diff --git a/.github/workflows/positron-python-ci.yml b/.github/workflows/positron-python-ci.yml
index d66abcb266d2..498137d59a64 100644
--- a/.github/workflows/positron-python-ci.yml
+++ b/.github/workflows/positron-python-ci.yml
@@ -15,11 +15,13 @@ on:
 
 defaults:
  run:
-  working-directory: './extensions/positron-python'
+  working-directory: 'extensions/positron-python'
 
 env:
   NODE_VERSION: '18.17.1'
   PYTHON_VERSION: '3.10'
+  PROJECT_DIR: 'extensions/positron-python'
+  PYTHON_SRC_DIR: 'extensions/positron-python/pythonFiles'
   # Force a path with spaces and to test extension works in these scenarios
   # Unicode characters are causing 2.7 failures so skip that for now.
   special-working-directory: './path with spaces'
@@ -67,13 +69,13 @@ jobs:
         run: |
           python -m pip install -U black
           python -m black . --check
-        working-directory: pythonFiles
+        working-directory: ${{ env.PYTHON_SRC_DIR }}
 
       - name: Run Ruff
         run: |
           python -m pip install -U ruff
           python -m ruff check .
-        working-directory: pythonFiles
+        working-directory: ${{ env.PYTHON_SRC_DIR }}
 
   check-types:
     name: Check Python types
@@ -89,9 +91,7 @@ jobs:
           cache: 'pip'
 
       - name: Install base Python requirements
-        uses: brettcannon/pip-secure-install@v1
-        with:
-          options: '-t ./pythonFiles/lib/python --no-cache-dir --implementation py'
+        run: 'python -m pip install --no-deps --require-hashes --only-binary :all: -t ./pythonFiles/lib/python --no-cache-dir --implementation py -r requirements.txt'
 
       - name: Install Positron IPyKernel requirements
         run: python scripts/vendor.py
@@ -106,7 +106,7 @@ jobs:
         uses: jakebailey/pyright-action@v2
         with:
           version: 1.1.308
-          working-directory: 'pythonFiles'
+          working-directory: ${{ env.PYTHON_SRC_DIR }}
 
   python-tests:
     name: Python Tests
@@ -114,7 +114,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     defaults:
       run:
-        working-directory: ${{ env.special-working-directory }}
+        working-directory: ${{ env.special-working-directory }}/${{ env.PROJECT_DIR}}
     strategy:
       fail-fast: false
       matrix:
@@ -167,10 +167,7 @@ jobs:
         run: python -m pytest --version
 
       - name: Install base Python requirements
-        uses: brettcannon/pip-secure-install@v1
-        with:
-          requirements-file: '"${{ env.special-working-directory-relative }}/requirements.txt"'
-          options: '-t "${{ env.special-working-directory-relative }}/pythonFiles/lib/python" --no-cache-dir --implementation py'
+        run: 'python -m pip install --no-deps --require-hashes --only-binary :all: -t ./pythonFiles/lib/python --no-cache-dir --implementation py -r requirements.txt'
 
       - name: Install test requirements
         run: python -m pip install -r build/test-requirements.txt
@@ -248,7 +245,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     defaults:
       run:
-        working-directory: ${{ env.special-working-directory }}
+        working-directory: ${{ env.special-working-directory }}/${{ env.PROJECT_DIR}}
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
@@ -285,7 +282,7 @@ jobs:
         with:
           node-version: ${{ env.NODE_VERSION }}
           cache: 'yarn'
-          cache-dependency-path: ${{ env.special-working-directory-relative }}/yarn.lock
+          cache-dependency-path: ${{ env.special-working-directory-relative }}/${{ env.PROJECT_DIR }}/yarn.lock
 
