Merge branch 'main' into feat/pdm-support

.github/workflows/build-and-release.yml

@@ -101,6 +101,7 @@ jobs:
 
   publish-npm:
     name: Publish to npm
+    if: github.event_name == 'release'
     runs-on: ubuntu-latest
 
     steps:

.github/workflows/test-on-pr.yml

@@ -93,11 +93,6 @@ jobs:
             npm_version: "latest"
             yarn_version: "latest"
             pnpm_version: "latest"
-          # EOL compatibility testing - Node 16 (EOL Sept 2023)
-          - node_version: "16"
-            npm_version: "8.0.0"
-            yarn_version: "1.22.0"
-            pnpm_version: "8.0.0"
 
     steps:
       - name: Checkout code

README.md

@@ -23,6 +23,7 @@ Aikido Safe Chain supports the following package managers:
 - 📦 **pip3**
 - 📦 **uv**
 - 📦 **poetry**
+- 📦 **uvx**
 - 📦 **pipx**
 - 📦 **pdm**
 
@@ -30,6 +31,12 @@ Aikido Safe Chain supports the following package managers:
 
 ![Aikido Safe Chain demo](https://raw.githubusercontent.com/AikidoSec/safe-chain/main/docs/safe-package-manager-demo.gif)
 
+# Using Safe Chain across a team?
+
+[Aikido Endpoint](https://www.aikido.dev/protect/endpoint-protection) builds on Safe Chain, extending package and extension security across more ecosystems: **npm**, **PyPI**, **Maven**, **NuGet**, **VS Code**, **Open VSX** - (Cursor, Windsurf, Kiro, Vs Codium, ...), **Chrome extensions**, **Skills.sh AI skills** and more.
+
+Get centralized policy management, request-and-approval workflows, and visibility across every developer workstation in your org. Powered by the same Aikido Intel feed. Deploy it manually or manage it through your MDM tool (Jamf, Fleet, or Iru).
+
 ## Installation
 
 Installing the Aikido Safe Chain is easy with our one-line installer.
@@ -67,7 +74,7 @@ You can find all available versions on the [releases page](https://github.com/Ai
 ### Verify the installation
 
 1. **❗Restart your terminal** to start using the Aikido Safe Chain.
-   - This step is crucial as it ensures that the shell aliases for npm, npx, yarn, pnpm, pnpx, bun, bunx, pip, pip3, poetry, uv, pipx and pdm are loaded correctly. If you do not restart your terminal, the aliases will not be available.
+   - This step is crucial as it ensures that the shell aliases for npm, npx, yarn, pnpm, pnpx, bun, bunx, pip, pip3, poetry, uv, uvx, pipx and pdm are loaded correctly. If you do not restart your terminal, the aliases will not be available.
 
 2. **Verify the installation** by running the verification command:
 
@@ -98,7 +105,7 @@ You can find all available versions on the [releases page](https://github.com/Ai
 
    - The output should show that Aikido Safe Chain is blocking the installation of these test packages as they are flagged as malware.
 
-When running `npm`, `npx`, `yarn`, `pnpm`, `pnpx`, `bun`, `bunx`, `pip`, `pip3`, `uv`, `poetry`, `pipx` and `pdm` commands, the Aikido Safe Chain will automatically check for malware in the packages you are trying to install. It also intercepts Python module invocations for pip when available (e.g., `python -m pip install ...`, `python3 -m pip download ...`). If any malware is detected, it will prompt you to exit the command.
+When running `npm`, `npx`, `yarn`, `pnpm`, `pnpx`, `bun`, `bunx`, `pip`, `pip3`, `uv`, `uvx`, `poetry`, `pipx` and `pdm` commands, the Aikido Safe Chain will automatically check for malware in the packages you are trying to install. It also intercepts Python module invocations for pip when available (e.g., `python -m pip install ...`, `python3 -m pip download ...`). If any malware is detected, it will prompt you to exit the command.
 
 You can check the installed version by running:
 
@@ -110,7 +117,7 @@ safe-chain --version
 
 ### Malware Blocking
 
-The Aikido Safe Chain works by running a lightweight proxy server that intercepts package downloads from the npm registry and PyPI. When you run npm, npx, yarn, pnpm, pnpx, bun, bunx, pip, pip3, uv, poetry or pipx commands, all package downloads are routed through this local proxy, which verifies packages in real-time against **[Aikido Intel - Open Sources Threat Intelligence](https://intel.aikido.dev/?tab=malware)**. If malware is detected in any package (including deep dependencies), the proxy blocks the download before the malicious code reaches your machine.
+The Aikido Safe Chain works by running a lightweight proxy server that intercepts package downloads from the npm registry and PyPI. When you run npm, npx, yarn, pnpm, pnpx, bun, bunx, pip, pip3, uv, uvx, poetry or pipx commands, all package downloads are routed through this local proxy, which verifies packages in real-time against **[Aikido Intel - Open Sources Threat Intelligence](https://intel.aikido.dev/?tab=malware)**. If malware is detected in any package (including deep dependencies), the proxy blocks the download before the malicious code reaches your machine.
 
