diff --git a/.github/workflows/build-and-release.yml b/.github/workflows/build-and-release.yml
index f9ca4da..7423778 100644
--- a/.github/workflows/build-and-release.yml
+++ b/.github/workflows/build-and-release.yml
@@ -44,9 +44,7 @@ jobs:
           NODE_AUTH_TOKEN: ${{ secrets.NPM_PUBLISH_TOKEN }}
 
       - name: Setup safe-chain
-        run: |
-          npm i -g @aikidosec/safe-chain
-          safe-chain setup-ci
+        run: curl -fsSL https://raw.githubusercontent.com/AikidoSec/safe-chain/main/install-scripts/install-safe-chain.sh | sh -s -- --ci
 
       - name: Set the version in safe-chain package
         run: npm --no-git-tag-version version ${{ needs.set-version.outputs.version }} --workspace=packages/safe-chain
@@ -77,21 +75,35 @@ jobs:
 
       - name: Rename binaries to include platform and architecture
         run: |
-          mv binaries/safe-chain-macos-x64/safe-chain binaries/safe-chain-macos-x64/safe-chain-macos-x64
-          mv binaries/safe-chain-macos-arm64/safe-chain binaries/safe-chain-macos-arm64/safe-chain-macos-arm64
-          mv binaries/safe-chain-linux-x64/safe-chain binaries/safe-chain-linux-x64/safe-chain-linux-x64
-          mv binaries/safe-chain-linux-arm64/safe-chain binaries/safe-chain-linux-arm64/safe-chain-linux-arm64
-          mv binaries/safe-chain-win-x64/safe-chain.exe binaries/safe-chain-win-x64/safe-chain-win-x64.exe
-          mv binaries/safe-chain-win-arm64/safe-chain.exe binaries/safe-chain-win-arm64/safe-chain-win-arm64.exe
+          mkdir release-artifacts
+          mv binaries/safe-chain-macos-x64/safe-chain release-artifacts/safe-chain-macos-x64
+          mv binaries/safe-chain-macos-arm64/safe-chain release-artifacts/safe-chain-macos-arm64
+          mv binaries/safe-chain-linux-x64/safe-chain release-artifacts/safe-chain-linux-x64
+          mv binaries/safe-chain-linux-arm64/safe-chain release-artifacts/safe-chain-linux-arm64
+          mv binaries/safe-chain-win-x64/safe-chain.exe release-artifacts/safe-chain-win-x64.exe
+          mv binaries/safe-chain-win-arm64/safe-chain.exe release-artifacts/safe-chain-win-arm64.exe
+
+      - name: Move install scripts and hard-code version
+        env:
+          VERSION: ${{ needs.set-version.outputs.version }}
+        run: |
+          sed "s/\$(fetch_latest_version)/${VERSION}/" install-scripts/install-safe-chain.sh > release-artifacts/install-safe-chain.sh
+          sed "s/\$Version = Get-LatestVersion/\$Version = \"${VERSION}\"/" install-scripts/install-safe-chain.ps1 > release-artifacts/install-safe-chain.ps1
+          cp install-scripts/uninstall-safe-chain.sh release-artifacts/uninstall-safe-chain.sh
+          cp install-scripts/uninstall-safe-chain.ps1 release-artifacts/uninstall-safe-chain.ps1
 
       - name: Upload binaries to existing GitHub Release
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
           gh release upload ${{ needs.set-version.outputs.version }} \
-            binaries/safe-chain-macos-x64/* \
-            binaries/safe-chain-macos-arm64/* \
-            binaries/safe-chain-linux-x64/* \
-            binaries/safe-chain-linux-arm64/* \
-            binaries/safe-chain-win-x64/* \
-            binaries/safe-chain-win-arm64/*
+            release-artifacts/safe-chain-macos-x64 \
+            release-artifacts/safe-chain-macos-arm64 \
+            release-artifacts/safe-chain-linux-x64 \
+            release-artifacts/safe-chain-linux-arm64 \
+            release-artifacts/safe-chain-win-x64.exe \
+            release-artifacts/safe-chain-win-arm64.exe \
+            release-artifacts/install-safe-chain.sh \
+            release-artifacts/install-safe-chain.ps1 \
+            release-artifacts/uninstall-safe-chain.sh \
+            release-artifacts/uninstall-safe-chain.ps1
diff --git a/.github/workflows/create-artifact.yml b/.github/workflows/create-artifact.yml
index ad43a9d..d57bce9 100644
--- a/.github/workflows/create-artifact.yml
+++ b/.github/workflows/create-artifact.yml
@@ -5,7 +5,7 @@ on:
   workflow_call:
     inputs:
       version:
-        description: 'Version to set in package.json'
+        description: "Version to set in package.json"
         required: false
         type: string
 
@@ -59,18 +59,22 @@ jobs:
         with:
           node-version: "20.x"
 
-      - name: Setup safe-chain
-        run: |
-          npm i -g @aikidosec/safe-chain
-          safe-chain setup-ci
+      - name: Setup safe-chain (Mac/Linux)
+        if: runner.os != 'Windows'
+        run: curl -fsSL https://raw.githubusercontent.com/AikidoSec/safe-chain/main/install-scripts/install-safe-chain.sh | sh -s -- --ci
 
-      - name: Set the version in safe-chain package
-        if: inputs.version != ''
-        run: npm --no-git-tag-version version ${{ inputs.version }} --workspace=packages/safe-chain
+      - name: Setup safe-chain (Windows)
+        if: runner.os == 'Windows'
+        shell: pwsh
+        run: iex "& { $(iwr 'https://raw.githubusercontent.com/AikidoSec/safe-chain/main/install-scripts/install-safe-chain.ps1' -UseBasicParsing) } -ci"
 
       - name: Install dependencies
         run: npm ci --ignore-scripts
 
+      - name: Set the version in safe-chain package
+        if: inputs.version != ''
+        run: npm --no-git-tag-version version ${{ inputs.version }} --workspace=packages/safe-chain --ignore-scripts
+
       - name: Create binary
         run: |
           node build.js ${{ matrix.target }}
diff --git a/.github/workflows/test-on-pr.yml b/.github/workflows/test-on-pr.yml
index f754931..8811944 100644
--- a/.github/workflows/test-on-pr.yml
+++ b/.github/workflows/test-on-pr.yml
@@ -110,9 +110,7 @@ jobs:
           node-version: "lts/*"
 
       - name: Setup safe-chain
-        run: |
-          npm i -g @aikidosec/safe-chain@1.0.24
-          safe-chain setup-ci
+        run: curl -fsSL https://raw.githubusercontent.com/AikidoSec/safe-chain/main/install-scripts/install-safe-chain.sh | sh -s -- --ci
 
       - name: Install dependencies (root)
         run: npm ci
diff --git a/README.md b/README.md
index 28b94cf..6b424f1 100644
--- a/README.md
+++ b/README.md
@@ -19,10 +19,10 @@ Aikido Safe Chain supports the following package managers:
 - 📦 **pnpx**
 - 📦 **bun**
 - 📦 **bunx**
-- 📦 **pip** (beta)
-- 📦 **pip3** (beta)
-- 📦 **uv** (beta)
-- 📦 **poetry** (beta)
+- 📦 **pip**
+- 📦 **pip3**
+- 📦 **uv**
+- 📦 **poetry**
 
 # Usage
 
@@ -34,32 +34,32 @@ Installing the Aikido Safe Chain is easy with our one-line installer.
 
 ### Unix/Linux/macOS
 
-**Default installation (JavaScript packages only):**
-
 ```shell
-curl -fsSL https://raw.githubusercontent.com/AikidoSec/safe-chain/main/install-scripts/install-safe-chain.sh | sh
-```
-
-**Include Python support (pip/pip3/uv):**
-
-```shell
-curl -fsSL https://raw.githubusercontent.com/AikidoSec/safe-chain/main/install-scripts/install-safe-chain.sh | sh -s -- --include-python
+curl -fsSL https://github.com/AikidoSec/safe-chain/releases/latest/download/install-safe-chain.sh | sh
 ```
 
 ### Windows (PowerShell)
 
-**Default installation (JavaScript packages only):**
-
 ```powershell
-iex (iwr "https://raw.githubusercontent.com/AikidoSec/safe-chain/main/install-scripts/install-safe-chain.ps1" -UseBasicParsing)
+iex (iwr "https://github.com/AikidoSec/safe-chain/releases/latest/download/install-safe-chain.ps1" -UseBasicParsing)
 ```
 