       - name: Install Yarn
         run: npm install -g yarn
@@ -406,31 +403,31 @@ jobs:
         env:
           TEST_FILES_SUFFIX: testvirtualenvs
           CI_PYTHON_VERSION: ${{ matrix.python }}
-          POSITRON_GITHUB_PAT: ${{ secrets.POSITRON_GITHUB_RO_PAT }}
+          POSITRON_GITHUB_PAT: ${{ secrets.POSITRON_GITHUB_PAT }}
         uses: GabrielBB/xvfb-action@v1.6
         with:
           run: yarn testSingleWorkspace
-          working-directory: ${{ env.special-working-directory }}
+          working-directory: ${{ env.special-working-directory }}/${{ env.PROJECT_DIR }}
         if: matrix.test-suite == 'venv'
 
       - name: Run single-workspace tests
         env:
           CI_PYTHON_VERSION: ${{ matrix.python }}
-          POSITRON_GITHUB_PAT: ${{ secrets.POSITRON_GITHUB_RO_PAT }}
+          POSITRON_GITHUB_PAT: ${{ secrets.POSITRON_GITHUB_PAT }}
         uses: GabrielBB/xvfb-action@v1.6
         with:
           run: yarn testSingleWorkspace
-          working-directory: ${{ env.special-working-directory }}
+          working-directory: ${{ env.special-working-directory }}/${{ env.PROJECT_DIR }}
         if: matrix.test-suite == 'single-workspace'
 
       - name: Run debugger tests
         env:
           CI_PYTHON_VERSION: ${{ matrix.python }}
-          POSITRON_GITHUB_PAT: ${{ secrets.POSITRON_GITHUB_RO_PAT }}
+          POSITRON_GITHUB_PAT: ${{ secrets.POSITRON_GITHUB_PAT }}
         uses: GabrielBB/xvfb-action@v1.6
         with:
           run: yarn testDebugger
-          working-directory: ${{ env.special-working-directory }}
+          working-directory: ${{ env.special-working-directory }}/${{ env.PROJECT_DIR }}
         if: matrix.test-suite == 'debugger'
 
       - name: Run TypeScript functional tests
@@ -439,6 +436,6 @@ jobs:
 
