file) => {
     if (existsSync(file)) {
-      Deno.removeSync(file);
+      safeRemoveSync(file);
     }
   });
 
@@ -141,7 +141,7 @@ export async function runIndexEngine(
 
   // Clean any log file from previous runs
   if (existsSync(log)) {
-    Deno.removeSync(log);
+    safeRemoveSync(log);
   }
 
   const result = await runLatexCommand(
@@ -176,7 +176,7 @@ export async function runBibEngine(
 
   // Clean any log file from previous runs
   if (existsSync(log)) {
-    Deno.removeSync(log);
+    safeRemoveSync(log);
   }
 
   const result = await runLatexCommand(
diff --git a/src/command/render/latexmk/pdf.ts b/src/command/render/latexmk/pdf.ts
index 81fdd746972..bf501aa8215 100644
--- a/src/command/render/latexmk/pdf.ts
+++ b/src/command/render/latexmk/pdf.ts
@@ -5,7 +5,7 @@
  */
 
 import { dirname, join } from "../../../deno_ral/path.ts";
-import { existsSync } from "../../../deno_ral/fs.ts";
+import { existsSync, safeRemoveSync } from "../../../deno_ral/fs.ts";
 
 import { PdfEngine } from "../../../config/types.ts";
 import { LatexmkOptions } from "./types.ts";
@@ -594,7 +594,7 @@ function cleanup(workingDir: string, stem: string) {
 
   auxFiles.forEach((auxFile) => {
     if (existsSync(auxFile)) {
-      Deno.removeSync(auxFile);
+      safeRemoveSync(auxFile);
     }
   });
 }
diff --git a/src/command/render/output-tex.ts b/src/command/render/output-tex.ts
index ac09b70eb99..768e8051f9e 100644
--- a/src/command/render/output-tex.ts
+++ b/src/command/render/output-tex.ts
@@ -5,7 +5,7 @@
  */
 
 import { dirname, join, normalize, relative } from "../../deno_ral/path.ts";
-import { ensureDirSync } from "../../deno_ral/fs.ts";
+import { ensureDirSync, safeRemoveSync } from "../../deno_ral/fs.ts";
 
 import { writeFileToStdout } from "../../core/console.ts";
 import { dirAndStem, expandPath } from "../../core/path.ts";
@@ -78,14 +78,14 @@ export function texToPdfOutputRecipe(
     // keep tex if requested
     const compileTex = join(inputDir, output);
     if (!format.render[kKeepTex]) {
-      Deno.removeSync(compileTex);
+      safeRemoveSync(compileTex);
     }
 
     // copy (or write for stdout) compiled pdf to final output location
     if (finalOutput) {
       if (finalOutput === kStdOut) {
         writeFileToStdout(pdfOutput);
-        Deno.removeSync(pdfOutput);
+        safeRemoveSync(pdfOutput);
       } else {
         const outputPdf = expandPath(finalOutput);
 
@@ -99,9 +99,10 @@ export function texToPdfOutputRecipe(
 
       // Clean the output directory if it is empty
       if (pdfOutputDir) {
+        console.log({ pdfOutputDir });
         try {
           // Remove the outputDir if it is empty
-          Deno.removeSync(pdfOutputDir, { recursive: false });
+          safeRemoveSync(pdfOutputDir, { recursive: false });
         } catch {
           // This is ok, just means the directory wasn't empty
         }
diff --git a/src/command/render/output-typst.ts b/src/command/render/output-typst.ts
index f714e7b6fbf..83a5b3f9cac 100644
--- a/src/command/render/output-typst.ts
+++ b/src/command/render/output-typst.ts
@@ -5,7 +5,7 @@
  */
 
 import { dirname, join, normalize, relative } from "../../deno_ral/path.ts";
-import { ensureDirSync } from "../../deno_ral/fs.ts";
+import { ensureDirSync, safeRemoveSync } from "../../deno_ral/fs.ts";
 
 import {
   kFontPaths,
@@ -81,14 +81,14 @@ export function typstPdfOutputRecipe(
 
     // keep typ if requested
     if (!format.render[kKeepTyp]) {
-      Deno.removeSync(input);
+      safeRemoveSync(input);
     }
 
