diff --git a/.circleci/config.yml b/.circleci/config.yml
index ec679f49bf8a..748e7f3eb45e 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -27,6 +27,7 @@ mainBuildFilters: &mainBuildFilters
     branches:
       only:
         - develop
+        - 'ryanm/fix/improve-binary-cleanup-to-look-at-binary-rather-than-monorepo'
 
 # usually we don't build Mac app - it takes a long time
 # but sometimes we want to really confirm we are doing the right thing
@@ -35,6 +36,7 @@ macWorkflowFilters: &darwin-workflow-filters
   when:
     or:
     - equal: [ develop, << pipeline.git.branch >> ]
+    - equal: [ 'ryanm/fix/improve-binary-cleanup-to-look-at-binary-rather-than-monorepo', << pipeline.git.branch >> ]
     - matches:
           pattern: "-release$"
           value: << pipeline.git.branch >>
@@ -43,6 +45,7 @@ linuxArm64WorkflowFilters: &linux-arm64-workflow-filters
   when:
     or:
     - equal: [ develop, << pipeline.git.branch >> ]
+    - equal: [ 'ryanm/fix/improve-binary-cleanup-to-look-at-binary-rather-than-monorepo', << pipeline.git.branch >> ]
     - matches:
           pattern: "-release$"
           value: << pipeline.git.branch >>
@@ -60,6 +63,7 @@ windowsWorkflowFilters: &windows-workflow-filters
   when:
     or:
     - equal: [ develop, << pipeline.git.branch >> ]
+    - equal: [ 'ryanm/fix/improve-binary-cleanup-to-look-at-binary-rather-than-monorepo', << pipeline.git.branch >> ]
     - matches:
           pattern: "-release$"
           value: << pipeline.git.branch >>
@@ -126,7 +130,7 @@ commands:
       - run:
           name: Check current branch to persist artifacts
           command: |
-            if [[ "$CIRCLE_BRANCH" != "develop" ]]; then
+            if [[ "$CIRCLE_BRANCH" != "develop" && "$CIRCLE_BRANCH" != "ryanm/fix/improve-binary-cleanup-to-look-at-binary-rather-than-monorepo" ]]; then
               echo "Not uploading artifacts or posting install comment for this branch."
               circleci-agent step halt
             fi
diff --git a/scripts/binary/binary-cleanup.js b/scripts/binary/binary-cleanup.js
index 47ac4c68676c..68dc96ac1df6 100644
--- a/scripts/binary/binary-cleanup.js
+++ b/scripts/binary/binary-cleanup.js
@@ -36,22 +36,22 @@ async function removeEmptyDirectories (directory) {
   }
 }
 
-const getDependencyPathsToKeep = async () => {
+const getDependencyPathsToKeep = async (buildAppDir) => {
   let entryPoints = new Set([
     // This is the entry point for the server bundle. It will not have access to the snapshot yet. It needs to be kept in the binary
-    require.resolve('@packages/server/index.js'),
+    require.resolve('@packages/server/index.js', { paths: [buildAppDir] }),
     // This is a dynamic import that is used to load the snapshot require logic. It will not have access to the snapshot yet. It needs to be kept in the binary
-    require.resolve('@packages/server/hook-require.js'),
+    require.resolve('@packages/server/hook-require.js', { paths: [buildAppDir] }),
     // These dependencies are started in a new process or thread and will not have access to the snapshot. They need to be kept in the binary
-    require.resolve('@packages/server/lib/plugins/child/require_async_child.js'),
-    require.resolve('@packages/server/lib/plugins/child/register_ts_node.js'),
-    require.resolve('@packages/rewriter/lib/threads/worker.ts'),
+    require.resolve('@packages/server/lib/plugins/child/require_async_child.js', { paths: [buildAppDir] }),
+    require.resolve('@packages/server/lib/plugins/child/register_ts_node.js', { paths: [buildAppDir] }),
+    require.resolve('@packages/rewriter/lib/threads/worker.ts', { paths: [buildAppDir] }),
     // These dependencies use the `require.resolve(<dependency>, { paths: [<path>] })` pattern where <path> is a path within the cypress monorepo. These will not be
     // pulled in by esbuild but still need to be kept in the binary.
-    require.resolve('webpack'),
-    require.resolve('webpack-dev-server', { paths: [path.join(__dirname, '..', '..', 'npm', 'webpack-dev-server')] }),
-    require.resolve('html-webpack-plugin-4', { paths: [path.join(__dirname, '..', '..', 'npm', 'webpack-dev-server')] }),
-    require.resolve('html-webpack-plugin-5', { paths: [path.join(__dirname, '..', '..', 'npm', 'webpack-dev-server')] }),
+    require.resolve('webpack', { paths: [buildAppDir] }),
+    require.resolve('webpack-dev-server', { paths: [buildAppDir] }),
+    require.resolve('html-webpack-plugin-4', { paths: [buildAppDir] }),
+    require.resolve('html-webpack-plugin-5', { paths: [buildAppDir] }),
     // These dependencies are completely dynamic using the pattern `require(`./${name}`)` and will not be pulled in by esbuild but still need to be kept in the binary.
     ...['ibmi',
       'sunos',
@@ -61,7 +61,7 @@ const getDependencyPathsToKeep = async () => {
       'linux',
       'openbsd',
       'sunos',
-      'win32'].map((platform) => require.resolve(`default-gateway/${platform}`)),
+      'win32'].map((platform) => require.resolve(`default-gateway/${platform}`, { paths: [buildAppDir] })),
   ])
   let esbuildResult
   let newEntryPointsFound = true
@@ -77,7 +77,9 @@ const getDependencyPathsToKeep = async () => {
       outdir: workingDir,
       platform: 'node',
       metafile: true,
+      absWorkingDir: buildAppDir,
       external: [
+        './packages/packherd-require/dist/transpile-ts',
         './packages/server/server-entry',
         'fsevents',
         'pnpapi',
@@ -95,9 +97,9 @@ const getDependencyPathsToKeep = async () => {
         let entryPoint
 
         if (warningSubject.startsWith('.')) {
-          entryPoint = path.join(__dirname, '..', '..', path.dirname(warning.location.file), warningSubject)
+          entryPoint = path.join(buildAppDir, path.dirname(warning.location.file), warningSubject)
         } else {
-          entryPoint = require.resolve(warningSubject)
+          entryPoint = require.resolve(warningSubject, { paths: [path.join(buildAppDir, path.dirname(warning.location.file))] })
         }
 
         if (path.extname(entryPoint) !== '' && !entryPoints.has(entryPoint)) {
@@ -114,7 +116,7 @@ const getDependencyPathsToKeep = async () => {
 const cleanup = async (buildAppDir) => {
   // 1. Retrieve all dependencies that still need to be kept in the binary. In theory, we could use the bundles generated here as single files within the binary,
   // but for now, we just track on the dependencies that get pulled in
-  const keptDependencies = [...await getDependencyPathsToKeep(), 'package.json', 'packages/server/server-entry.js']
+  const keptDependencies = [...await getDependencyPathsToKeep(buildAppDir), 'package.json', 'packages/server/server-entry.js']
 
   // 2. Gather the dependencies that could potentially be removed from the binary due to being in the snapshot
   const potentiallyRemovedDependencies = [...snapshotMetadata.healthy, ...snapshotMetadata.deferred, ...snapshotMetadata.norewrite]