 ### Minimum package age
 
@@ -129,7 +136,7 @@ By default, the minimum package age is 48 hours. This provides an additional sec
 
 ### Shell Integration
 
-The Aikido Safe Chain integrates with your shell to provide a seamless experience when using npm, npx, yarn, pnpm, pnpx, bun, bunx, and Python package managers (pip, uv, poetry, pipx). It sets up aliases for these commands so that they are wrapped by the Aikido Safe Chain commands, which manage the proxy server before executing the original commands. We currently support:
+The Aikido Safe Chain integrates with your shell to provide a seamless experience when using npm, npx, yarn, pnpm, pnpx, bun, bunx, and Python package managers (pip, uv, uvx, poetry, pipx). It sets up aliases for these commands so that they are wrapped by the Aikido Safe Chain commands, which manage the proxy server before executing the original commands. We currently support:
 
 - ✅ **Bash**
 - ✅ **Zsh**
@@ -317,6 +324,24 @@ The base URL should point to a server that mirrors the structure of `https://mal
 - `/releases/npm.json` (JavaScript new packages list)
 - `/releases/pypi.json` (Python new packages list)
 
+## Custom Install Directory
+
+By default, Safe Chain installs itself into `~/.safe-chain`. You can change this by passing an explicit install directory to the installer. This is useful for system-wide installations (e.g. inside a Docker image) or when you need to avoid conflicts with other tools.
+
+When set, all Safe Chain data (binary, shims, scripts, config) is placed under the custom directory instead of `~/.safe-chain`.
+
+### Unix/Linux/macOS
+
+```shell
+curl -fsSL https://github.com/AikidoSec/safe-chain/releases/latest/download/install-safe-chain.sh | sh -s -- --install-dir /usr/local/.safe-chain
+```
+
+### Windows
+
+```powershell
+iex "& { $(iwr 'https://github.com/AikidoSec/safe-chain/releases/latest/download/install-safe-chain.ps1' -UseBasicParsing) } -InstallDir 'C:\ProgramData\safe-chain'"
+```
+
 # Usage in CI/CD
 
 You can protect your CI/CD pipelines from malicious packages by integrating Aikido Safe Chain into your build process. This ensures that any packages installed during your automated builds are checked for malware before installation.
@@ -407,6 +432,7 @@ pipeline {
   environment {
     // Jenkins does not automatically persist PATH updates from setup-ci,
     // so add the shims + binary directory explicitly for all stages.
+    // If you installed into a custom directory, replace ~/.safe-chain with that path here.
     PATH = "${env.HOME}/.safe-chain/shims:${env.HOME}/.safe-chain/bin:${env.PATH}"
   }
 
@@ -462,7 +488,7 @@ To add safe-chain in GitLab pipelines, you need to install it in the image runni
    # Install safe-chain
    RUN curl -fsSL https://github.com/AikidoSec/safe-chain/releases/latest/download/install-safe-chain.sh | sh -s -- --ci
 
-   # Add safe-chain to PATH
+   # Add safe-chain to PATH (update paths if you used a custom install dir)
    ENV PATH="/root/.safe-chain/shims:/root/.safe-chain/bin:${PATH}"
    ```
 

docs/Release.md

@@ -0,0 +1,25 @@
+# Release Guide
+
+## Steps
+
+### 1. Create and push a version tag
+
+```bash
+git tag 1.0.0
+git push origin 1.0.0
+```
+
+This triggers the build pipeline, which compiles binaries for all platforms and creates a draft GitHub release.
+
+### 2. Wait for artifacts to build
+
+Monitor the [Actions tab](https://github.com/AikidoSec/safe-chain/actions) until the `Create Release` workflow completes.
+
+### 3. Publish the GitHub release
+
+1. Go to the [Releases page](https://github.com/AikidoSec/safe-chain/releases)
+2. Open the draft release created for your tag
+3. Add release notes
+4. Click **Publish release**
+
+Publishing the release automatically triggers an npm publish. Pre-release versions (e.g. `1.0.0-beta`) are published to npm under a tag matching the pre-release identifier (e.g. `beta`). Stable versions are published to the `latest` tag.

docs/shell-integration.md

@@ -2,7 +2,7 @@
 
 ## Overview
 
-The shell integration automatically wraps common package manager commands (`npm`, `npx`, `yarn`, `pnpm`, `pnpx`, `bun`, `bunx`, `pip`, `pip3`, `uv`, `poetry`, `pipx`) with Aikido's security scanning functionality. It also intercepts Python module invocations for pip when available: `python -m pip`, `python -m pip3`, `python3 -m pip`, `python3 -m pip3`. This is achieved by sourcing startup scripts that define shell functions to wrap these commands with their Aikido-protected equivalents.
+The shell integration automatically wraps common package manager commands (`npm`, `npx`, `yarn`, `pnpm`, `pnpx`, `bun`, `bunx`, `pip`, `pip3`, `uv`, `uvx`, `poetry`, `pipx`) with Aikido's security scanning functionality. It also intercepts Python module invocations for pip when available: `python -m pip`, `python -m pip3`, `python3 -m pip`, `python3 -m pip3`. This is achieved by sourcing startup scripts that define shell functions to wrap these commands with their Aikido-protected equivalents.
 
 ## Supported Shells
 
@@ -28,7 +28,7 @@ This command:
 
 - Copies necessary startup scripts to Safe Chain's installation directory (`~/.safe-chain/scripts`)
 - Detects all supported shells on your system
-- Sources each shell's startup file to add Safe Chain functions for `npm`, `npx`, `yarn`, `pnpm`, `pnpx`, `bun`, `bunx`, `pip`, `pip3`, `uv`, `poetry` and `pipx`
+- Sources each shell's startup file to add Safe Chain functions for `npm`, `npx`, `yarn`, `pnpm`, `pnpx`, `bun`, `bunx`, `pip`, `pip3`, `uv`, `uvx`, `poetry` and `pipx`
 - Adds lightweight interceptors so `python -m pip[...]` and `python3 -m pip[...]` route through Safe Chain when invoked by name
 
 ❗ After running this command, **you must restart your terminal** for the changes to take effect. This ensures that the startup scripts are sourced correctly.
@@ -78,7 +78,7 @@ The system modifies the following files to source Safe Chain startup scripts:
 This means the shell functions are working but the Aikido commands aren't installed or available in your PATH:
 
 - Make sure Aikido Safe Chain is properly installed on your system
-- Verify the `aikido-npm`, `aikido-npx`, `aikido-yarn`, `aikido-pnpm`, `aikido-pnpx`, `aikido-bun`, `aikido-bunx`, `aikido-pip`, `aikido-pip3`, `aikido-uv`, `aikido-poetry` and `aikido-pipx` commands exist
+- Verify the `aikido-npm`, `aikido-npx`, `aikido-yarn`, `aikido-pnpm`, `aikido-pnpx`, `aikido-bun`, `aikido-bunx`, `aikido-pip`, `aikido-pip3`, `aikido-uv`, `aikido-uvx`, `aikido-poetry` and `aikido-pipx` commands exist
 - Check that these commands are in your system's PATH
 