     // copy (or write for stdout) compiled pdf to final output location
     if (finalOutput) {
       if (finalOutput === kStdOut) {
         writeFileToStdout(pdfOutput);
-        Deno.removeSync(pdfOutput);
+        safeRemoveSync(pdfOutput);
       } else {
         const outputPdf = expandPath(finalOutput);
 
diff --git a/src/command/render/output.ts b/src/command/render/output.ts
index cf08086e6f1..9ae7e057e7a 100644
--- a/src/command/render/output.ts
+++ b/src/command/render/output.ts
@@ -15,7 +15,7 @@ import {
 } from "../../deno_ral/path.ts";
 
 import { writeFileToStdout } from "../../core/console.ts";
-import { dirAndStem, expandPath } from "../../core/path.ts";
+import { dirAndStem, expandPath, safeRemoveSync } from "../../core/path.ts";
 import {
   parse as parseYaml,
   partitionYamlFrontMatter,
@@ -209,7 +209,7 @@ export function outputRecipe(
       recipe.isOutputTransient = true;
       completeActions.push(() => {
         writeFileToStdout(join(inputDir, recipe.output));
-        Deno.removeSync(join(inputDir, recipe.output));
+        safeRemoveSync(join(inputDir, recipe.output));
       });
     } else if (!isAbsolute(recipe.output)) {
       // relatve output file on the command line: make it relative to the input dir
diff --git a/src/command/render/project.ts b/src/command/render/project.ts
index 76fbbeb175d..6e50bcdd0d0 100644
--- a/src/command/render/project.ts
+++ b/src/command/render/project.ts
@@ -4,7 +4,14 @@
  * Copyright (C) 2020-2022 Posit Software, PBC
  */
 
-import { ensureDirSync, existsSync, safeMoveSync } from "../../deno_ral/fs.ts";
+import {
+  ensureDirSync,
+  existsSync,
+  safeMoveSync,
+  safeRemoveDirSync,
+  safeRemoveSync,
+  UnsafeRemovalError,
+} from "../../deno_ral/fs.ts";
 import { dirname, isAbsolute, join, relative } from "../../deno_ral/path.ts";
 import { info, warning } from "../../deno_ral/log.ts";
 import { mergeProjectMetadata } from "../../config/metadata.ts";
@@ -481,7 +488,18 @@ export async function renderProject(
         return;
       }
       if (existsSync(targetDir)) {
-        Deno.removeSync(targetDir, { recursive: true });
+        try {
+          safeRemoveDirSync(targetDir, context.dir);
+        } catch (e) {
+          if (e instanceof UnsafeRemovalError) {
+            warning(
+              `Refusing to remove directory ${targetDir} since it is not a subdirectory of the main project directory.`,
+            );
+            warning(
+              `Quarto did not expect the path configuration being used in this project, and strange behavior may result.`,
+            );
+          }
+        }
       }
       ensureDirSync(dirname(targetDir));
       if (copy) {
@@ -494,7 +512,7 @@ export async function renderProject(
           // because src and target are in different file systems.
           // In that case, try to recursively copy from src
           copyTo(srcDir, targetDir);
-          Deno.removeSync(srcDir, { recursive: true });
+          safeRemoveDirSync(targetDir, context.dir);
         }
       }
     };
@@ -906,7 +924,7 @@ export async function renderProject(
   if (projectRenderConfig.options.forceClean) {
     const scratchDir = join(projDir, kQuartoScratch);
     if (existsSync(scratchDir)) {
-      Deno.removeSync(scratchDir, { recursive: true });
+      safeRemoveSync(scratchDir, { recursive: true });
     }
   }
 
diff --git a/src/command/render/render.ts b/src/command/render/render.ts
index 80986a16016..e8e0d70dcb3 100644
--- a/src/command/render/render.ts
+++ b/src/command/render/render.ts
@@ -377,6 +377,7 @@ export async function renderPandoc(
             context.target.input,
             finalOutput!,
             format,
+            file.context.project,
             cleanupSelfContained,
             executionEngineKeepMd(context),
           ));
diff --git a/src/core/copy.ts b/src/core/copy.ts
index a05636cddce..c2d5712910f 100644
--- a/src/core/copy.ts
+++ b/src/core/copy.ts
@@ -18,6 +18,7 @@ import {
   existsSync,
   getFileInfoType,
   isSubdir,
+  safeRemoveSync,
   walkSync,
 } from "../deno_ral/fs.ts";
 