-**Include Python support (pip/pip3/uv):**
+### Pinning to a specific version
 
-```powershell
-iex "& { $(iwr 'https://raw.githubusercontent.com/AikidoSec/safe-chain/main/install-scripts/install-safe-chain.ps1' -UseBasicParsing) } -includepython"
+To install a specific version instead of the latest, replace `latest` with the version number in the URL (available from version 1.3.2 onwards):
+
+**Unix/Linux/macOS:**
+```shell
+curl -fsSL https://github.com/AikidoSec/safe-chain/releases/download/x.x.x/install-safe-chain.sh | sh
 ```
 
+**Windows (PowerShell):**
+```powershell
+iex (iwr "https://github.com/AikidoSec/safe-chain/releases/download/x.x.x/install-safe-chain.ps1" -UseBasicParsing)
+```
+
+You can find all available versions on the [releases page](https://github.com/AikidoSec/safe-chain/releases).
+
 ### Verify the installation
 
 1. **❗Restart your terminal** to start using the Aikido Safe Chain.
@@ -74,7 +74,7 @@ iex "& { $(iwr 'https://raw.githubusercontent.com/AikidoSec/safe-chain/main/inst
    npm install safe-chain-test
    ```
 
-   For Python (if you enabled Python support):
+   For Python:
 
    ```shell
    pip3 install safe-chain-pi-test
@@ -121,13 +121,13 @@ To uninstall the Aikido Safe Chain, use our one-line uninstaller:
 ### Unix/Linux/macOS
 
 ```shell
-curl -fsSL https://raw.githubusercontent.com/AikidoSec/safe-chain/main/install-scripts/uninstall-safe-chain.sh | sh
+curl -fsSL https://github.com/AikidoSec/safe-chain/releases/latest/download/uninstall-safe-chain.sh | sh
 ```
 
 ### Windows (PowerShell)
 
 ```powershell
-iex (iwr "https://raw.githubusercontent.com/AikidoSec/safe-chain/main/install-scripts/uninstall-safe-chain.ps1" -UseBasicParsing)
+iex (iwr "https://github.com/AikidoSec/safe-chain/releases/latest/download/uninstall-safe-chain.ps1" -UseBasicParsing)
 ```
 
 **❗Restart your terminal** after uninstalling to ensure all aliases are removed.
@@ -193,30 +193,14 @@ Use the `--ci` flag to automatically configure Aikido Safe Chain for CI/CD envir
 
 ### Unix/Linux/macOS (GitHub Actions, Azure Pipelines, etc.)
 
-**JavaScript only:**
-
 ```shell
-curl -fsSL https://raw.githubusercontent.com/AikidoSec/safe-chain/main/install-scripts/install-safe-chain.sh | sh -s -- --ci
-```
-
-**With Python support:**
-
-```shell
-curl -fsSL https://raw.githubusercontent.com/AikidoSec/safe-chain/main/install-scripts/install-safe-chain.sh | sh -s -- --ci --include-python
+curl -fsSL https://github.com/AikidoSec/safe-chain/releases/latest/download/install-safe-chain.sh | sh -s -- --ci
 ```
 
 ### Windows (Azure Pipelines, etc.)
 
-**JavaScript only:**
-
 ```powershell
-iex "& { $(iwr 'https://raw.githubusercontent.com/AikidoSec/safe-chain/main/install-scripts/install-safe-chain.ps1' -UseBasicParsing) } -ci"
-```
-
-**With Python support:**
-
-```powershell
-iex "& { $(iwr 'https://raw.githubusercontent.com/AikidoSec/safe-chain/main/install-scripts/install-safe-chain.ps1' -UseBasicParsing) } -ci -includepython"
+iex "& { $(iwr 'https://github.com/AikidoSec/safe-chain/releases/latest/download/install-safe-chain.ps1' -UseBasicParsing) } -ci"
 ```
 
 ## Supported Platforms
@@ -234,14 +218,12 @@ iex "& { $(iwr 'https://raw.githubusercontent.com/AikidoSec/safe-chain/main/inst
     cache: "npm"
 
 - name: Install safe-chain
-  run: curl -fsSL https://raw.githubusercontent.com/AikidoSec/safe-chain/main/install-scripts/install-safe-chain.sh | sh -s -- --ci --include-python
+  run: curl -fsSL https://github.com/AikidoSec/safe-chain/releases/latest/download/install-safe-chain.sh | sh -s -- --ci
 
 - name: Install dependencies
   run: npm ci
 ```
 
-> **Note:** Remove `--include-python` if you don't need Python (pip/pip3/uv/poetry) support.
-
 ## Azure DevOps Example
 
 ```yaml
@@ -250,13 +232,11 @@ iex "& { $(iwr 'https://raw.githubusercontent.com/AikidoSec/safe-chain/main/inst
     versionSpec: "22.x"
   displayName: "Install Node.js"
 
-- script: curl -fsSL https://raw.githubusercontent.com/AikidoSec/safe-chain/main/install-scripts/install-safe-chain.sh | sh -s -- --ci --include-python
+- script: curl -fsSL https://github.com/AikidoSec/safe-chain/releases/latest/download/install-safe-chain.sh | sh -s -- --ci
   displayName: "Install safe-chain"
 
 - script: npm ci
   displayName: "Install dependencies"
 ```
 
-> **Note:** Remove `--include-python` if you don't need Python (pip/pip3/uv/poetry) support.
-
 After setup, all subsequent package manager commands in your CI pipeline will automatically be protected by Aikido Safe Chain's malware detection.
diff --git a/install-scripts/install-safe-chain.ps1 b/install-scripts/install-safe-chain.ps1
index 081d232..51d15ba 100644
--- a/install-scripts/install-safe-chain.ps1
+++ b/install-scripts/install-safe-chain.ps1
@@ -31,6 +31,46 @@ function Write-Error-Custom {
     exit 1
 }
 
+# Get currently installed version of safe-chain
+function Get-InstalledVersion {
+    # Check if safe-chain command exists
+    if (-not (Get-Command safe-chain -ErrorAction SilentlyContinue)) {
+        return $null
+    }
+
+    try {
+        # Execute safe-chain -v and capture output
+        $output = & safe-chain -v 2>&1
+
+        # Extract version from "Current safe-chain version: X.Y.Z" output
+        if ($output -match "Current safe-chain version:\s*(.+)") {
+            return $matches[1].Trim()
+        }
+
+        return $null
+    }
+    catch {
+        return $null
+    }
+}
+
+# Check if the requested version is already installed
+function Test-VersionInstalled {
+    param([string]$RequestedVersion)
+
+    $installedVersion = Get-InstalledVersion
+
+    if ([string]::IsNullOrWhiteSpace($installedVersion)) {
+        return $false
+    }
+
+    # Strip leading 'v' from versions if present for comparison
+    $requestedClean = $RequestedVersion -replace '^v', ''
+    $installedClean = $installedVersion -replace '^v', ''
+
+    return $requestedClean -eq $installedClean
+}
+
 # Fetch latest release version tag from GitHub
 function Get-LatestVersion {
     try {
@@ -115,14 +155,20 @@ function Install-SafeChain {
         $Version = Get-LatestVersion
     }
 
+    # Check if the requested version is already installed
+    if (Test-VersionInstalled -RequestedVersion $Version) {
+        Write-Info "safe-chain $Version is already installed"
+        return
+    }
+
     # Build installation message
     $installMsg = "Installing safe-chain $Version"
-    if ($includepython) {
-        $installMsg += " with python"
-    }
     if ($ci) {
         $installMsg += " in ci"
     }
+    if ($includepython) {
+        Write-Warn "-includepython is deprecated and ignored. Python ecosystem is now included by default."
+    }
 
     Write-Info $installMsg
 
@@ -181,9 +227,6 @@ function Install-SafeChain {
     # Build setup command based on parameters
     $setupCmd = if ($ci) { "setup-ci" } else { "setup" }
     $setupArgs = @()
-    if ($includepython) {
-        $setupArgs += "--include-python"
-    }
 
     # Execute safe-chain setup
     Write-Info "Running safe-chain $setupCmd $(if ($setupArgs) { $setupArgs -join ' ' })..."
diff --git a/install-scripts/install-safe-chain.sh b/install-scripts/install-safe-chain.sh
index 2afb583..94a9b55 100755
--- a/install-scripts/install-safe-chain.sh
+++ b/install-scripts/install-safe-chain.sh
@@ -54,6 +54,38 @@ command_exists() {
     command -v "$1" >/dev/null 2>&1
 }
 