 ### Manual Verification
@@ -121,7 +121,7 @@ npm() {
 }
 ```
 
-Repeat this pattern for `npx`, `yarn`, `pnpm`, `pnpx`, `bun`, `bunx`, `pip`, `pip3`, `uv`, `poetry` and `pipx` using their respective `aikido-*` commands. After adding these functions, restart your terminal to apply the changes.
+Repeat this pattern for `npx`, `yarn`, `pnpm`, `pnpx`, `bun`, `bunx`, `pip`, `pip3`, `uv`, `uvx`, `poetry` and `pipx` using their respective `aikido-*` commands. After adding these functions, restart your terminal to apply the changes.
 
 To intercept Python module invocations for pip without altering Python itself, you can add small forwarding functions:
 

install-scripts/install-endpoint-mac.sh

@@ -7,8 +7,8 @@
 set -e  # Exit on error
 
 # Configuration
-INSTALL_URL="https://github.com/AikidoSec/safechain-internals/releases/download/v1.2.12/EndpointProtection.pkg"
+INSTALL_URL="https://github.com/AikidoSec/safechain-internals/releases/download/v1.2.20/EndpointProtection.pkg"
-DOWNLOAD_SHA256="26492f3cbb1094532dc298199842eb97d60cc670552c9c256314960b298ee784"
+DOWNLOAD_SHA256="def6c01caac6a4ce93eb68157a5a6b81028c9203fa13a0f5c539cceb92cc7e7b"
 TOKEN_FILE="/tmp/aikido_endpoint_token.txt"
 
 # Colors for output

install-scripts/install-endpoint-windows.ps1

@@ -7,8 +7,8 @@ param(
 )
 
 # Configuration
-$InstallUrl = "https://github.com/AikidoSec/safechain-internals/releases/download/v1.2.12/EndpointProtection.msi"
+$InstallUrl = "https://github.com/AikidoSec/safechain-internals/releases/download/v1.2.20/EndpointProtection.msi"
-$DownloadSha256 = "06308fc06f95f4b2ad9e48bfd978eb8d02c2928f2ee3c8bba2c81ef2fde21e4f"
+$DownloadSha256 = "46fe377a4ce6204e1cc4a031e80f92f85cb8e1ef6b9690b542438c0870937be3"
 
 # Ensure TLS 1.2 is enabled for downloads
 [Net.ServicePointManager]::SecurityProtocol = [Net.SecurityProtocolType]::Tls12

install-scripts/install-safe-chain.ps1

@@ -4,11 +4,52 @@
 
 param(
     [switch]$ci,
-    [switch]$includepython
+    [switch]$includepython,
+    [string]$InstallDir
 )
 
+# Validates and normalizes the requested install directory.
+# Rejects non-absolute, root, PATH-like, and traversal-containing paths.
+function Test-InstallDir {
+    param([string]$Dir)
+
+    if ([string]::IsNullOrWhiteSpace($Dir)) {
+        return @{ Ok = $true; Normalized = $null }
+    }
+
+    if (-not [System.IO.Path]::IsPathRooted($Dir)) {
+        return @{ Ok = $false; Reason = "-InstallDir must be an absolute path, got: $Dir" }
+    }
+
+    if ($Dir.Contains([System.IO.Path]::PathSeparator)) {
+        return @{ Ok = $false; Reason = "-InstallDir must not contain the PATH separator ($([System.IO.Path]::PathSeparator))" }
+    }
+
+    $inputSegments = $Dir.Split([char[]]@('\', '/'), [System.StringSplitOptions]::RemoveEmptyEntries)
+    if ($inputSegments -contains "..") {
+        return @{ Ok = $false; Reason = "-InstallDir must not contain path traversal segments" }
+    }
+
+    $normalized = [System.IO.Path]::GetFullPath($Dir)
+    $root = [System.IO.Path]::GetPathRoot($normalized)
+    if ($normalized.TrimEnd('\', '/') -eq $root.TrimEnd('\', '/')) {
+        return @{ Ok = $false; Reason = "-InstallDir cannot be a root or drive-root directory" }
+    }
+
+    return @{ Ok = $true; Normalized = $normalized }
+}
+
 $Version = $env:SAFE_CHAIN_VERSION  # Will be fetched from latest release if not set
-$InstallDir = Join-Path $env:USERPROFILE ".safe-chain\bin"
+$SafeChainBase = if ($InstallDir) { $InstallDir } else { Join-Path $HOME ".safe-chain" }
+
+$installDirValidation = Test-InstallDir -Dir $SafeChainBase
+if (-not $installDirValidation.Ok) {
+    Write-Host "[ERROR] $($installDirValidation.Reason)" -ForegroundColor Red
+    exit 1
+}
+
+$SafeChainBase = $installDirValidation.Normalized
+$InstallDir = Join-Path $SafeChainBase "bin"
 $RepoUrl = "https://github.com/AikidoSec/safe-chain"
 
 # Ensure TLS 1.2 is enabled for downloads
@@ -98,6 +139,59 @@ function Get-Architecture {
     }
 }
 
+# Emits the deprecation warning for SAFE_CHAIN_VERSION and prints the version-pinned install command.
+# Returns immediately when no version was provided through the environment.
+function Write-VersionDeprecationWarning {
+    if ([string]::IsNullOrWhiteSpace($env:SAFE_CHAIN_VERSION)) {
+        return
+    }
+
+    Write-Warn "SAFE_CHAIN_VERSION environment variable is deprecated."
+    Write-Warn ""
+    Write-Warn "Please use direct download URLs for version pinning instead:"
+    Write-Warn ""
+    if ($ci) {
+        Write-Warn "  iex `"& { `$(iwr 'https://github.com/AikidoSec/safe-chain/releases/download/$env:SAFE_CHAIN_VERSION/install-safe-chain.ps1' -UseBasicParsing) } -ci`""
+    } else {
+        Write-Warn "  iex (iwr `"https://github.com/AikidoSec/safe-chain/releases/download/$env:SAFE_CHAIN_VERSION/install-safe-chain.ps1`" -UseBasicParsing)"
+    }
+    Write-Warn ""
+}
+
+# Builds the Windows release binary filename for the detected architecture.
+# Centralizes binary name generation for the download step.
+function Get-BinaryName {
+    param([string]$Architecture)
+
+    return "safe-chain-win-$Architecture.exe"