@@ -146,7 +147,7 @@ function copyFileSync(
   // multiple users/owners in play). see this code for where this occurs:
   // https://github.com/denoland/deno/blob/1c05e41f37da022971f0090b2a92e6340d230055/runtime/ops/fs.rs#L914-L916
   if (existsSync(dest)) {
-    Deno.removeSync(dest);
+    safeRemoveSync(dest);
   }
   Deno.copyFileSync(src, dest);
 
@@ -196,7 +197,7 @@ function copySymlinkSync(
   ensureValidCopySync(src, dest, options);
   // remove dest if it exists
   if (existsSync(dest)) {
-    Deno.removeSync(dest);
+    safeRemoveSync(dest);
   }
   const originSrcFilePath = Deno.readLinkSync(src);
   const type = getFileInfoType(Deno.lstatSync(src));
diff --git a/src/core/deno/debug.ts b/src/core/deno/debug.ts
index d5c68326cb4..01a94641175 100644
--- a/src/core/deno/debug.ts
+++ b/src/core/deno/debug.ts
@@ -122,6 +122,19 @@ export const getStackAsArray = (
           col: m4[5] + (m4[1] ? 6 : 0),
         };
       }
+
+      // at Array.map (<anonymous>)
+      const m5 = s.match(
+        /^.*at (.*)\(<anonymous>\)$/,
+      );
+      if (m5) {
+        return {
+          pos: "",
+          name: `${m5[1]}`,
+          line: "",
+          col: "",
+        };
+      }
       throw new Error(`Unexpected stack entry: ${s}`);
     });
 
diff --git a/src/core/deno/monkey-patch.ts b/src/core/deno/monkey-patch.ts
index 5119e882c06..7f6fb6a8840 100644
--- a/src/core/deno/monkey-patch.ts
+++ b/src/core/deno/monkey-patch.ts
@@ -6,8 +6,9 @@
 
 import { debug } from "../../deno_ral/log.ts";
 import { normalizePath } from "../path.ts";
+import { getStack } from "./debug.ts";
 
-// Window UNC paths can be mishandled by realPathSync
+// Windows UNC paths can be mishandled by realPathSync
 // (see https://github.com/quarto-dev/quarto-vscode/issues/67)
 // so we monkey-patch to implement the absolute path and normalize
 // parts of realPathSync (we aren't interested in the symlink
diff --git a/src/core/run/lua.ts b/src/core/run/lua.ts
index d9e797ed274..dfb9c801d04 100644
--- a/src/core/run/lua.ts
+++ b/src/core/run/lua.ts
@@ -7,7 +7,7 @@
 import { info } from "../../deno_ral/log.ts";
 
 import { dirname, extname } from "../../deno_ral/path.ts";
-import { normalizePath } from "../path.ts";
+import { normalizePath, safeRemoveSync } from "../path.ts";
 import { isWindows } from "../platform.ts";
 import { execProcess } from "../process.ts";
 import { pandocBinaryPath, resourcePath } from "../resources.ts";
@@ -109,7 +109,7 @@ setmetatable(_G, meta)
   } finally {
     // remove temp script
     if (tempScript) {
-      Deno.removeSync(tempScript);
+      safeRemoveSync(tempScript);
     }
   }
 }
diff --git a/src/core/windows.ts b/src/core/windows.ts
index 8ed9c990c7f..38dde5acec3 100644
--- a/src/core/windows.ts
+++ b/src/core/windows.ts
@@ -3,7 +3,7 @@
  *
  * Copyright (C) 2020-2022 Posit Software, PBC
  */
-import { existsSync } from "../deno_ral/fs.ts";
+import { existsSync, safeRemoveSync } from "../deno_ral/fs.ts";
 import { join } from "../deno_ral/path.ts";
 import { quartoCacheDir } from "./appdirs.ts";
 import { removeIfExists } from "./path.ts";
@@ -79,7 +79,7 @@ export async function cacheCodePage() {
 
 export function clearCodePageCache() {
   if (existsSync(tokenPath)) {
-    Deno.removeSync(tokenPath);
+    safeRemoveSync(tokenPath);
   }
 }
 
diff --git a/src/deno_ral/fs.ts b/src/deno_ral/fs.ts
index cf229454518..d408f1ad261 100644
--- a/src/deno_ral/fs.ts
+++ b/src/deno_ral/fs.ts
@@ -36,6 +36,7 @@ export function getFileInfoType(fileInfo: Deno.FileInfo): PathType | undefined {
 }
 