       - name: Run smoke tests
         env:
-          POSITRON_GITHUB_PAT: ${{ secrets.POSITRON_GITHUB_RO_PAT }}
+          POSITRON_GITHUB_PAT: ${{ secrets.POSITRON_GITHUB_PAT }}
         run: yarn tsc && node ./out/test/smokeTest.js
         if: matrix.test-suite == 'smoke'
diff --git a/.vscode/settings.json b/.vscode/settings.json
index d31c1786e5b4..0f62a0752e2a 100644
--- a/.vscode/settings.json
+++ b/.vscode/settings.json
@@ -122,6 +122,9 @@
 		"editor.defaultFormatter": "rust-lang.rust-analyzer",
 		"editor.formatOnSave": true,
 	},
+	"[diff]": {
+		"files.trimTrailingWhitespace": false
+	},
 	"rust-analyzer.linkedProjects": [
 		"cli/Cargo.toml"
 	],
diff --git a/extensions/positron-python/scripts/patches/jedi-language-server.patch b/extensions/positron-python/scripts/patches/jedi-language-server.patch
index b9527ce3af52..948c9638341e 100644
--- a/extensions/positron-python/scripts/patches/jedi-language-server.patch
+++ b/extensions/positron-python/scripts/patches/jedi-language-server.patch
@@ -4,7 +4,7 @@ index 4f3ba7bd5..52524daa2 100644
 +++ b/extensions/positron-python/pythonFiles/positron/positron_ipykernel/_vendor/jedi_language_server/jedi_utils.py
 @@ -12,9 +12,9 @@ from inspect import Parameter
  from typing import Any, Callable, Dict, Iterator, List, Optional, Tuple, Union
-
+ 
  import docstring_to_markdown
 -import jedi.api.errors
 -import jedi.inference.references
@@ -27,7 +27,7 @@ index 4f3ba7bd5..52524daa2 100644
              + initialization_options.jedi_settings.auto_import_modules
          )
      )
-
+ 
 -    jedi.settings.case_insensitive_completion = (
 +    settings.case_insensitive_completion = (
          initialization_options.jedi_settings.case_insensitive_completion
@@ -35,8 +35,8 @@ index 4f3ba7bd5..52524daa2 100644
      if initialization_options.jedi_settings.debug:
 @@ -284,7 +284,7 @@ def lsp_document_symbols(names: List[Name]) -> List[DocumentSymbol]:
      return results
-
-
+ 
+ 
 -def lsp_diagnostic(error: jedi.api.errors.SyntaxError) -> Diagnostic:
 +def lsp_diagnostic(error: JediSyntaxError) -> Diagnostic:
      """Get LSP Diagnostic from Jedi SyntaxError."""
@@ -49,6 +49,6 @@ index ba6eaf9fe..28266bd95 100644
 @@ -1,4 +1,3 @@
  """Jedi Language Server."""
 -from importlib.metadata import version
-
+ 
 -__version__ = version("jedi-language-server")
 +__version__ = "unknown"
diff --git a/extensions/positron-python/scripts/patches/jedi.patch b/extensions/positron-python/scripts/patches/jedi.patch
index 128d18db5f13..eabb923f86a3 100644
--- a/extensions/positron-python/scripts/patches/jedi.patch
+++ b/extensions/positron-python/scripts/patches/jedi.patch
@@ -4,19 +4,19 @@ index e0f23d19b..f30731476 100644
 +++ b/extensions/positron-python/pythonFiles/positron/positron_ipykernel/_vendor/jedi/api/replstartup.py
 @@ -17,13 +17,13 @@ Then you will be able to use Jedi completer in your Python interpreter::
      ..dex   ..sert
-
+ 
  """
 -import jedi.utils
 +from jedi.utils import setup_readline
  from jedi import __version__ as __jedi_version__
-
+ 
  print('REPL completion using Jedi %s' % __jedi_version__)
 -jedi.utils.setup_readline(fuzzy=False)
 +setup_readline(fuzzy=False)
-
+ 
 -del jedi
 +del setup_readline
-
+ 
  # Note: try not to do many things here, as it will contaminate global
  # namespace of the interpreter.
 diff --git a/extensions/positron-python/pythonFiles/positron/positron_ipykernel/_vendor/jedi/inference/compiled/subprocess/__main__.py b/extensions/positron-python/pythonFiles/positron/positron_ipykernel/_vendor/jedi/inference/compiled/subprocess/__main__.py
@@ -24,8 +24,8 @@ index f044e2ee1..beec3f0cf 100644
 --- a/extensions/positron-python/pythonFiles/positron/positron_ipykernel/_vendor/jedi/inference/compiled/subprocess/__main__.py