+}
+
+# Runs safe-chain setup or setup-ci after the binary is installed.
+# Temporarily appends the install directory to PATH and downgrades setup failures to warnings.
+function Invoke-SafeChainSetup {
+    param(
+        [string]$BinaryPath,
+        [string]$InstallDirectory
+    )
+
+    $setupCmd = if ($ci) { "setup-ci" } else { "setup" }
+
+    Write-Info "Running safe-chain $setupCmd..."
+    try {
+        $env:Path = "$env:Path;$InstallDirectory"
+        & $BinaryPath $setupCmd
+
+        if ($LASTEXITCODE -ne 0) {
+            Write-Warn "safe-chain was installed but setup encountered issues."
+            Write-Warn "You can run 'safe-chain $setupCmd' manually later."
+        }
+    }
+    catch {
+        Write-Warn "safe-chain was installed but setup encountered issues: $_"
+        Write-Warn "You can run 'safe-chain $setupCmd' manually later."
+    }
+}
+
 # Check and uninstall npm global package if present
 function Remove-NpmInstallation {
     # Check if npm is available
@@ -149,19 +243,7 @@ function Remove-VoltaInstallation {
 
 # Main installation
 function Install-SafeChain {
-    # Show deprecation warning if SAFE_CHAIN_VERSION is set
+    Write-VersionDeprecationWarning
-    if (-not [string]::IsNullOrWhiteSpace($env:SAFE_CHAIN_VERSION)) {
-        Write-Warn "SAFE_CHAIN_VERSION environment variable is deprecated."
-        Write-Warn ""
-        Write-Warn "Please use direct download URLs for version pinning instead:"
-        Write-Warn ""
-        if ($ci) {
-            Write-Warn "  iex `"& { `$(iwr 'https://github.com/AikidoSec/safe-chain/releases/download/$env:SAFE_CHAIN_VERSION/install-safe-chain.ps1' -UseBasicParsing) } -ci`""
-        } else {
-            Write-Warn "  iex (iwr `"https://github.com/AikidoSec/safe-chain/releases/download/$env:SAFE_CHAIN_VERSION/install-safe-chain.ps1`" -UseBasicParsing)"
-        }
-        Write-Warn ""
-    }
 
     # Fetch latest version if VERSION is not set
     if ([string]::IsNullOrWhiteSpace($Version)) {
@@ -192,7 +274,7 @@ function Install-SafeChain {
 
     # Detect platform
     $arch = Get-Architecture
-    $binaryName = "safe-chain-win-$arch.exe"
+    $binaryName = Get-BinaryName -Architecture $arch
 
     Write-Info "Detected architecture: $arch"
 
@@ -238,31 +320,7 @@ function Install-SafeChain {
 
     Write-Info "Binary installed to: $finalFile"
 
-    # Build setup command based on parameters
+    Invoke-SafeChainSetup -BinaryPath $finalFile -InstallDirectory $InstallDir
-    $setupCmd = if ($ci) { "setup-ci" } else { "setup" }
-    $setupArgs = @()
-
-    # Execute safe-chain setup
-    Write-Info "Running safe-chain $setupCmd $(if ($setupArgs) { $setupArgs -join ' ' })..."
-    try {
-        $env:Path = "$env:Path;$InstallDir"
-
-        if ($setupArgs) {
-            & $finalFile $setupCmd $setupArgs
-        }
-        else {
-            & $finalFile $setupCmd
-        }
-
-        if ($LASTEXITCODE -ne 0) {
-            Write-Warn "safe-chain was installed but setup encountered issues."
-            Write-Warn "You can run 'safe-chain $setupCmd $(if ($setupArgs) { $setupArgs -join ' ' })' manually later."
-        }
-    }
-    catch {
-        Write-Warn "safe-chain was installed but setup encountered issues: $_"
-        Write-Warn "You can run 'safe-chain $setupCmd $(if ($setupArgs) { $setupArgs -join ' ' })' manually later."
-    }
 }
 
 # Run installation

install-scripts/install-safe-chain.sh

@@ -6,9 +6,53 @@
 
 set -e  # Exit on error
 
+# Validates a user-provided install dir and exits on unsafe values.
+# Rejects relative paths, root paths, PATH separators, and traversal segments.
+validate_install_dir() {
+    dir="$1"
+
+    if [ -z "$dir" ]; then
+        return 0
+    fi
+
+    case "$dir" in
+        /*) ;;
+        *)
+            printf '[ERROR] --install-dir must be an absolute path, got: %s\n' "$dir" >&2
+            exit 1
+            ;;
+    esac
+
+    case "$dir" in
+        *:*)
+            printf '[ERROR] --install-dir must not contain the PATH separator (:)\n' >&2
+            exit 1
+            ;;
+    esac
+
+    if [ "$dir" = "/" ]; then
+        printf '[ERROR] --install-dir cannot be a root or drive-root directory\n' >&2
+        exit 1
+    fi
+
+    old_ifs=$IFS
+    IFS='/'
+    set -- $dir
+    IFS=$old_ifs
+
+    for segment in "$@"; do
+        if [ "$segment" = ".." ]; then
+            printf '[ERROR] --install-dir must not contain path traversal segments\n' >&2
+            exit 1
+        fi
+    done
+}
+
 # Configuration
 VERSION="${SAFE_CHAIN_VERSION:-}"  # Will be fetched from latest release if not set
-INSTALL_DIR="${HOME}/.safe-chain/bin"
+SAFE_CHAIN_BASE="${HOME}/.safe-chain"
+
+INSTALL_DIR="${SAFE_CHAIN_BASE}/bin"
 REPO_URL="https://github.com/AikidoSec/safe-chain"
 
 # Colors for output
@@ -126,6 +170,75 @@ download() {
     fi
 }
 
+# Prints the deprecation warning for SAFE_CHAIN_VERSION and the replacement install command.
+# Returns immediately when no version was pinned through the environment.
+warn_deprecated_version_env() {