 // from https://jsr.io/@std/fs/1.0.3/_is_subdir.ts
+// 2024-15-11: isSubDir("foo", "foo/bar") returns true, which gets src and dest exactly backwards?!
 /**
  * Checks whether `src` is a sub-directory of `dest`.
  *
@@ -104,3 +105,22 @@ export function safeRemoveSync(
     }
   }
 }
+
+export class UnsafeRemovalError extends Error {
+  constructor(msg: string) {
+    super(msg);
+  }
+}
+
+export function safeRemoveDirSync(
+  path: string,
+  boundary: string,
+) {
+  // note the comment above about isSubdir getting src and dest backwards
+  if (path === boundary || isSubdir(path, boundary)) {
+    throw new UnsafeRemovalError(
+      `Refusing to remove directory ${path} that isn't a subdirectory of ${boundary}`,
+    );
+  }
+  return safeRemoveSync(path, { recursive: true });
+}
diff --git a/src/execute/julia.ts b/src/execute/julia.ts
index f95ab3d2a6b..622fed63114 100644
--- a/src/execute/julia.ts
+++ b/src/execute/julia.ts
@@ -39,7 +39,7 @@ import { isInteractiveSession } from "../core/platform.ts";
 import { runningInCI } from "../core/ci-info.ts";
 import { sleep } from "../core/async.ts";
 import { JupyterNotebook } from "../core/jupyter/types.ts";
-import { existsSync } from "../deno_ral/fs.ts";
+import { existsSync, safeRemoveSync } from "../deno_ral/fs.ts";
 import { encodeBase64 } from "encoding/base64";
 import {
   executeResultEngineDependencies,
@@ -468,7 +468,7 @@ async function getJuliaServerConnection(
         options,
         "Connecting to server failed, a transport file was reused so it might be stale. Delete transport file and retry.",
       );
-      Deno.removeSync(juliaTransportFile());
+      safeRemoveSync(juliaTransportFile());
       return await getJuliaServerConnection(options);
     } else {
       error(
diff --git a/src/execute/jupyter/jupyter-kernel.ts b/src/execute/jupyter/jupyter-kernel.ts
index 71c89d4ef6f..d94c2c65794 100644
--- a/src/execute/jupyter/jupyter-kernel.ts
+++ b/src/execute/jupyter/jupyter-kernel.ts
@@ -4,7 +4,7 @@
  * Copyright (C) 2020-2022 Posit Software, PBC
  */
 
-import { existsSync } from "../../deno_ral/fs.ts";
+import { existsSync, safeRemoveSync } from "../../deno_ral/fs.ts";
 import { join } from "../../deno_ral/path.ts";
 import { error, info, warning } from "../../deno_ral/log.ts";
 
@@ -148,7 +148,7 @@ export async function executeKernelKeepalive(
     // in that case remove the connection file and re-throw the exception
     const transportFile = kernelTransportFile(options.target.input);
     if (existsSync(transportFile)) {
-      Deno.removeSync(transportFile);
+      safeRemoveSync(transportFile);
     }
     throw e;
   } finally {
@@ -174,7 +174,7 @@ async function abortKernel(options: JupyterExecuteOptions) {
     } finally {
       const transportFile = kernelTransportFile(options.target.input);
       if (existsSync(transportFile)) {
-        Deno.removeSync(transportFile);
+        safeRemoveSync(transportFile);
       }
       conn.close();
     }
@@ -360,7 +360,7 @@ function readKernelTransportFile(
           "Error reading kernel transport file: " + e.toString() +
             "(removing file)",
         );
-        Deno.removeSync(transportFile);
+        safeRemoveSync(transportFile);
         return null;
       }
     } else {
@@ -408,7 +408,7 @@ async function connectToKernel(
     } catch {
       // remove the transport file
       if (existsSync(transportFile)) {
-        Deno.removeSync(transportFile);
+        safeRemoveSync(transportFile);
       }
     }
   }
@@ -453,7 +453,7 @@ async function connectToKernel(
         return await denoConnectToKernel(kernelTransport);
       } catch (e) {
         // remove the transport file
-        Deno.removeSync(transportFile);
+        safeRemoveSync(transportFile);
         error("Error connecting to Jupyter kernel: " + e.toString());
         return Promise.reject();
       }
diff --git a/src/execute/ojs/extract-resources.ts b/src/execute/ojs/extract-resources.ts
index f56c674477e..95eb5a3de66 100644
--- a/src/execute/ojs/extract-resources.ts
+++ b/src/execute/ojs/extract-resources.ts
@@ -34,6 +34,7 @@ import { stripColor } from "../../core/lib/external/colors.ts";
 import { lines } from "../../core/lib/text.ts";
 import { InternalError } from "../../core/lib/error.ts";
 import { kRenderServicesLifetime } from "../../config/constants.ts";
+import { safeRemoveSync } from "../../deno_ral/fs.ts";
 