 +++ b/extensions/positron-python/pythonFiles/positron/positron_ipykernel/_vendor/jedi/inference/compiled/subprocess/__main__.py
 @@ -9,12 +9,9 @@ del sys.path[0]
-
-
+ 
+ 
  def _get_paths():
 -    # Get the path to jedi.
 +    # Get the path to positron, in which jedi and parso are vendored.
@@ -35,6 +35,6 @@ index f044e2ee1..beec3f0cf 100644
 -    # The paths are the directory that jedi and parso lie in.
 -    return {'jedi': _jedi_path, 'parso': _parso_path}
 +    return {"positron_ipykernel": _d(_d(_d(_d(_d(_d(_d(__file__)))))))}
-
-
+ 
+ 
  class _ExactImporter(MetaPathFinder):
diff --git a/extensions/positron-python/scripts/patches/parso.patch b/extensions/positron-python/scripts/patches/parso.patch
index 4e443e95e8e7..3121436e9357 100644
--- a/extensions/positron-python/scripts/patches/parso.patch
+++ b/extensions/positron-python/scripts/patches/parso.patch
@@ -9,7 +9,7 @@ index 5592a9fdd..98b903aaa 100644
 @@ -49,7 +49,7 @@ are regarded as incompatible.
  - A __slot__ of a class is changed.
  """
-
+ 
 -_VERSION_TAG = '%s-%s%s-%s' % (
 +_VERSION_TAG = '%s-%s%s-%s-Positron' % (
      platform.python_implementation(),
diff --git a/extensions/positron-python/scripts/patches/pydantic.patch b/extensions/positron-python/scripts/patches/pydantic.patch
index 567e86171898..4302de1b0428 100644
--- a/extensions/positron-python/scripts/patches/pydantic.patch
+++ b/extensions/positron-python/scripts/patches/pydantic.patch
@@ -4,13 +4,13 @@ index 0c529620f..ce9df7a36 100644
 +++ b/extensions/positron-python/pythonFiles/positron/positron_ipykernel/_vendor/pydantic/_hypothesis_plugin.py
 @@ -33,7 +33,7 @@ from typing import Callable, Dict, Type, Union, cast, overload
  import hypothesis.strategies as st
-
+ 
  import pydantic
 -import pydantic.color
 +import pydantic.color as pydantic_color
  import pydantic.types
  from pydantic.utils import lenient_issubclass
-
+ 
 @@ -88,23 +88,23 @@ st.register_type_strategy(
  _color_regexes = (
      '|'.join(
@@ -51,29 +51,29 @@ index ce9df7a36..93ff17077 100644
 --- a/extensions/positron-python/pythonFiles/positron/positron_ipykernel/_vendor/pydantic/_hypothesis_plugin.py
 +++ b/extensions/positron-python/pythonFiles/positron/positron_ipykernel/_vendor/pydantic/_hypothesis_plugin.py
 @@ -34,7 +34,7 @@ import hypothesis.strategies as st
-
+ 
  import pydantic
  import pydantic.color as pydantic_color
 -import pydantic.types
 +import pydantic.types as pydantic_types
  from pydantic.utils import lenient_issubclass
-
+ 
  # FilePath and DirectoryPath are explicitly unsupported, as we'd have to create
 @@ -182,22 +182,22 @@ RESOLVERS: Dict[type, Callable[[type], st.SearchStrategy]] = {}  # type: ignore[
-
-
+ 
+ 
  @overload
 -def _registered(typ: Type[pydantic.types.T]) -> Type[pydantic.types.T]:
 +def _registered(typ: Type[pydantic_types.T]) -> Type[pydantic.types.T]:
      pass
-
-
+ 
+ 
  @overload
 -def _registered(typ: pydantic.types.ConstrainedNumberMeta) -> pydantic.types.ConstrainedNumberMeta:
 +def _registered(typ: pydantic_types.ConstrainedNumberMeta) -> pydantic.types.ConstrainedNumberMeta:
      pass
-
-
+ 
+ 
  def _registered(
 -    typ: Union[Type[pydantic.types.T], pydantic.types.ConstrainedNumberMeta]
 -) -> Union[Type[pydantic.types.T], pydantic.types.ConstrainedNumberMeta]:
@@ -89,8 +89,8 @@ index ce9df7a36..93ff17077 100644
          if issubclass(typ, supertype):
              st.register_type_strategy(typ, resolver(typ))  # type: ignore
 @@ -206,7 +206,7 @@ def _registered(
-
-
+ 
+ 
  def resolves(
 -    typ: Union[type, pydantic.types.ConstrainedNumberMeta]
 +    typ: Union[type, pydantic_types.ConstrainedNumberMeta]
@@ -98,8 +98,8 @@ index ce9df7a36..93ff17077 100644
      def inner(f):  # type: ignore
          assert f not in RESOLVERS
 @@ -385,7 +385,7 @@ def resolve_constr(cls):  # type: ignore[no-untyped-def]  # pragma: no cover