+    if [ -z "$SAFE_CHAIN_VERSION" ]; then
+        return
+    fi
+
+    warn "SAFE_CHAIN_VERSION environment variable is deprecated."
+    warn ""
+    warn "Please use direct download URLs for version pinning instead:"
+    warn ""
+    if [ "$USE_CI_SETUP" = "true" ]; then
+        warn "  curl -fsSL https://github.com/AikidoSec/safe-chain/releases/download/${SAFE_CHAIN_VERSION}/install-safe-chain.sh | sh -s -- --ci"
+    else
+        warn "  curl -fsSL https://github.com/AikidoSec/safe-chain/releases/download/${SAFE_CHAIN_VERSION}/install-safe-chain.sh | sh"
+    fi
+    warn ""
+}
+
+# Ensures VERSION is populated before installation continues.
+# Fetches the latest release only when no explicit version was provided.
+ensure_version() {
+    if [ -n "$VERSION" ]; then
+        return
+    fi
+
+    info "Fetching latest release version..."
+    VERSION=$(fetch_latest_version)
+}
+
+# Constructs platform-specific binary filename to match GitHub release asset naming convention.
+get_binary_name() {
+    os="$1"
+    arch="$2"
+
+    if [ "$os" = "win" ]; then
+        printf 'safe-chain-%s-%s.exe\n' "$os" "$arch"
+    else
+        printf 'safe-chain-%s-%s\n' "$os" "$arch"
+    fi
+}
+
+# Returns the final installation path for the downloaded safe-chain binary.
+# Uses INSTALL_DIR and the platform-specific executable name.
+get_final_binary_path() {
+    os="$1"
+
+    if [ "$os" = "win" ]; then
+        printf '%s/safe-chain.exe\n' "$INSTALL_DIR"
+    else
+        printf '%s/safe-chain\n' "$INSTALL_DIR"
+    fi
+}
+
+run_setup_command() {
+    final_file="$1"
+
+    setup_cmd="setup"
+    if [ "$USE_CI_SETUP" = "true" ]; then
+        setup_cmd="setup-ci"
+    fi
+
+    info "Running safe-chain $setup_cmd..."
+    if ! "$final_file" "$setup_cmd"; then
+        warn "safe-chain was installed but setup encountered issues."
+        warn "You can run 'safe-chain $setup_cmd' manually later."
+    fi
+}
+
 # Check and uninstall npm global package if present
 remove_npm_installation() {
     if ! command_exists npm; then
@@ -229,19 +342,39 @@ remove_nvm_installation() {
 
 # Parse command-line arguments
 parse_arguments() {
-    for arg in "$@"; do
+    while [ $# -gt 0 ]; do
-        case "$arg" in
+        case "$1" in
             --ci)
                 USE_CI_SETUP=true
                 ;;
+            --install-dir)
+                shift
+                if [ $# -eq 0 ]; then
+                    error "Missing value for --install-dir"
+                fi
+                if [ -z "$1" ]; then
+                    error "--install-dir must not be empty"
+                fi
+                SAFE_CHAIN_BASE="$1"
+                ;;
+            --install-dir=*)
+                SAFE_CHAIN_BASE="${1#--install-dir=}"
+                if [ -z "$SAFE_CHAIN_BASE" ]; then
+                    error "--install-dir must not be empty"
+                fi
+                ;;
             --include-python)
                 warn "--include-python is deprecated and ignored. Python ecosystem is now included by default."
                 ;;
             *)
-                error "Unknown argument: $arg"
+                error "Unknown argument: $1"
                 ;;
         esac
+        shift
     done
+
+    validate_install_dir "${SAFE_CHAIN_BASE}"
+    INSTALL_DIR="${SAFE_CHAIN_BASE}/bin"
 }
 
 # Main installation
@@ -252,25 +385,9 @@ main() {
     # Parse command-line arguments
     parse_arguments "$@"
 
-    # Show deprecation warning if SAFE_CHAIN_VERSION is set
+    warn_deprecated_version_env
-    if [ -n "$SAFE_CHAIN_VERSION" ]; then
-        warn "SAFE_CHAIN_VERSION environment variable is deprecated."
-        warn ""
-        warn "Please use direct download URLs for version pinning instead:"
-        warn ""
-        if [ "$USE_CI_SETUP" = "true" ]; then
-            warn "  curl -fsSL https://github.com/AikidoSec/safe-chain/releases/download/${SAFE_CHAIN_VERSION}/install-safe-chain.sh | sh -s -- --ci"
-        else
-            warn "  curl -fsSL https://github.com/AikidoSec/safe-chain/releases/download/${SAFE_CHAIN_VERSION}/install-safe-chain.sh | sh"
-        fi
-        warn ""
-    fi
 
-    # Fetch latest version if VERSION is not set
+    ensure_version
-    if [ -z "$VERSION" ]; then
-        info "Fetching latest release version..."
-        VERSION=$(fetch_latest_version)
-    fi
 
     # Check if the requested version is already installed
     if is_version_installed "$VERSION"; then
@@ -294,11 +411,7 @@ main() {
     # Detect platform
     OS=$(detect_os)
     ARCH=$(detect_arch)
-    if [ "$OS" = "win" ]; then
+    BINARY_NAME=$(get_binary_name "$OS" "$ARCH")
-        BINARY_NAME="safe-chain-${OS}-${ARCH}.exe"
-    else
-        BINARY_NAME="safe-chain-${OS}-${ARCH}"
-    fi
 
     info "Detected platform: ${OS}-${ARCH}"
 
@@ -316,11 +429,7 @@ main() {
     download "$DOWNLOAD_URL" "$TEMP_FILE"
 
     # Rename and make executable
-    if [ "$OS" = "win" ]; then
+    FINAL_FILE=$(get_final_binary_path "$OS")
-        FINAL_FILE="${INSTALL_DIR}/safe-chain.exe"
-    else