 // ResourceDescription filenames are always project-relative
 export interface ResourceDescription {
@@ -571,7 +572,7 @@ export async function extractResourceDescriptionsFromOJSChunk(
             // more than once, so we could end up with more than one request
             // to delete it. Fail gracefully if so.
             try {
-              Deno.removeSync(res.filename);
+              safeRemoveSync(res.filename);
             } catch (e) {
               if (e.name !== "NotFound") {
                 throw e;
diff --git a/src/extension/install.ts b/src/extension/install.ts
index 51784c96b42..fef12c6764c 100644
--- a/src/extension/install.ts
+++ b/src/extension/install.ts
@@ -4,7 +4,7 @@
  * Copyright (C) 2020-2022 Posit Software, PBC
  */
 
-import { ensureDirSync, existsSync } from "../deno_ral/fs.ts";
+import { ensureDirSync, existsSync, safeRemoveSync } from "../deno_ral/fs.ts";
 import { Confirm } from "cliffy/prompt/mod.ts";
 import { Table } from "cliffy/table/mod.ts";
 import { basename, dirname, join, relative } from "../deno_ral/path.ts";
@@ -587,7 +587,7 @@ export async function completeInstallation(
         // Move from the staging path to the install dir
         const installPath = join(installExtDir, extensionRelativeDir);
         if (existsSync(installPath)) {
-          Deno.removeSync(installPath, { recursive: true });
+          safeRemoveSync(installPath, { recursive: true });
         }
 
         // Ensure the parent directory exists
@@ -596,7 +596,7 @@ export async function completeInstallation(
       });
     } finally {
       // Clean up the staging directory
-      Deno.removeSync(stagingDir, { recursive: true });
+      safeRemoveSync(stagingDir, { recursive: true });
     }
     return Promise.resolve();
   });
diff --git a/src/preview/preview-text.ts b/src/preview/preview-text.ts
index 24bb0eeafc3..a0820e58f8f 100644
--- a/src/preview/preview-text.ts
+++ b/src/preview/preview-text.ts
@@ -19,6 +19,7 @@ import {
   pandocBinaryPath,
   textHighlightThemePath,
 } from "../core/resources.ts";
+import { safeRemoveSync } from "../deno_ral/fs.ts";
 
 import { basename, extname, join } from "../deno_ral/path.ts";
 
@@ -254,6 +255,6 @@ async function gfmPreview(file: string, request: Request) {
       );
     }
   } finally {
-    Deno.removeSync(workingDir, { recursive: true });
+    safeRemoveSync(workingDir, { recursive: true });
   }
 }
diff --git a/src/project/project-shared.ts b/src/project/project-shared.ts
index 13b28744a93..ec9bcfb619f 100644
--- a/src/project/project-shared.ts
+++ b/src/project/project-shared.ts
@@ -350,7 +350,7 @@ export async function directoryMetadataForInputFile(
 }
 
 const mdForFile = async (
-  project: ProjectContext,
+  _project: ProjectContext,
   engine: ExecutionEngine | undefined,
   file: string,
 ): Promise<MappedString> => {
diff --git a/src/project/serve/serve.ts b/src/project/serve/serve.ts
index b2822e6f8b1..cca9218cf51 100644
--- a/src/project/serve/serve.ts
+++ b/src/project/serve/serve.ts
@@ -5,7 +5,7 @@
  */
 
 import { info, warning } from "../../deno_ral/log.ts";
-import { existsSync } from "../../deno_ral/fs.ts";
+import { existsSync, safeRemoveSync } from "../../deno_ral/fs.ts";
 import {
   basename,
   dirname,
@@ -918,7 +918,7 @@ function acquirePreviewLock(project: ProjectContext) {
 