+# Get currently installed version of safe-chain
+get_installed_version() {
+    if ! command_exists safe-chain; then
+        echo ""
+        return
+    fi
+
+    # Extract version from "Current safe-chain version: X.Y.Z" output
+    installed_version=$(safe-chain -v 2>/dev/null | grep "Current safe-chain version:" | sed -E 's/.*: (.*)/\1/')
+    echo "$installed_version"
+}
+
+# Check if the requested version is already installed
+is_version_installed() {
+    requested_version="$1"
+    installed_version=$(get_installed_version)
+
+    if [ -z "$installed_version" ]; then
+        return 1  # Not installed
+    fi
+
+    # Strip leading 'v' from versions if present for comparison
+    requested_clean=$(echo "$requested_version" | sed 's/^v//')
+    installed_clean=$(echo "$installed_version" | sed 's/^v//')
+
+    if [ "$requested_clean" = "$installed_clean" ]; then
+        return 0  # Same version installed
+    else
+        return 1  # Different version installed
+    fi
+}
+
 # Fetch latest release version tag from GitHub
 fetch_latest_version() {
     # Try using GitHub API to get the latest release tag
@@ -135,7 +167,7 @@ parse_arguments() {
                 USE_CI_SETUP=true
                 ;;
             --include-python)
-                INCLUDE_PYTHON=true
+                warn "--include-python is deprecated and ignored. Python ecosystem is now included by default."
                 ;;
             *)
                 error "Unknown argument: $arg"
@@ -148,7 +180,6 @@ parse_arguments() {
 main() {
     # Initialize argument flags
     USE_CI_SETUP=false
-    INCLUDE_PYTHON=false
 
     # Parse command-line arguments
     parse_arguments "$@"
@@ -159,11 +190,14 @@ main() {
         VERSION=$(fetch_latest_version)
     fi
 
+    # Check if the requested version is already installed
+    if is_version_installed "$VERSION"; then
+        info "safe-chain ${VERSION} is already installed"
+        exit 0
+    fi
+
     # Build installation message
     INSTALL_MSG="Installing safe-chain ${VERSION}"
-    if [ "$INCLUDE_PYTHON" = "true" ]; then
-        INSTALL_MSG="${INSTALL_MSG} with python"
-    fi
     if [ "$USE_CI_SETUP" = "true" ]; then
         INSTALL_MSG="${INSTALL_MSG} in ci"
     fi
@@ -209,10 +243,6 @@ main() {
         SETUP_CMD="setup-ci"
     fi
 
-    if [ "$INCLUDE_PYTHON" = "true" ]; then
-        SETUP_ARGS="--include-python"
-    fi
-
     # Execute safe-chain setup
     info "Running safe-chain $SETUP_CMD $SETUP_ARGS..."
     if ! "$FINAL_FILE" $SETUP_CMD $SETUP_ARGS; then
diff --git a/packages/safe-chain/bin/safe-chain.js b/packages/safe-chain/bin/safe-chain.js
index 802005b..aed77f0 100755
--- a/packages/safe-chain/bin/safe-chain.js
+++ b/packages/safe-chain/bin/safe-chain.js
@@ -95,11 +95,6 @@ function writeHelp() {
       "safe-chain setup"
     )}: This will setup your shell to wrap safe-chain around npm, npx, yarn, pnpm, pnpx, bun, bunx, pip and pip3.`
   );
-  ui.writeInformation(
-    `    ${chalk.yellow(
-      "--include-python"
-    )}: Experimental: include Python package managers (pip, pip3) in the setup.`
-  );
   ui.writeInformation(
     `- ${chalk.cyan(
       "safe-chain teardown"
@@ -110,11 +105,6 @@ function writeHelp() {
       "safe-chain setup-ci"
     )}: This will setup safe-chain for CI environments by creating shims and modifying the PATH.`
   );
-  ui.writeInformation(
-    `    ${chalk.yellow(
-      "--include-python"
-    )}: Experimental: include Python package managers (pip, pip3) in the setup.`
-  );
   ui.writeInformation(
     `- ${chalk.cyan("safe-chain --version")} (or ${chalk.cyan(
       "-v"
diff --git a/packages/safe-chain/src/config/cliArguments.js b/packages/safe-chain/src/config/cliArguments.js
index ddcd8b9..25013fb 100644
--- a/packages/safe-chain/src/config/cliArguments.js
+++ b/packages/safe-chain/src/config/cliArguments.js
@@ -1,11 +1,12 @@
+import { ui } from "../environment/userInteraction.js";
+
 /**
- * @type {{loggingLevel: string | undefined, skipMinimumPackageAge: boolean | undefined, minimumPackageAgeHours: string | undefined, includePython: boolean}}
+ * @type {{loggingLevel: string | undefined, skipMinimumPackageAge: boolean | undefined, minimumPackageAgeHours: string | undefined}}
  */
 const state = {
   loggingLevel: undefined,
   skipMinimumPackageAge: undefined,
   minimumPackageAgeHours: undefined,
-  includePython: false,
 };
 
 const SAFE_CHAIN_ARG_PREFIX = "--safe-chain-";
@@ -34,8 +35,7 @@ export function initializeCliArguments(args) {
   setLoggingLevel(safeChainArgs);
   setSkipMinimumPackageAge(safeChainArgs);
   setMinimumPackageAgeHours(safeChainArgs);
-  setIncludePython(args);
-
+  checkDeprecatedPythonFlag(args);
   return remainingArgs;
 }
 
@@ -109,20 +109,6 @@ export function getMinimumPackageAgeHours() {
   return state.minimumPackageAgeHours;
 }
 
-/**
- * @param {string[]} args
- */
-function setIncludePython(args) {
-  // This flag doesn't have the --safe-chain- prefix because
-  // it is only used for the safe-chain command itself and
-  // not when wrapped around package manager commands.
-  state.includePython = hasFlagArg(args, "--include-python");
-}
-
-export function includePython() {
-  return state.includePython;
-}
-
 /**
  * @param {string[]} args
  * @param {string} flagName
@@ -136,3 +122,17 @@ function hasFlagArg(args, flagName) {
   }
   return false;
 }
+
+/**
+ * Emits a deprecation warning for legacy --include-python flag
+ *
+ * @param {string[]} args
+ * @returns {void}
+ */
+export function checkDeprecatedPythonFlag(args) {
+  if (hasFlagArg(args, "--include-python")) {
+    ui.writeWarning(
+      "--include-python is deprecated and ignored. Python tooling is included by default."
+    );
+  }
+}
diff --git a/packages/safe-chain/src/config/cliArguments.spec.js b/packages/safe-chain/src/config/cliArguments.spec.js
index bbd5121..8b505be 100644
--- a/packages/safe-chain/src/config/cliArguments.spec.js
+++ b/packages/safe-chain/src/config/cliArguments.spec.js
@@ -6,6 +6,7 @@ import {
   getSkipMinimumPackageAge,
   getMinimumPackageAgeHours,
 } from "./cliArguments.js";
+import { ui } from "../environment/userInteraction.js";
 
 describe("initializeCliArguments", () => {
   it("should return all args when no safe-chain args are present", () => {
@@ -271,4 +272,40 @@ describe("initializeCliArguments", () => {
 
     assert.strictEqual(getMinimumPackageAgeHours(), "-24");
   });
+
+  it("should warn on deprecated --include-python for setup", () => {
+    const warnings = [];
+    const originalWriteWarning = ui.writeWarning;
+    ui.writeWarning = (msg, ..._rest) => {
+      warnings.push(String(msg));
+    };
+    try {
+      const argv = ["node", "safe-chain", "setup", "--include-python"];
+      initializeCliArguments(argv);
+      assert.ok(
+        warnings.some((m) => m.includes("--include-python is deprecated")),
+        "Expected a deprecation warning for --include-python in setup"
+      );
+    } finally {
+      ui.writeWarning = originalWriteWarning;
+    }
+  });
+
+  it("should warn on deprecated --include-python for setup-ci", () => {
+    const warnings = [];
+    const originalWriteWarning = ui.writeWarning;
+    ui.writeWarning = (msg, ..._rest) => {
+      warnings.push(String(msg));
+    };
+    try {
+      const argv = ["node", "safe-chain", "setup-ci", "--include-python"];
+      initializeCliArguments(argv);
+      assert.ok(
+        warnings.some((m) => m.includes("--include-python is deprecated")),
+        "Expected a deprecation warning for --include-python in setup-ci"
+      );
+    } finally {
+      ui.writeWarning = originalWriteWarning;
+    }
+  });
 });
diff --git a/packages/safe-chain/src/config/configFile.spec.js b/packages/safe-chain/src/config/configFile.spec.js
index 17a7577..7da7e8d 100644
--- a/packages/safe-chain/src/config/configFile.spec.js
+++ b/packages/safe-chain/src/config/configFile.spec.js
@@ -1,32 +1,24 @@
 import { describe, it, beforeEach, afterEach, mock } from "node:test";
 import assert from "node:assert";
 