-        FINAL_FILE="${INSTALL_DIR}/safe-chain"
-    fi
     mv "$TEMP_FILE" "$FINAL_FILE" || error "Failed to move binary to $FINAL_FILE"
     if [ "$OS" != "win" ]; then
         chmod +x "$FINAL_FILE" || error "Failed to make binary executable"
@@ -328,20 +437,7 @@ main() {
 
     info "Binary installed to: $FINAL_FILE"
 
-    # Build setup command based on arguments
+    run_setup_command "$FINAL_FILE"
-    SETUP_CMD="setup"
-    SETUP_ARGS=""
-
-    if [ "$USE_CI_SETUP" = "true" ]; then
-        SETUP_CMD="setup-ci"
-    fi
-
-    # Execute safe-chain setup
-    info "Running safe-chain $SETUP_CMD $SETUP_ARGS..."
-    if ! "$FINAL_FILE" $SETUP_CMD $SETUP_ARGS; then
-        warn "safe-chain was installed but setup encountered issues."
-        warn "You can run 'safe-chain $SETUP_CMD $SETUP_ARGS' manually later."
-    fi
 }
 
 main "$@"

install-scripts/uninstall-safe-chain.ps1

@@ -4,8 +4,6 @@
 
 # Use HOME on Unix, USERPROFILE on Windows (PowerShell Core is cross-platform)
 $HomeDir = if ($env:HOME) { $env:HOME } else { $env:USERPROFILE }
-$DotSafeChain = Join-Path $HomeDir ".safe-chain"
-$InstallDir = Join-Path $DotSafeChain "bin"
 
 # Helper functions
 function Write-Info {
@@ -24,6 +22,146 @@ function Write-Error-Custom {
     exit 1
 }
 
+# Derives the safe-chain base install directory from a resolved binary path.
+# Rejects wrapper scripts and paths that do not match the packaged bin layout.
+function Get-InstallDirFromBinaryPath {
+    param([string]$BinaryPath)
+
+    if ([string]::IsNullOrWhiteSpace($BinaryPath)) {
+        return $null
+    }
+
+    try {
+        $resolvedPath = (Resolve-Path -LiteralPath $BinaryPath -ErrorAction Stop).Path
+    }
+    catch {
+        $resolvedPath = [System.IO.Path]::GetFullPath($BinaryPath)
+    }
+
+    $fileName = [System.IO.Path]::GetFileName($resolvedPath)
+    if (($fileName -ne "safe-chain") -and ($fileName -ne "safe-chain.exe")) {
+        return $null
+    }
+
+    if ($resolvedPath -match '\.(js|cjs|mjs|cmd|ps1)$') {
+        return $null
+    }
+
+    $binDir = Split-Path -Parent $resolvedPath
+    if ((Split-Path -Leaf $binDir) -ne "bin") {
+        return $null
+    }
+
+    return (Split-Path -Parent $binDir)
+}
+
+# Returns the first safe-chain command found on PATH, if any.
+# Used as the starting point for install-dir discovery.
+function Get-SafeChainCommand {
+    return Get-Command safe-chain -ErrorAction SilentlyContinue | Select-Object -First 1
+}
+
+# Returns the safe-chain command path only when it points to a valid packaged binary install.
+# Prevents teardown from invoking arbitrary wrappers or scripts from PATH.
+function Get-ValidatedSafeChainCommandPath {
+    $command = Get-SafeChainCommand
+    if (-not $command -or [string]::IsNullOrWhiteSpace($command.Path)) {
+        return $null
+    }
+
+    $installDir = Get-InstallDirFromBinaryPath -BinaryPath $command.Path
+    if (-not $installDir) {
+        return $null
+    }
+
+    return $command.Path
+}
+
+# Invokes the validated safe-chain binary with get-install-dir and returns the reported base directory.
+# Safely returns $null when the command is unavailable or the lookup fails.
+function Get-ReportedInstallDir {
+    $safeChainPath = Get-ValidatedSafeChainCommandPath
+    if (-not $safeChainPath) {
+        return $null
+    }
+
+    try {
+        $reportedInstallDir = & $safeChainPath get-install-dir 2>$null | Select-Object -First 1
+        if ($reportedInstallDir) {
+            $reportedInstallDir = $reportedInstallDir.Trim()
+        }
+        if ($reportedInstallDir) {
+            return $reportedInstallDir
+        }
+    }
+    catch {
+        return $null
+    }
+
+    return $null
+}
+
+# Determines the safe-chain base install directory for uninstall.
+# Prefers the binary-reported location, then derives it from PATH, then falls back to the default home-dir layout.
+function Get-SafeChainInstallDir {
+    $reportedInstallDir = Get-ReportedInstallDir
+    if ($reportedInstallDir) {
+        return $reportedInstallDir
+    }
+
+    $command = Get-SafeChainCommand
+    if ($command -and $command.Path) {
+        $discoveredInstallDir = Get-InstallDirFromBinaryPath -BinaryPath $command.Path
+        if ($discoveredInstallDir) {
+            return $discoveredInstallDir
+        }
+    }
+
+    return (Join-Path $HomeDir ".safe-chain")
+}
+
+# Finds the installed safe-chain binary inside the resolved install directory.
+# Falls back to a validated safe-chain command when the expected file is missing.
+function Find-SafeChainBinary {
+    param([string]$DotSafeChain)
+
+    $safeChainExe = Join-Path $DotSafeChain "bin/safe-chain.exe"
+    $safeChainBin = Join-Path $DotSafeChain "bin/safe-chain"
+
+    if (Test-Path $safeChainExe) {
+        return $safeChainExe
+    }
+
+    if (Test-Path $safeChainBin) {
+        return $safeChainBin
+    }
+
+    return Get-ValidatedSafeChainCommandPath
+}
+
+# Runs safe-chain teardown before removing the installation directory.
+# Converts teardown failures into warnings so uninstall can still complete.