-
-
+ 
+ 
  # Finally, register all previously-defined types, and patch in our new function
 -for typ in list(pydantic.types._DEFINED_TYPES):
 +for typ in list(pydantic_types._DEFINED_TYPES):
diff --git a/extensions/positron-python/scripts/patches/pygments.patch b/extensions/positron-python/scripts/patches/pygments.patch
index eed86d1d782e..5e4968342f4f 100644
--- a/extensions/positron-python/scripts/patches/pygments.patch
+++ b/extensions/positron-python/scripts/patches/pygments.patch
@@ -14,7 +14,7 @@ index 435231e65..b75a9d7f4 100644
 -            outfile = colorama.initialise.wrap_stream(
 +            outfile = colorama_initialise.wrap_stream(
                  outfile, convert=None, strip=None, autoreset=False, wrap=True)
-
+ 
      # When using the LaTeX formatter and the option `escapeinside` is
 diff --git a/extensions/positron-python/pythonFiles/positron/positron_ipykernel/_vendor/pygments/__main__.py b/extensions/positron-python/pythonFiles/positron/positron_ipykernel/_vendor/pygments/__main__.py
 index 5eb2c747a..b8b833ec4 100644
@@ -22,11 +22,11 @@ index 5eb2c747a..b8b833ec4 100644
 +++ b/extensions/positron-python/pythonFiles/positron/positron_ipykernel/_vendor/pygments/__main__.py
 @@ -9,9 +9,9 @@
  """
-
+ 
  import sys
 -import pygments.cmdline
 +from pygments.cmdline import main
-
+ 
  try:
 -    sys.exit(pygments.cmdline.main(sys.argv))
 +    sys.exit(main(sys.argv))
@@ -43,14 +43,14 @@ index f935688f1..4c293489f 100644
 -        import pygments.lexers
 +        from pygments.lexers import find_lexer_class
          out = []
-
+ 
          table = []
 @@ -102,7 +102,7 @@ class PygmentsDoc(Directive):
              return name
-
+ 
          for classname, data in sorted(LEXERS.items(), key=lambda x: x[1][1].lower()):
 -            lexer_cls = pygments.lexers.find_lexer_class(data[1])
 +            lexer_cls = find_lexer_class(data[1])
              extensions = lexer_cls.filenames + lexer_cls.alias_filenames
-
+ 
              table.append({
diff --git a/extensions/positron-python/src/test/positron/constants.ts b/extensions/positron-python/src/test/positron/constants.ts
new file mode 100644
index 000000000000..ca006eef4b2b
--- /dev/null
+++ b/extensions/positron-python/src/test/positron/constants.ts
@@ -0,0 +1,22 @@
+/*---------------------------------------------------------------------------------------------
+ *  Copyright (C) 2024 Posit Software, PBC. All rights reserved.
+ *--------------------------------------------------------------------------------------------*/
+
+import * as fs from 'fs-extra';
+import * as os from 'os';
+import * as path from 'path';
+
+/**
+ * Get the path to the user data directory for tests.
+ *
+ * Uses the environment variable POSITRON_USER_DATA_DIR if set, otherwise creates a new temporary
+ * directory and sets the environment variable.
+ *
+ * @returns The path to the user data directory.
+ */
+export async function getUserDataDir(): Promise<string> {
+    if (!process.env.POSITRON_USER_DATA_DIR) {
+        process.env.POSITRON_USER_DATA_DIR = await fs.mkdtemp(path.join(os.tmpdir(), 'positron-'));
+    }
+    return process.env.POSITRON_USER_DATA_DIR;
+}
diff --git a/extensions/positron-python/src/test/positron/testElectron.ts b/extensions/positron-python/src/test/positron/testElectron.ts
index e5b929b92ba1..da47896571a1 100644
--- a/extensions/positron-python/src/test/positron/testElectron.ts
+++ b/extensions/positron-python/src/test/positron/testElectron.ts
@@ -11,6 +11,7 @@ import * as path from 'path';
 import { defaultCachePath } from '@vscode/test-electron/out/download';
 import { TestOptions } from '@vscode/test-electron/out/runTest';
 import { runTests as vscodeRunTests } from '@vscode/test-electron';
+import { getUserDataDir } from './constants';
 