-describe("getScanTimeout", () => {
+let configFileContent = undefined;
+mock.module("fs", {
+  namedExports: {
+    existsSync: () => configFileContent !== undefined,
+    readFileSync: () => configFileContent,
+    writeFileSync: (content) => (configFileContent = content),
+    mkdirSync: () => {},
+  },
+});
+
+describe("getScanTimeout", async () => {
   let originalEnv;
-  let fsMock;
-  let getScanTimeout;
+
+  const { getScanTimeout } = await import("./configFile.js");
 
   beforeEach(async () => {
     // Save original environment
     originalEnv = process.env.AIKIDO_SCAN_TIMEOUT_MS;
-
-    // Mock fs module
-    fsMock = {
-      existsSync: mock.fn(() => false),
-      readFileSync: mock.fn(() => "{}"),
-      writeFileSync: mock.fn(),
-      mkdirSync: mock.fn(),
-    };
-
-    mock.module("fs", {
-      namedExports: fsMock,
-    });
-
-    // Re-import the module to get the mocked version
-    const configFileModule = await import(
-      `./configFile.js?update=${Date.now()}`
-    );
-    getScanTimeout = configFileModule.getScanTimeout;
   });
 
   afterEach(() => {
@@ -37,14 +29,12 @@ describe("getScanTimeout", () => {
       delete process.env.AIKIDO_SCAN_TIMEOUT_MS;
     }
 
-    // Reset all mocks
-    mock.restoreAll();
+    configFileContent = undefined;
   });
 
   it("should return default timeout of 10000ms when no config or env var is set", () => {
     delete process.env.AIKIDO_SCAN_TIMEOUT_MS;
-    // Mock: config file doesn't exist
-    fsMock.existsSync.mock.mockImplementation(() => false);
+    configFileContent = undefined;
 
     const timeout = getScanTimeout();
 
@@ -53,11 +43,7 @@ describe("getScanTimeout", () => {
 
   it("should return timeout from config file when set", () => {
     delete process.env.AIKIDO_SCAN_TIMEOUT_MS;
-    // Mock: config file exists with scanTimeout: 5000
-    fsMock.existsSync.mock.mockImplementation(() => true);
-    fsMock.readFileSync.mock.mockImplementation(() =>
-      JSON.stringify({ scanTimeout: 5000 })
-    );
+    configFileContent = JSON.stringify({ scanTimeout: 5000 });
 
     const timeout = getScanTimeout();
 
@@ -66,11 +52,7 @@ describe("getScanTimeout", () => {
 
   it("should prioritize environment variable over config file", () => {
     process.env.AIKIDO_SCAN_TIMEOUT_MS = "20000";
-    // Mock: config file exists with scanTimeout: 5000
-    fsMock.existsSync.mock.mockImplementation(() => true);
-    fsMock.readFileSync.mock.mockImplementation(() =>
-      JSON.stringify({ scanTimeout: 5000 })
-    );
+    configFileContent = JSON.stringify({ scanTimeout: 5000 });
 
     const timeout = getScanTimeout();
 
@@ -79,11 +61,7 @@ describe("getScanTimeout", () => {
 
   it("should handle invalid environment variable and fall back to config", () => {
     process.env.AIKIDO_SCAN_TIMEOUT_MS = "invalid";
-    // Mock: config file exists with scanTimeout: 7000
-    fsMock.existsSync.mock.mockImplementation(() => true);
-    fsMock.readFileSync.mock.mockImplementation(() =>
-      JSON.stringify({ scanTimeout: 7000 })
-    );
+    configFileContent = JSON.stringify({ scanTimeout: 7000 });
 
     const timeout = getScanTimeout();
 
@@ -91,8 +69,7 @@ describe("getScanTimeout", () => {
   });
 
   it("should ignore zero and negative values and fall back to default", () => {
-    // Mock: config file doesn't exist
-    fsMock.existsSync.mock.mockImplementation(() => false);
+    configFileContent = undefined;
 
     process.env.AIKIDO_SCAN_TIMEOUT_MS = "0";
 
@@ -107,11 +84,7 @@ describe("getScanTimeout", () => {
 
   it("should ignore textual non-numeric values in environment variable and fall back to config", () => {
     process.env.AIKIDO_SCAN_TIMEOUT_MS = "fast";
-    // Mock: config file exists with scanTimeout: 8000
-    fsMock.existsSync.mock.mockImplementation(() => true);
-    fsMock.readFileSync.mock.mockImplementation(() =>
-      JSON.stringify({ scanTimeout: 8000 })
-    );
+    configFileContent = JSON.stringify({ scanTimeout: 8000 });
 
     const timeout = getScanTimeout();
 
@@ -120,11 +93,7 @@ describe("getScanTimeout", () => {
 
   it("should ignore textual non-numeric values in config file and fall back to default", () => {
     delete process.env.AIKIDO_SCAN_TIMEOUT_MS;
-    // Mock: config file exists with scanTimeout: "slow"
-    fsMock.existsSync.mock.mockImplementation(() => true);
-    fsMock.readFileSync.mock.mockImplementation(() =>
-      JSON.stringify({ scanTimeout: "slow" })
-    );
+    configFileContent = JSON.stringify({ scanTimeout: "slow" });
 
     const timeout = getScanTimeout();
 
@@ -133,11 +102,7 @@ describe("getScanTimeout", () => {
 
   it("should ignore textual non-numeric values in both env and config, fall back to default", () => {
     process.env.AIKIDO_SCAN_TIMEOUT_MS = "quick";
-    // Mock: config file exists with scanTimeout: "medium"
-    fsMock.existsSync.mock.mockImplementation(() => true);
-    fsMock.readFileSync.mock.mockImplementation(() =>
-      JSON.stringify({ scanTimeout: "medium" })
-    );
+    configFileContent = JSON.stringify({ scanTimeout: "medium" });
 
     const timeout = getScanTimeout();
 
@@ -146,11 +111,7 @@ describe("getScanTimeout", () => {
 
   it("should ignore mixed alphanumeric strings in environment variable", () => {
     process.env.AIKIDO_SCAN_TIMEOUT_MS = "5000ms";
-    // Mock: config file exists with scanTimeout: 6000
-    fsMock.existsSync.mock.mockImplementation(() => true);
-    fsMock.readFileSync.mock.mockImplementation(() =>
-      JSON.stringify({ scanTimeout: 6000 })
-    );
+    configFileContent = JSON.stringify({ scanTimeout: 6000 });
 
     const timeout = getScanTimeout();
 
@@ -159,11 +120,7 @@ describe("getScanTimeout", () => {
 
   it("should ignore mixed alphanumeric strings in config file", () => {
     delete process.env.AIKIDO_SCAN_TIMEOUT_MS;
-    // Mock: config file exists with scanTimeout: "3000ms"
-    fsMock.existsSync.mock.mockImplementation(() => true);
-    fsMock.readFileSync.mock.mockImplementation(() =>
-      JSON.stringify({ scanTimeout: "3000ms" })
-    );
+    configFileContent = JSON.stringify({ scanTimeout: "3000ms" });
 
     const timeout = getScanTimeout();
 
@@ -171,37 +128,15 @@ describe("getScanTimeout", () => {
   });
 });
 
-describe("getMinimumPackageAgeHours", () => {
-  let fsMock;
-  let getMinimumPackageAgeHours;
-
-  beforeEach(async () => {
-    // Mock fs module
-    fsMock = {
-      existsSync: mock.fn(() => false),
-      readFileSync: mock.fn(() => "{}"),
-      writeFileSync: mock.fn(),
-      mkdirSync: mock.fn(),
-    };
-
-    mock.module("fs", {
-      namedExports: fsMock,
-    });
-
-    // Re-import the module to get the mocked version
-    const configFileModule = await import(
-      `./configFile.js?update=${Date.now()}`
-    );
-    getMinimumPackageAgeHours = configFileModule.getMinimumPackageAgeHours;
-  });
+describe("getMinimumPackageAgeHours", async () => {
+  const { getMinimumPackageAgeHours } = await import("./configFile.js");
 
   afterEach(() => {
-    // Reset all mocks
-    mock.restoreAll();
+    configFileContent = undefined;
   });
 
   it("should return null when config file doesn't exist", () => {
-    fsMock.existsSync.mock.mockImplementation(() => false);
+    configFileContent = undefined;
 
     const hours = getMinimumPackageAgeHours();
 
@@ -209,10 +144,7 @@ describe("getMinimumPackageAgeHours", () => {
   });
 
   it("should return null when config file exists but minimumPackageAgeHours is not set", () => {
-    fsMock.existsSync.mock.mockImplementation(() => true);
-    fsMock.readFileSync.mock.mockImplementation(() =>
-      JSON.stringify({ scanTimeout: 5000 })
-    );
+    configFileContent = JSON.stringify({ scanTimeout: 5000 });
 
     const hours = getMinimumPackageAgeHours();
 