+function Invoke-SafeChainTeardown {
+    param([string]$SafeChainPath)
+
+    if (-not $SafeChainPath) {
+        Write-Warn "safe-chain command not found. Proceeding with uninstallation."
+        return
+    }
+
+    Write-Info "Running safe-chain teardown..."
+    try {
+        & $SafeChainPath teardown
+        if ($LASTEXITCODE -ne 0) {
+            Write-Warn "safe-chain teardown encountered issues, continuing with uninstallation..."
+        }
+    }
+    catch {
+        Write-Warn "safe-chain teardown encountered issues: $_"
+        Write-Warn "Continuing with uninstallation..."
+    }
+}
+
 # Check and uninstall npm global package if present
 function Remove-NpmInstallation {
     # Check if npm is available
@@ -76,49 +214,9 @@ function Remove-VoltaInstallation {
 # Main uninstallation
 function Uninstall-SafeChain {
     Write-Info "Uninstalling safe-chain..."
-
+    $DotSafeChain = Get-SafeChainInstallDir
-    # Run teardown if safe-chain is available
+    $safeChainPath = Find-SafeChainBinary -DotSafeChain $DotSafeChain
-    # Check for both safe-chain.exe (Windows) and safe-chain (Unix) since PowerShell Core runs on all platforms
+    Invoke-SafeChainTeardown -SafeChainPath $safeChainPath
-    $safeChainExe = Join-Path $InstallDir "safe-chain.exe"
-    $safeChainBin = Join-Path $InstallDir "safe-chain"
-
-    $safeChainPath = $null
-    if (Test-Path $safeChainExe) {
-        $safeChainPath = $safeChainExe
-    }
-    elseif (Test-Path $safeChainBin) {
-        $safeChainPath = $safeChainBin
-    }
-
-    if ($safeChainPath) {
-        Write-Info "Running safe-chain teardown..."
-        try {
-            & $safeChainPath teardown
-            if ($LASTEXITCODE -ne 0) {
-                Write-Warn "safe-chain teardown encountered issues, continuing with uninstallation..."
-            }
-        }
-        catch {
-            Write-Warn "safe-chain teardown encountered issues: $_"
-            Write-Warn "Continuing with uninstallation..."
-        }
-    }
-    elseif (Get-Command safe-chain -ErrorAction SilentlyContinue) {
-        Write-Info "Running safe-chain teardown..."
-        try {
-            safe-chain teardown
-            if ($LASTEXITCODE -ne 0) {
-                Write-Warn "safe-chain teardown encountered issues, continuing with uninstallation..."
-            }
-        }
-        catch {
-            Write-Warn "safe-chain teardown encountered issues: $_"
-            Write-Warn "Continuing with uninstallation..."
-        }
-    }
-    else {
-        Write-Warn "safe-chain command not found. Proceeding with uninstallation."
-    }
 
     # Remove npm and Volta installations
     Remove-NpmInstallation

install-scripts/uninstall-safe-chain.sh

@@ -7,7 +7,6 @@
 set -e  # Exit on error
 
 # Configuration
-DOT_SAFE_CHAIN="${HOME}/.safe-chain"
 
 # Colors for output
 RED='\033[0;31m'
@@ -34,6 +33,159 @@ command_exists() {
     command -v "$1" >/dev/null 2>&1
 }
 
+# Resolves a path to its canonical filesystem location when possible.
+# Follows symlinks so binary validation can inspect the real installed path.
+resolve_path() {
+    target="$1"
+
+    while [ -L "$target" ]; do
+        link_target=$(readlink "$target" 2>/dev/null || echo "")
+        if [ -z "$link_target" ]; then
+            break
+        fi
+
+        case "$link_target" in
+            /*) target="$link_target" ;;
+            *)
+                target="$(dirname "$target")/$link_target"
+                ;;
+        esac
+    done
+
+    target_dir=$(dirname "$target")
+    target_name=$(basename "$target")
+
+    if cd "$target_dir" 2>/dev/null; then
+        printf '%s/%s\n' "$(pwd -P)" "$target_name"
+    else
+        printf '%s\n' "$target"
+    fi
+}
+
+# Derives the safe-chain base install directory from a packaged binary path.
+# Rejects wrapper scripts and paths that do not match the expected bin layout.
+derive_install_dir_from_binary() {
+    binary_path="$1"
+
+    if [ -z "$binary_path" ]; then
+        return 1
+    fi
+
+    resolved_path=$(resolve_path "$binary_path")
+    binary_name=$(basename "$resolved_path")
+    case "$binary_name" in
+        safe-chain|safe-chain.exe) ;;
+        *) return 1 ;;
+    esac
+
+    case "$resolved_path" in
+        *.js|*.cjs|*.mjs|*.cmd|*.ps1) return 1 ;;
+    esac
+
+    binary_dir=$(dirname "$resolved_path")
+    if [ "$(basename "$binary_dir")" != "bin" ]; then
+        return 1
+    fi
+
+    dirname "$binary_dir"
+}
+
+# Determines the installed safe-chain base directory for uninstall.
+# Prefers the binary-reported location, then infers it from PATH, then falls back to ~/.safe-chain.
+get_install_dir() {
+    reported_install_dir=$(get_reported_install_dir || true)
+    if [ -n "$reported_install_dir" ]; then
+        printf '%s\n' "$reported_install_dir"
+        return 0
+    fi
+
+    command_path=$(get_safe_chain_command_path || true)
+    install_dir=$(derive_install_dir_from_binary "$command_path" || true)
+    if [ -n "$install_dir" ]; then
+        printf '%s\n' "$install_dir"
+        return 0
+    fi
+