 const rmrf = require('rimraf');
 
@@ -341,9 +342,16 @@ export async function downloadAndUnzipPositron(): Promise<{ version: string; exe
 }
 
 /**
- * Wrap `@vscode/test-electron/runTests` to download and use the latest Positron release.
+ * Wrap `@vscode/test-electron/runTests` to support Positron.
  */
 export async function runTests(options: TestOptions): Promise<number> {
     const { version, executablePath: vscodeExecutablePath } = await downloadAndUnzipPositron();
+
+    // Run tests with a temporary user data dir to ensure no leftover state.
+    // This is also necessary for upstream debugger tests on CI since otherwise the debugger tests
+    // fail due to the path being too long.
+    options.launchArgs = options.launchArgs || [];
+    options.launchArgs.push('--user-data-dir', await getUserDataDir());
+
     return vscodeRunTests({ version, vscodeExecutablePath, ...options });
 }
diff --git a/extensions/positron-python/src/test/smokeTest.ts b/extensions/positron-python/src/test/smokeTest.ts
index 47fd24992cc0..15aa2d04de1d 100644
--- a/extensions/positron-python/src/test/smokeTest.ts
+++ b/extensions/positron-python/src/test/smokeTest.ts
@@ -13,6 +13,10 @@ import * as path from 'path';
 import { unzip } from './common';
 import { EXTENSION_ROOT_DIR_FOR_TESTS, SMOKE_TEST_EXTENSIONS_DIR } from './constants';
 
+// --- Start Positron ---
+import { getUserDataDir } from './positron/constants';
+// --- End Positron ---
+
 class TestRunner {
     public async start() {
         console.log('Start Test Runner');
@@ -55,7 +59,7 @@ class TestRunner {
     }
     // --- Start Positron ---
     private async enableExperiments() {
-        const settingsFile = path.join('.vscode-test', 'user-data', 'User', 'settings.json');
+        const settingsFile = path.join(await getUserDataDir(), 'User', 'settings.json');
 
         await fs.mkdir(path.dirname(settingsFile), { recursive: true });
 
diff --git a/extensions/positron-python/src/test/standardTest.ts b/extensions/positron-python/src/test/standardTest.ts
index beb840917c3e..9aa552b62b6c 100644
--- a/extensions/positron-python/src/test/standardTest.ts
+++ b/extensions/positron-python/src/test/standardTest.ts
@@ -8,6 +8,10 @@ import { EXTENSION_ROOT_DIR_FOR_TESTS } from './constants';
 import { downloadAndUnzipPositron } from './positron/testElectron';
 import { TestOptions } from '@vscode/test-electron/out/runTest';
 
+// --- Start Positron ---
+import { getUserDataDir } from './positron/constants';
+// --- End Positron ---
+
 // If running smoke tests, we don't have access to this.
 if (process.env.TEST_FILES_SUFFIX !== 'smoke.test') {
     const logger = require('./testLogger');
@@ -91,6 +95,12 @@ async function start() {
         .concat([workspacePath])
         .concat(channel === 'insiders' ? ['--enable-proposed-api'] : [])
         .concat(['--timeout', '5000']);
+    // --- Start Positron ---
+    // Run tests with a temporary user data dir to ensure no leftover state.
+    // This is also necessary for upstream debugger tests on CI since otherwise the debugger tests
+    // fail due to the path being too long.
+    launchArgs.push('--user-data-dir', await getUserDataDir());
+    // --- End Positron ---
     console.log(`Starting vscode ${channel} with args ${launchArgs.join(' ')}`);
     const options: TestOptions = {
         // --- Start Positron ---