@@ -220,10 +152,7 @@ describe("getMinimumPackageAgeHours", () => {
   });
 
   it("should return value from config file when set to valid number", () => {
-    fsMock.existsSync.mock.mockImplementation(() => true);
-    fsMock.readFileSync.mock.mockImplementation(() =>
-      JSON.stringify({ minimumPackageAgeHours: 48 })
-    );
+    configFileContent = JSON.stringify({ minimumPackageAgeHours: 48 });
 
     const hours = getMinimumPackageAgeHours();
 
@@ -231,10 +160,7 @@ describe("getMinimumPackageAgeHours", () => {
   });
 
   it("should handle string numbers in config file", () => {
-    fsMock.existsSync.mock.mockImplementation(() => true);
-    fsMock.readFileSync.mock.mockImplementation(() =>
-      JSON.stringify({ minimumPackageAgeHours: "72" })
-    );
+    configFileContent = JSON.stringify({ minimumPackageAgeHours: "72" });
 
     const hours = getMinimumPackageAgeHours();
 
@@ -242,10 +168,7 @@ describe("getMinimumPackageAgeHours", () => {
   });
 
   it("should handle decimal values", () => {
-    fsMock.existsSync.mock.mockImplementation(() => true);
-    fsMock.readFileSync.mock.mockImplementation(() =>
-      JSON.stringify({ minimumPackageAgeHours: 1.5 })
-    );
+    configFileContent = JSON.stringify({ minimumPackageAgeHours: 1.5 });
 
     const hours = getMinimumPackageAgeHours();
 
@@ -253,21 +176,15 @@ describe("getMinimumPackageAgeHours", () => {
   });
 
   it("should return null for non-numeric strings", () => {
-    fsMock.existsSync.mock.mockImplementation(() => true);
-    fsMock.readFileSync.mock.mockImplementation(() =>
-      JSON.stringify({ minimumPackageAgeHours: "invalid" })
-    );
+    configFileContent = JSON.stringify({ minimumPackageAgeHours: "invalid" });
 
     const hours = getMinimumPackageAgeHours();
 
     assert.strictEqual(hours, undefined);
   });
 
-  it("should return null for values with units suffix", () => {
-    fsMock.existsSync.mock.mockImplementation(() => true);
-    fsMock.readFileSync.mock.mockImplementation(() =>
-      JSON.stringify({ minimumPackageAgeHours: "48h" })
-    );
+  it("should return undefined for values with units suffix", () => {
+    configFileContent = JSON.stringify({ minimumPackageAgeHours: "48h" });
 
     const hours = getMinimumPackageAgeHours();
 
@@ -275,8 +192,7 @@ describe("getMinimumPackageAgeHours", () => {
   });
 
   it("should handle malformed JSON and return null", () => {
-    fsMock.existsSync.mock.mockImplementation(() => true);
-    fsMock.readFileSync.mock.mockImplementation(() => "{ invalid json");
+    configFileContent = "{ invalid json";
 
     const hours = getMinimumPackageAgeHours();
 
@@ -284,10 +200,7 @@ describe("getMinimumPackageAgeHours", () => {
   });
 
   it("should return 0 when minimumPackageAgeHours is set to 0", () => {
-    fsMock.existsSync.mock.mockImplementation(() => true);
-    fsMock.readFileSync.mock.mockImplementation(() =>
-      JSON.stringify({ minimumPackageAgeHours: 0 })
-    );
+    configFileContent = JSON.stringify({ minimumPackageAgeHours: 0 });
 
     const hours = getMinimumPackageAgeHours();
 
@@ -295,10 +208,7 @@ describe("getMinimumPackageAgeHours", () => {
   });
 
   it("should return 0 when minimumPackageAgeHours is set to string '0'", () => {
-    fsMock.existsSync.mock.mockImplementation(() => true);
-    fsMock.readFileSync.mock.mockImplementation(() =>
-      JSON.stringify({ minimumPackageAgeHours: "0" })
-    );
+    configFileContent = JSON.stringify({ minimumPackageAgeHours: "0" });
 
     const hours = getMinimumPackageAgeHours();
 
@@ -306,10 +216,7 @@ describe("getMinimumPackageAgeHours", () => {
   });
 
   it("should handle negative numeric values", () => {
-    fsMock.existsSync.mock.mockImplementation(() => true);
-    fsMock.readFileSync.mock.mockImplementation(() =>
-      JSON.stringify({ minimumPackageAgeHours: -24 })
-    );
+    configFileContent = JSON.stringify({ minimumPackageAgeHours: -24 });
 
     const hours = getMinimumPackageAgeHours();
 
@@ -317,86 +224,10 @@ describe("getMinimumPackageAgeHours", () => {
   });
 
   it("should handle negative string values", () => {
-    fsMock.existsSync.mock.mockImplementation(() => true);
-    fsMock.readFileSync.mock.mockImplementation(() =>
-      JSON.stringify({ minimumPackageAgeHours: "-48" })
-    );
+    configFileContent = JSON.stringify({ minimumPackageAgeHours: "-48" });
 
     const hours = getMinimumPackageAgeHours();
 
     assert.strictEqual(hours, -48);
   });
 });
-
-describe("environmentVariables - getMinimumPackageAgeHours", () => {
-  let originalEnv;
-  let getMinimumPackageAgeHours;
-
-  beforeEach(async () => {
-    // Save original environment
-    originalEnv = process.env.SAFE_CHAIN_MINIMUM_PACKAGE_AGE_HOURS;
-
-    // Re-import the module to get fresh version
-    const envModule = await import(
-      `./environmentVariables.js?update=${Date.now()}`
-    );
-    getMinimumPackageAgeHours = envModule.getMinimumPackageAgeHours;
-  });
-
-  afterEach(() => {
-    // Restore original environment
-    if (originalEnv !== undefined) {
-      process.env.SAFE_CHAIN_MINIMUM_PACKAGE_AGE_HOURS = originalEnv;
-    } else {
-      delete process.env.SAFE_CHAIN_MINIMUM_PACKAGE_AGE_HOURS;
-    }
-  });
-
-  it("should return undefined when environment variable is not set", () => {
-    delete process.env.SAFE_CHAIN_MINIMUM_PACKAGE_AGE_HOURS;
-
-    const hours = getMinimumPackageAgeHours();
-
-    assert.strictEqual(hours, undefined);
-  });
-
-  it("should return value when environment variable is set to a number", () => {
-    process.env.SAFE_CHAIN_MINIMUM_PACKAGE_AGE_HOURS = "48";
-
-    const hours = getMinimumPackageAgeHours();
-
-    assert.strictEqual(hours, "48");
-  });
-
-  it("should return '0' when environment variable is set to '0'", () => {
-    process.env.SAFE_CHAIN_MINIMUM_PACKAGE_AGE_HOURS = "0";
-
-    const hours = getMinimumPackageAgeHours();
-
-    assert.strictEqual(hours, "0");
-  });
-
-  it("should return value when set to decimal", () => {
-    process.env.SAFE_CHAIN_MINIMUM_PACKAGE_AGE_HOURS = "1.5";
-
-    const hours = getMinimumPackageAgeHours();
-
-    assert.strictEqual(hours, "1.5");
-  });
-
-  it("should return value even if non-numeric (validation happens in settings.js)", () => {
-    process.env.SAFE_CHAIN_MINIMUM_PACKAGE_AGE_HOURS = "invalid";
-
-    const hours = getMinimumPackageAgeHours();
-
-    assert.strictEqual(hours, "invalid");
-  });
-
-  it("should return negative values (validation happens in settings.js)", () => {
-    process.env.SAFE_CHAIN_MINIMUM_PACKAGE_AGE_HOURS = "-24";
-
-    const hours = getMinimumPackageAgeHours();
-
-    assert.strictEqual(hours, "-24");
-  });
-});
diff --git a/packages/safe-chain/src/shell-integration/setup-ci.js b/packages/safe-chain/src/shell-integration/setup-ci.js
index b0a8c83..14510f9 100644
--- a/packages/safe-chain/src/shell-integration/setup-ci.js
+++ b/packages/safe-chain/src/shell-integration/setup-ci.js
@@ -5,8 +5,6 @@ import fs from "fs";
 import os from "os";
 import path from "path";
 import { fileURLToPath } from "url";
-import { includePython } from "../config/cliArguments.js";
-import { ECOSYSTEM_PY } from "../config/settings.js";
 