 function releasePreviewLock(project: ProjectContext) {
   try {
-    Deno.removeSync(previewLockFile(project));
+    safeRemoveSync(previewLockFile(project));
   } catch {
     //
   }
diff --git a/src/project/types/book/book-render.ts b/src/project/types/book/book-render.ts
index 87f3f593b21..b83c881dfc7 100644
--- a/src/project/types/book/book-render.ts
+++ b/src/project/types/book/book-render.ts
@@ -681,6 +681,7 @@ function cleanupExecutedFile(
     file.context.target.input,
     finalOutput,
     file.recipe.format,
+    file.context.project,
     file.executeResult.supporting,
     executionEngineKeepMd(file.context),
   );
diff --git a/src/project/types/manuscript/manuscript.ts b/src/project/types/manuscript/manuscript.ts
index abf093bfcab..bab820b2f4c 100644
--- a/src/project/types/manuscript/manuscript.ts
+++ b/src/project/types/manuscript/manuscript.ts
@@ -107,7 +107,12 @@ import { isQmdFile } from "../../../execute/qmd.ts";
 import * as ld from "../../../core/lodash.ts";
 import { safeExistsSync } from "../../../core/path.ts";
 
-import { copySync, ensureDirSync, existsSync } from "../../../deno_ral/fs.ts";
+import {
+  copySync,
+  ensureDirSync,
+  existsSync,
+  safeRemoveSync,
+} from "../../../deno_ral/fs.ts";
 import { kTitleBlockStyle } from "../../../format/html/format-html-title.ts";
 import { resolveProjectInputLinks } from "../website/website-utils.ts";
 
@@ -751,7 +756,7 @@ const createTexOutputBundle = (
       texInputFile,
       texOutputFile,
     );
-    Deno.removeSync(texInputFile);
+    safeRemoveSync(texInputFile);
 
     // Create the resulting bundle descriptor
     const texBundle: { manuscript: string; supporting: string[] } = {
@@ -767,7 +772,7 @@ const createTexOutputBundle = (
         const outPath = join(texDirAbs, relative(context.dir, supportingAbs));
         ensureDirSync(dirname(outPath));
         copySync(supportingAbs, outPath, { overwrite: true });
-        Deno.removeSync(supportingAbs, { recursive: true });
+        safeRemoveSync(supportingAbs, { recursive: true });
         texBundle.supporting.push(outPath);
       }
     }
diff --git a/src/project/types/website/listing/website-listing-feed.ts b/src/project/types/website/listing/website-listing-feed.ts
index b23f144dd73..a22a945d6b5 100644
--- a/src/project/types/website/listing/website-listing-feed.ts
+++ b/src/project/types/website/listing/website-listing-feed.ts
@@ -40,7 +40,11 @@ import {
   renderedContentReader,
   RenderedContents,
 } from "./website-listing-shared.ts";
-import { dirAndStem, resolvePathGlobs } from "../../../../core/path.ts";
+import {
+  dirAndStem,
+  resolvePathGlobs,
+  safeRemoveSync,
+} from "../../../../core/path.ts";
 import { ProjectOutputFile } from "../../types.ts";
 import { resolveInputTarget } from "../../../project-index.ts";
 import { projectOutputDir } from "../../../project-shared.ts";
@@ -372,7 +376,7 @@ export function completeStagedFeeds(
             );
           } finally {
             try {
-              Deno.removeSync(feedFile);
+              safeRemoveSync(feedFile);
             } catch {
               // Just ignore this and move on
             }
diff --git a/src/project/types/website/listing/website-listing-index.ts b/src/project/types/website/listing/website-listing-index.ts
index 0cb928f861c..0a6bb0cbcf8 100644
--- a/src/project/types/website/listing/website-listing-index.ts
+++ b/src/project/types/website/listing/website-listing-index.ts
@@ -5,7 +5,7 @@
  */
 
 import { join, relative } from "../../../../deno_ral/path.ts";
-import { existsSync } from "../../../../deno_ral/fs.ts";
+import { existsSync, safeRemoveSync } from "../../../../deno_ral/fs.ts";
 
 import { ProjectContext } from "../../../types.ts";
 import { ListingDescriptor, ListingItem } from "./website-listing-shared.ts";
@@ -124,7 +124,7 @@ export function updateGlobalListingIndex(
             listingPaths.push(indexJson);
           }
 