 /** @type {string} */
 // This checks the current file's dirname in a way that's compatible with:
@@ -162,9 +160,5 @@ function modifyPathForCi(shimsDir, binDir) {
 }
 
 function getToolsToSetup() {
-  if (includePython()) {
-    return knownAikidoTools;
-  } else {
-    return knownAikidoTools.filter((tool) => tool.ecoSystem !== ECOSYSTEM_PY);
-  }
+  return knownAikidoTools;
 }
diff --git a/packages/safe-chain/src/shell-integration/setup.js b/packages/safe-chain/src/shell-integration/setup.js
index 065de75..7e64c0b 100644
--- a/packages/safe-chain/src/shell-integration/setup.js
+++ b/packages/safe-chain/src/shell-integration/setup.js
@@ -4,7 +4,6 @@ import { detectShells } from "./shellDetection.js";
 import { knownAikidoTools, getPackageManagerList, getScriptsDir } from "./helpers.js";
 import fs from "fs";
 import path from "path";
-import { includePython } from "../config/cliArguments.js";
 import { fileURLToPath } from "url";
 
 /** @type {string} */
@@ -118,7 +117,7 @@ function copyStartupFiles() {
     // Use absolute path for source
     const sourcePath = path.join(
       dirname,
-      includePython() ? "startup-scripts/include-python" : "startup-scripts",
+      "startup-scripts",
       file
     );
     fs.copyFileSync(sourcePath, targetPath);
diff --git a/packages/safe-chain/src/shell-integration/startup-scripts/include-python/init-fish.fish b/packages/safe-chain/src/shell-integration/startup-scripts/include-python/init-fish.fish
deleted file mode 100644
index 386144c..0000000
--- a/packages/safe-chain/src/shell-integration/startup-scripts/include-python/init-fish.fish
+++ /dev/null
@@ -1,98 +0,0 @@
-set -gx PATH $PATH $HOME/.safe-chain/bin
-
-function npx
-    wrapSafeChainCommand "npx" $argv
-end
-
-function yarn
-    wrapSafeChainCommand "yarn" $argv
-end
-
-function pnpm
-    wrapSafeChainCommand "pnpm" $argv
-end
-
-function pnpx
-    wrapSafeChainCommand "pnpx" $argv
-end
-
-function bun
-    wrapSafeChainCommand "bun" $argv
-end
-
-function bunx
-    wrapSafeChainCommand "bunx" $argv
-end
-
-function npm
-    # If args is just -v or --version and nothing else, just run the `npm -v` command
-    # This is because nvm uses this to check the version of npm
-    set argc (count $argv)
-    if test $argc -eq 1
-        switch $argv[1]
-            case "-v" "--version"
-                command npm $argv
-                return
-        end
-    end
-
-    wrapSafeChainCommand "npm" $argv
-end
-
-
-function pip
-    wrapSafeChainCommand "pip" $argv
-end
-
-function pip3
-    wrapSafeChainCommand "pip3" $argv
-end
-
-function uv
-    wrapSafeChainCommand "uv" $argv
-end
-
-function poetry
-    wrapSafeChainCommand "poetry" $argv
-end
-
-# `python -m pip`, `python -m pip3`.
-function python
-    wrapSafeChainCommand "python" $argv
-end
-
-# `python3 -m pip`, `python3 -m pip3'.
-function python3
-    wrapSafeChainCommand "python3" $argv
-end
-
-function printSafeChainWarning
-    set original_cmd $argv[1]
-    
-    # Fish equivalent of ANSI color codes: yellow background, black text for "Warning:"
-    set_color -b yellow black
-    printf "Warning:"
-    set_color normal
-    printf " safe-chain is not available to protect you from installing malware. %s will run without it.\n" $original_cmd
-    
-    # Cyan text for the install command
-    printf "Install safe-chain by using "
-    set_color cyan
-    printf "npm install -g @aikidosec/safe-chain"
-    set_color normal
-    printf ".\n"
-end
-
-function wrapSafeChainCommand
-    set original_cmd $argv[1]
-    set cmd_args $argv[2..-1]
-
-    if type -q safe-chain
-        # If the safe-chain command is available, just run it with the provided arguments
-        safe-chain $original_cmd $cmd_args
-    else
-        # If the safe-chain command is not available, print a warning and run the original command
-        printSafeChainWarning $original_cmd
-        command $original_cmd $cmd_args
-    end
-end
diff --git a/packages/safe-chain/src/shell-integration/startup-scripts/include-python/init-posix.sh b/packages/safe-chain/src/shell-integration/startup-scripts/include-python/init-posix.sh
deleted file mode 100644
index c71c741..0000000
--- a/packages/safe-chain/src/shell-integration/startup-scripts/include-python/init-posix.sh
+++ /dev/null
@@ -1,85 +0,0 @@
-export PATH="$PATH:$HOME/.safe-chain/bin"
-
-function npx() {
-  wrapSafeChainCommand "npx" "$@"
-}
-
-function yarn() {
-  wrapSafeChainCommand "yarn" "$@"
-}
-
-function pnpm() {
-  wrapSafeChainCommand "pnpm" "$@"
-}
-
-function pnpx() {
-  wrapSafeChainCommand "pnpx" "$@"
-}
-
-function bun() {
-  wrapSafeChainCommand "bun" "$@"
-}
-
-function bunx() {
-  wrapSafeChainCommand "bunx" "$@"
-}
-
-function npm() {
-  if [[ "$1" == "-v" || "$1" == "--version" ]] && [[ $# -eq 1 ]]; then
-    # If args is just -v or --version and nothing else, just run the npm version command
-    # This is because nvm uses this to check the version of npm
-    command npm "$@"
-    return
-  fi
-
-  wrapSafeChainCommand "npm" "$@"
-}
-
-
-function pip() {
-  wrapSafeChainCommand "pip" "$@"
-}
-
-function pip3() {
-  wrapSafeChainCommand "pip3" "$@"
-}
-
-function uv() {
-  wrapSafeChainCommand "uv" "$@"
-}
-
-function poetry() {
-  wrapSafeChainCommand "poetry" "$@"
-}
-
-# `python -m pip`, `python -m pip3`.
-function python() {
-  wrapSafeChainCommand "python" "$@"
-}
-
-# `python3 -m pip`, `python3 -m pip3'.
-function python3() {
-  wrapSafeChainCommand "python3" "$@"
-}
-
-function printSafeChainWarning() {
-  # \033[43;30m is used to set the background color to yellow and text color to black
-  # \033[0m is used to reset the text formatting
-  printf "\033[43;30mWarning:\033[0m safe-chain is not available to protect you from installing malware. %s will run without it.\n" "$1"
-  # \033[36m is used to set the text color to cyan
-  printf "Install safe-chain by using \033[36mnpm install -g @aikidosec/safe-chain\033[0m.\n"
-}
-
-function wrapSafeChainCommand() {
-  local original_cmd="$1"
-
-  if command -v safe-chain > /dev/null 2>&1; then
-    # If the aikido command is available, just run it with the provided arguments
-    safe-chain "$@"
-  else
-    # If the aikido command is not available, print a warning and run the original command
-    printSafeChainWarning "$original_cmd"
-
-    command "$original_cmd" "$@"
-  fi
-}
diff --git a/packages/safe-chain/src/shell-integration/startup-scripts/include-python/init-pwsh.ps1 b/packages/safe-chain/src/shell-integration/startup-scripts/include-python/init-pwsh.ps1
deleted file mode 100644
index 168556a..0000000
--- a/packages/safe-chain/src/shell-integration/startup-scripts/include-python/init-pwsh.ps1
+++ /dev/null
@@ -1,119 +0,0 @@
-# Use cross-platform path separator (: on Unix, ; on Windows)
-$pathSeparator = if ($IsWindows) { ';' } else { ':' }
-$safeChainBin = Join-Path (Join-Path $HOME '.safe-chain') 'bin'
-$env:PATH = "$env:PATH$pathSeparator$safeChainBin"
-
-function npx {
-    Invoke-WrappedCommand "npx" $args
-}
-
-function yarn {
-    Invoke-WrappedCommand "yarn" $args
-}
-
-function pnpm {
-    Invoke-WrappedCommand "pnpm" $args
-}
-
-function pnpx {
-    Invoke-WrappedCommand "pnpx" $args
-}
-
-function bun {
-    Invoke-WrappedCommand "bun" $args
-}
-
-function bunx {
-    Invoke-WrappedCommand "bunx" $args
-}
-
-function npm {
-    # If args is just -v or --version and nothing else, just run the npm version command
-    # This is because nvm uses this to check the version of npm
-    if (($args.Length -eq 1) -and (($args[0] -eq "-v") -or ($args[0] -eq "--version"))) {
-        Invoke-RealCommand "npm" $args
-        return
-    }
-
-    Invoke-WrappedCommand "npm" $args
-}
-
-function pip {
-    Invoke-WrappedCommand "pip" $args
-}
-
-function pip3 {
-    Invoke-WrappedCommand "pip3" $args
-}
-
-function uv {
-    Invoke-WrappedCommand "uv" $args
-}
-
-function poetry {
-    Invoke-WrappedCommand "poetry" $args
-}
-
-# `python -m pip`, `python -m pip3`.
-function python {
-    Invoke-WrappedCommand 'python' $args
-}
-
-# `python3 -m pip`, `python3 -m pip3'.
-function python3 {
-    Invoke-WrappedCommand 'python3' $args
-}
-
-
-function Write-SafeChainWarning {
-    param([string]$Command)
-    
-    # PowerShell equivalent of ANSI color codes: yellow background, black text for "Warning:"
-    Write-Host "Warning:" -BackgroundColor Yellow -ForegroundColor Black -NoNewline
-    Write-Host " safe-chain is not available to protect you from installing malware. $Command will run without it."
-    
-    # Cyan text for the install command
-    Write-Host "Install safe-chain by using " -NoNewline
-    Write-Host "npm install -g @aikidosec/safe-chain" -ForegroundColor Cyan -NoNewline
-    Write-Host "."
-}
-
-function Test-CommandAvailable {
-    param([string]$Command)
-    
-    try {
-        Get-Command $Command -ErrorAction Stop | Out-Null
-        return $true
-    }
-    catch {
-        return $false
-    }
-}
-
-function Invoke-RealCommand {
-    param(
-        [string]$Command,
-        [string[]]$Arguments
-    )
-    
-    # Find the real executable to avoid calling our wrapped functions
-    $realCommand = Get-Command -Name $Command -CommandType Application | Select-Object -First 1
-    if ($realCommand) {
-        & $realCommand.Source @Arguments
-    }
-}
-
-function Invoke-WrappedCommand {
-    param(
-        [string]$OriginalCmd,
-        [string[]]$Arguments
-    )
-
-    if (Test-CommandAvailable "safe-chain") {
-        & safe-chain $OriginalCmd @Arguments
-    }
-    else {
-        Write-SafeChainWarning $OriginalCmd
-        Invoke-RealCommand $OriginalCmd $Arguments
-    }
-}
diff --git a/packages/safe-chain/src/shell-integration/startup-scripts/init-fish.fish b/packages/safe-chain/src/shell-integration/startup-scripts/init-fish.fish
index b18ff96..386144c 100644
--- a/packages/safe-chain/src/shell-integration/startup-scripts/init-fish.fish
+++ b/packages/safe-chain/src/shell-integration/startup-scripts/init-fish.fish
@@ -39,6 +39,33 @@ function npm
     wrapSafeChainCommand "npm" $argv
 end
 
+
+function pip
+    wrapSafeChainCommand "pip" $argv
+end
+
+function pip3
+    wrapSafeChainCommand "pip3" $argv
+end
+
+function uv
+    wrapSafeChainCommand "uv" $argv
+end
+
+function poetry
+    wrapSafeChainCommand "poetry" $argv
+end
+
+# `python -m pip`, `python -m pip3`.
+function python
+    wrapSafeChainCommand "python" $argv
+end
+
+# `python3 -m pip`, `python3 -m pip3'.
+function python3
+    wrapSafeChainCommand "python3" $argv
+end
+
 function printSafeChainWarning
     set original_cmd $argv[1]
     
diff --git a/packages/safe-chain/src/shell-integration/startup-scripts/init-posix.sh b/packages/safe-chain/src/shell-integration/startup-scripts/init-posix.sh
index 5c32143..c71c741 100644
--- a/packages/safe-chain/src/shell-integration/startup-scripts/init-posix.sh
+++ b/packages/safe-chain/src/shell-integration/startup-scripts/init-posix.sh
@@ -35,6 +35,33 @@ function npm() {
   wrapSafeChainCommand "npm" "$@"
 }
 
+
+function pip() {
+  wrapSafeChainCommand "pip" "$@"
+}
+
+function pip3() {
+  wrapSafeChainCommand "pip3" "$@"
+}
+
+function uv() {
+  wrapSafeChainCommand "uv" "$@"
+}
+
+function poetry() {
+  wrapSafeChainCommand "poetry" "$@"
+}
+
+# `python -m pip`, `python -m pip3`.
+function python() {
+  wrapSafeChainCommand "python" "$@"
+}
+
+# `python3 -m pip`, `python3 -m pip3'.
+function python3() {
+  wrapSafeChainCommand "python3" "$@"
+}
+
 function printSafeChainWarning() {
   # \033[43;30m is used to set the background color to yellow and text color to black
   # \033[0m is used to reset the text formatting
diff --git a/packages/safe-chain/src/shell-integration/startup-scripts/init-pwsh.ps1 b/packages/safe-chain/src/shell-integration/startup-scripts/init-pwsh.ps1
index 78228a0..c3d21c4 100644
--- a/packages/safe-chain/src/shell-integration/startup-scripts/init-pwsh.ps1
+++ b/packages/safe-chain/src/shell-integration/startup-scripts/init-pwsh.ps1
@@ -1,5 +1,7 @@
 # Use cross-platform path separator (: on Unix, ; on Windows)
-$pathSeparator = if ($IsWindows) { ';' } else { ':' }
+# $IsWindows is only available in PowerShell Core 6.0+. If it doesn't exist, assume Windows PowerShell
+$isWindowsPlatform = if (Test-Path variable:IsWindows) { $IsWindows } else { $true }
+$pathSeparator = if ($isWindowsPlatform) { ';' } else { ':' }
 $safeChainBin = Join-Path (Join-Path $HOME '.safe-chain') 'bin'
 $env:PATH = "$env:PATH$pathSeparator$safeChainBin"
 
@@ -38,6 +40,33 @@ function npm {
     Invoke-WrappedCommand "npm" $args
 }
 
+function pip {
+    Invoke-WrappedCommand "pip" $args
+}
+
+function pip3 {
+    Invoke-WrappedCommand "pip3" $args
+}
+
+function uv {
+    Invoke-WrappedCommand "uv" $args
+}
+
+function poetry {
+    Invoke-WrappedCommand "poetry" $args
+}
+
+# `python -m pip`, `python -m pip3`.
+function python {
+    Invoke-WrappedCommand 'python' $args
+}
+
+# `python3 -m pip`, `python3 -m pip3'.
+function python3 {
+    Invoke-WrappedCommand 'python3' $args
+}
+
+
 function Write-SafeChainWarning {
     param([string]$Command)
     
diff --git a/test/e2e/certbundle.e2e.spec.js b/test/e2e/certbundle.e2e.spec.js
index caf4102..4b4ad84 100644
--- a/test/e2e/certbundle.e2e.spec.js
+++ b/test/e2e/certbundle.e2e.spec.js
@@ -231,7 +231,7 @@ describe("E2E: NODE_EXTRA_CA_CERTS merging", () => {
   it(`pip install works without NODE_EXTRA_CA_CERTS set`, async () => {
     const shell = await container.openShell("zsh");
     
-    await shell.runCommand("safe-chain setup --include-python");
+    await shell.runCommand("safe-chain setup");
     await shell.runCommand("unset NODE_EXTRA_CA_CERTS");
     
     const result = await shell.runCommand(
@@ -247,7 +247,7 @@ describe("E2E: NODE_EXTRA_CA_CERTS merging", () => {
   it(`pip install works with valid NODE_EXTRA_CA_CERTS set`, async () => {
     const shell = await container.openShell("zsh");
     
-    await shell.runCommand("safe-chain setup --include-python");
+    await shell.runCommand("safe-chain setup");
     
     // Create a temporary valid certificate
     await shell.runCommand("cp /etc/ssl/certs/ca-certificates.crt /tmp/pip-valid-certs.pem");
@@ -265,7 +265,7 @@ describe("E2E: NODE_EXTRA_CA_CERTS merging", () => {
   it(`pip install handles non-existent NODE_EXTRA_CA_CERTS gracefully`, async () => {
     const shell = await container.openShell("zsh");
     
-    await shell.runCommand("safe-chain setup --include-python");
+    await shell.runCommand("safe-chain setup");
     
     const result = await shell.runCommand(
       'export NODE_EXTRA_CA_CERTS="/tmp/nonexistent-pip-certs.pem" && pip3 install --break-system-packages requests'
@@ -281,7 +281,7 @@ describe("E2E: NODE_EXTRA_CA_CERTS merging", () => {
   it(`pip install handles invalid NODE_EXTRA_CA_CERTS gracefully`, async () => {
     const shell = await container.openShell("zsh");
     
-    await shell.runCommand("safe-chain setup --include-python");
+    await shell.runCommand("safe-chain setup");
     