-          Deno.removeSync(indexPath);
+          safeRemoveSync(indexPath);
         }
       }
     }
diff --git a/src/project/types/website/listing/website-listing-project.ts b/src/project/types/website/listing/website-listing-project.ts
index ae6b27b5485..b9dfa596e3d 100644
--- a/src/project/types/website/listing/website-listing-project.ts
+++ b/src/project/types/website/listing/website-listing-project.ts
@@ -4,7 +4,7 @@
  * Copyright (C) 2020-2022 Posit Software, PBC
  */
 
-import { ensureDirSync } from "../../../../deno_ral/fs.ts";
+import { ensureDirSync, safeRemoveSync } from "../../../../deno_ral/fs.ts";
 import { dirname, join } from "../../../../deno_ral/path.ts";
 
 import { projectScratchPath } from "../../../project-scratch.ts";
@@ -66,7 +66,7 @@ export function clearListingProjectData(project: ProjectContext) {
 function clearListingMap(project: ProjectContext) {
   const file = projectListingMapFile(project.dir);
   try {
-    Deno.removeSync(file);
+    safeRemoveSync(file);
   } catch {
     // No op
   }
diff --git a/src/tools/impl/tinytex.ts b/src/tools/impl/tinytex.ts
index 464e04bd91f..926fce63bf1 100644
--- a/src/tools/impl/tinytex.ts
+++ b/src/tools/impl/tinytex.ts
@@ -5,7 +5,7 @@
  */
 import { debug, warning } from "../../deno_ral/log.ts";
 
-import { existsSync } from "../../deno_ral/fs.ts";
+import { existsSync, safeRemoveSync } from "../../deno_ral/fs.ts";
 import { basename, join, relative } from "../../deno_ral/path.ts";
 
 import { expandPath, which } from "../../core/path.ts";
@@ -226,7 +226,7 @@ async function install(
             }
           }
 
-          Deno.removeSync(from, { recursive: true });
+          safeRemoveSync(from, { recursive: true });
 
           // Note the version that we have installed
           noteInstalledVersion(pkgInfo.version);
diff --git a/src/tools/tools.ts b/src/tools/tools.ts
index fedc442b26e..94053a08a29 100644
--- a/src/tools/tools.ts
+++ b/src/tools/tools.ts
@@ -20,6 +20,7 @@ import { chromiumInstallable } from "./impl/chromium.ts";
 import { downloadWithProgress } from "../core/download.ts";
 import { Confirm } from "cliffy/prompt/mod.ts";
 import { isWSL } from "../core/platform.ts";
+import { safeRemoveSync } from "../deno_ral/fs.ts";
 
 // The tools that are available to install
 const kInstallableTools: { [key: string]: InstallableTool } = {
@@ -152,7 +153,7 @@ export async function installTool(name: string, updatePath?: boolean) {
         }
       } finally {
         // Cleanup the working directory
-        Deno.removeSync(workingDir, { recursive: true });
+        safeRemoveSync(workingDir, { recursive: true });
       }
     }
   } else {
@@ -184,7 +185,7 @@ export async function uninstallTool(name: string, updatePath?: boolean) {
       } catch (e) {
         logError(e);
       } finally {
-        Deno.removeSync(workingDir, { recursive: true });
+        safeRemoveSync(workingDir, { recursive: true });
       }
     } else {
       info(
@@ -232,7 +233,7 @@ export async function updateTool(name: string) {
     } catch (e) {
       logError(e);
     } finally {
-      Deno.removeSync(workingDir, { recursive: true });
+      safeRemoveSync(workingDir, { recursive: true });
     }
   } else {
     info(
diff --git a/tests/test.ts b/tests/test.ts
index c346a0f2b60..f808d4fe14e 100644
--- a/tests/test.ts
+++ b/tests/test.ts
@@ -4,7 +4,7 @@
 * Copyright (C) 2020-2022 Posit Software, PBC
 *
 */
-import { existsSync } from "../src/deno_ral/fs.ts";
+import { existsSync, safeRemoveSync } from "../src/deno_ral/fs.ts";
 import { AssertionError, fail } from "testing/asserts";
 import { warning } from "../src/deno_ral/log.ts";
 import { initDenoDom } from "../src/core/deno-dom.ts";
@@ -301,7 +301,7 @@ export function test(test: TestDescriptor) {
           }
           fail(output.join("\n"));
         } finally {
-          Deno.removeSync(log);
+          safeRemoveSync(log);
           await cleanupLogOnce();
           if (test.context.teardown) {
             await test.context.teardown();