     // Create invalid cert
     await shell.runCommand(
diff --git a/test/e2e/include-python-deprecation.e2e.spec.js b/test/e2e/include-python-deprecation.e2e.spec.js
new file mode 100644
index 0000000..a7019b7
--- /dev/null
+++ b/test/e2e/include-python-deprecation.e2e.spec.js
@@ -0,0 +1,45 @@
+import { describe, it, before, beforeEach, afterEach } from "node:test";
+import { DockerTestContainer } from "./DockerTestContainer.js";
+import assert from "node:assert";
+
+describe("E2E: deprecated --include-python handling", () => {
+  let container;
+
+  before(async () => {
+    DockerTestContainer.buildImage();
+  });
+
+  beforeEach(async () => {
+    container = new DockerTestContainer();
+    await container.start();
+  });
+
+  afterEach(async () => {
+    if (container) {
+      await container.stop();
+      container = null;
+    }
+  });
+
+  for (let shell of ["bash", "zsh"]) {
+    it(`safe-chain setup warns and continues for ${shell}`, async () => {
+      const sh = await container.openShell(shell);
+      const result = await sh.runCommand("safe-chain setup --include-python");
+
+      assert.ok(
+        result.output.toLowerCase().includes("deprecated and ignored"),
+        `Expected warning about deprecated --include-python. Output was:\n${result.output}`
+      );
+    });
+
+    it(`safe-chain setup-ci warns and continues for ${shell}`, async () => {
+      const sh = await container.openShell(shell);
+      const result = await sh.runCommand("safe-chain setup-ci --include-python");
+
+      assert.ok(
+        result.output.toLowerCase().includes("deprecated and ignored"),
+        `Expected warning about deprecated --include-python. Output was:\n${result.output}`
+      );
+    });
+  }
+});
diff --git a/test/e2e/pip-ci.e2e.spec.js b/test/e2e/pip-ci.e2e.spec.js
index 85a4a46..49db6ce 100644
--- a/test/e2e/pip-ci.e2e.spec.js
+++ b/test/e2e/pip-ci.e2e.spec.js
@@ -86,7 +86,7 @@ describe("E2E: safe-chain setup-ci command for pip/pip3", () => {
       // Setup safe-chain CI shims
       const installationShell = await container.openShell(shell);
       await installationShell.runCommand(
-        "safe-chain setup-ci --include-python"
+        "safe-chain setup-ci"
       );
 
       // Add $HOME/.safe-chain/shims to PATH for subsequent shells
@@ -115,7 +115,7 @@ describe("E2E: safe-chain setup-ci command for pip/pip3", () => {
     it(`setup-ci routes python -m pip through safe-chain for ${shell}`, async () => {
       const installationShell = await container.openShell(shell);
       await installationShell.runCommand(
-        "safe-chain setup-ci --include-python"
+        "safe-chain setup-ci"
       );
       await installationShell.runCommand(
         "echo 'export PATH=\"$HOME/.safe-chain/shims:$PATH\"' >> ~/.zshrc"
@@ -138,7 +138,7 @@ describe("E2E: safe-chain setup-ci command for pip/pip3", () => {
     it(`setup-ci routes python3 -m pip through safe-chain for ${shell}`, async () => {
       const installationShell = await container.openShell(shell);
       await installationShell.runCommand(
-        "safe-chain setup-ci --include-python"
+        "safe-chain setup-ci"
       );
       await installationShell.runCommand(
         "echo 'export PATH=\"$HOME/.safe-chain/shims:$PATH\"' >> ~/.zshrc"
@@ -161,7 +161,7 @@ describe("E2E: safe-chain setup-ci command for pip/pip3", () => {
     it(`setup-ci routes pip through safe-chain for ${shell}`, async () => {
       const installationShell = await container.openShell(shell);
       await installationShell.runCommand(
-        "safe-chain setup-ci --include-python"
+        "safe-chain setup-ci"
       );
       await installationShell.runCommand(
         "echo 'export PATH=\"$HOME/.safe-chain/shims:$PATH\"' >> ~/.zshrc"
@@ -184,7 +184,7 @@ describe("E2E: safe-chain setup-ci command for pip/pip3", () => {
     it(`setup-ci routes pip3 through safe-chain for ${shell}`, async () => {
       const installationShell = await container.openShell(shell);
       await installationShell.runCommand(
-        "safe-chain setup-ci --include-python"
+        "safe-chain setup-ci"
       );
       await installationShell.runCommand(
         "echo 'export PATH=\"$HOME/.safe-chain/shims:$PATH\"' >> ~/.zshrc"
diff --git a/test/e2e/pip.e2e.spec.js b/test/e2e/pip.e2e.spec.js
index e02d1b3..b06978f 100644
--- a/test/e2e/pip.e2e.spec.js
+++ b/test/e2e/pip.e2e.spec.js
@@ -15,7 +15,7 @@ describe("E2E: pip coverage", () => {
     await container.start();
 
     const installationShell = await container.openShell("zsh");
-    await installationShell.runCommand("safe-chain setup --include-python");
+    await installationShell.runCommand("safe-chain setup");
 
     // Clear pip cache before each test to ensure fresh downloads through proxy
     await installationShell.runCommand("pip3 cache purge");
diff --git a/test/e2e/poetry.e2e.spec.js b/test/e2e/poetry.e2e.spec.js
index 3d19783..58b74fd 100644
--- a/test/e2e/poetry.e2e.spec.js
+++ b/test/e2e/poetry.e2e.spec.js
@@ -15,7 +15,7 @@ describe("E2E: poetry coverage", () => {
     await container.start();
 
     const installationShell = await container.openShell("zsh");
-    await installationShell.runCommand("safe-chain setup --include-python");
+    await installationShell.runCommand("safe-chain setup");
     
     // Clear poetry cache
     await installationShell.runCommand("command poetry cache clear pypi --all -n");
diff --git a/test/e2e/teardown-dirs.e2e.spec.js b/test/e2e/teardown-dirs.e2e.spec.js
index 0ed8bf6..853c503 100644
--- a/test/e2e/teardown-dirs.e2e.spec.js
+++ b/test/e2e/teardown-dirs.e2e.spec.js
@@ -57,20 +57,18 @@ describe("E2E: safe-chain teardown command", () => {
     assert.ok(checkScriptsGone.output.includes("missing"), "Scripts directory should be removed after teardown");
   });
 
-  it("safe-chain teardown removes shims directory created by setup-ci --include-python", async () => {
+  it("safe-chain teardown removes shims directory created by setup-ci", async () => {
     const shell = await container.openShell("bash");
 
-    // Run setup-ci with --include-python
-    await shell.runCommand("safe-chain setup-ci --include-python");
-
+    // Run setup-ci
+    await shell.runCommand("safe-chain setup-ci");
     // Verify shims directory exists
     const checkShimsExist = await shell.runCommand("test -d ~/.safe-chain/shims && echo 'exists' || echo 'missing'");
-    assert.ok(checkShimsExist.output.includes("exists"), "Shims directory should exist after setup-ci --include-python");
+    assert.ok(checkShimsExist.output.includes("exists"), "Shims directory should exist after setup-ci");
 
     // Verify Python shims were created
     const checkPythonShims = await shell.runCommand("test -f ~/.safe-chain/shims/pip && echo 'exists' || echo 'missing'");
-    assert.ok(checkPythonShims.output.includes("exists"), "Python shims should exist after setup-ci --include-python");
-
+    assert.ok(checkPythonShims.output.includes("exists"), "Python shims should exist after setup-ci");
     // Run teardown
     await shell.runCommand("safe-chain teardown");
 
@@ -79,15 +77,14 @@ describe("E2E: safe-chain teardown command", () => {
     assert.ok(checkShimsGone.output.includes("missing"), "Shims directory should be removed after teardown");
   });
 
-  it("safe-chain teardown removes scripts directory created by setup --include-python", async () => {
+  it("safe-chain teardown removes scripts directory created by setup", async () => {
     const shell = await container.openShell("bash");
 
-    // Run setup with --include-python
-    await shell.runCommand("safe-chain setup --include-python");
-
+    // Run setup
+    await shell.runCommand("safe-chain setup");
     // Verify scripts directory exists
     const checkScriptsExist = await shell.runCommand("test -d ~/.safe-chain/scripts && echo 'exists' || echo 'missing'");
-    assert.ok(checkScriptsExist.output.includes("exists"), "Scripts directory should exist after setup --include-python");
+    assert.ok(checkScriptsExist.output.includes("exists"), "Scripts directory should exist after setup");
 
     // Run teardown
     await shell.runCommand("safe-chain teardown");
diff --git a/test/e2e/uv.e2e.spec.js b/test/e2e/uv.e2e.spec.js
index 7e9daac..9d5f3b9 100644
--- a/test/e2e/uv.e2e.spec.js
+++ b/test/e2e/uv.e2e.spec.js
@@ -15,7 +15,7 @@ describe("E2E: uv coverage", () => {
     await container.start();
 
     const installationShell = await container.openShell("zsh");
-    await installationShell.runCommand("safe-chain setup --include-python");
+    await installationShell.runCommand("safe-chain setup");
 
     // Clear uv cache
     await installationShell.runCommand("uv cache clean");