+    printf '%s\n' "${HOME}/.safe-chain"
+}
+
+# Returns the current safe-chain command path from PATH.
+# Fails when safe-chain is not currently resolvable.
+get_safe_chain_command_path() {
+    if ! command_exists safe-chain; then
+        return 1
+    fi
+
+    command -v safe-chain
+}
+
+# Returns the safe-chain command path only when it resolves to a valid packaged binary install.
+# Prevents the uninstaller from invoking arbitrary PATH entries.
+get_validated_safe_chain_command_path() {
+    command_path=$(get_safe_chain_command_path || true)
+    if [ -z "$command_path" ]; then
+        return 1
+    fi
+
+    install_dir=$(derive_install_dir_from_binary "$command_path" || true)
+    if [ -z "$install_dir" ]; then
+        return 1
+    fi
+
+    printf '%s\n' "$command_path"
+}
+
+# Asks the validated safe-chain binary for its install directory via get-install-dir.
+# Returns nothing if the command is unavailable or the lookup fails.
+get_reported_install_dir() {
+    safe_chain_path=$(get_validated_safe_chain_command_path || true)
+    if [ -z "$safe_chain_path" ]; then
+        return 1
+    fi
+
+    install_dir=$("$safe_chain_path" get-install-dir 2>/dev/null || true)
+    if [ -n "$install_dir" ]; then
+        printf '%s\n' "$install_dir"
+        return 0
+    fi
+
+    return 1
+}
+
+# Locates the installed safe-chain binary to use for teardown.
+# Checks the discovered install dir first, then falls back to a validated PATH entry.
+find_installed_safe_chain_binary() {
+    dot_safe_chain="$1"
+
+    safe_chain_location="$dot_safe_chain/bin/safe-chain"
+    if [ -x "$safe_chain_location" ]; then
+        printf '%s\n' "$safe_chain_location"
+        return 0
+    fi
+
+    command_path=$(get_validated_safe_chain_command_path || true)
+    if [ -n "$command_path" ]; then
+        printf '%s\n' "$command_path"
+        return 0
+    fi
+
+    return 1
+}
+
+# Runs safe-chain teardown before removing files.
+# Continues with uninstall even if teardown is unavailable or fails.
+run_safe_chain_teardown() {
+    safe_chain_command="$1"
+
+    if [ -z "$safe_chain_command" ]; then
+        warn "safe-chain command not found. Proceeding with uninstallation."
+        return
+    fi
+
+    info "Running safe-chain teardown..."
+    "$safe_chain_command" teardown || warn "safe-chain teardown encountered issues, continuing with uninstallation..."
+}
+
 # Check and uninstall npm global package if present
 remove_npm_installation() {
     if ! command_exists npm; then
@@ -139,17 +291,9 @@ remove_nvm_installation() {
 
 # Main uninstallation
 main() {
-    SAFE_CHAIN_LOCATION="$DOT_SAFE_CHAIN/bin/safe-chain"
+    DOT_SAFE_CHAIN=$(get_install_dir)
-
+    SAFE_CHAIN_COMMAND=$(find_installed_safe_chain_binary "$DOT_SAFE_CHAIN" || true)
-    if [ -x "$SAFE_CHAIN_LOCATION" ]; then
+    run_safe_chain_teardown "$SAFE_CHAIN_COMMAND"
-        info "Running safe-chain teardown..."
-        "$SAFE_CHAIN_LOCATION" teardown || warn "safe-chain teardown encountered issues, continuing with uninstallation..."
-    elif command_exists safe-chain; then
-        info "Running safe-chain teardown..."
-        safe-chain teardown || warn "safe-chain teardown encountered issues, continuing with uninstallation..."
-    else
-        warn "safe-chain command not found. Proceeding with uninstallation."
-    fi
 
     # Check for existing safe-chain installation through nvm, volta, or npm
     remove_npm_installation

packages/safe-chain/bin/aikido-uvx.js

@@ -0,0 +1,16 @@
+#!/usr/bin/env node
+
+import { main } from "../src/main.js";
+import { initializePackageManager } from "../src/packagemanager/currentPackageManager.js";
+import { setEcoSystem, ECOSYSTEM_PY } from "../src/config/settings.js";
+
+// Set eco system
+setEcoSystem(ECOSYSTEM_PY);
+
+initializePackageManager("uvx");
+
+(async () => {
+  // Pass through only user-supplied uvx args
+  var exitCode = await main(process.argv.slice(2));
+  process.exit(exitCode);
+})();

packages/safe-chain/bin/safe-chain.js

@@ -16,6 +16,7 @@ import path from "path";
 import { fileURLToPath } from "url";
 import fs from "fs";
 import { knownAikidoTools } from "../src/shell-integration/helpers.js";
+import { getInstalledSafeChainDir } from "../src/installLocation.js";
 
 /** @type {string} */
 // This checks the current file's dirname in a way that's compatible with:
@@ -67,6 +68,17 @@ if (tool) {
   teardownDirectories();
 } else if (command === "setup-ci") {
   setupCi();
+} else if (command === "get-install-dir") {
+  const installDir = getInstalledSafeChainDir();
+  if (!installDir) {
+    ui.writeError(
+      "Install directory is only available for packaged safe-chain binaries.",
+    );
+    process.exit(1);
+  }
+
+  ui.writeInformation(installDir);
+  process.exit(0);
 } else if (command === "--version" || command === "-v" || command === "-v") {
   (async () => {
     ui.writeInformation(`Current safe-chain version: ${await getVersion()}`);
@@ -88,7 +100,7 @@ function writeHelp() {
   ui.writeInformation(
     `Available commands: ${chalk.cyan("setup")}, ${chalk.cyan(
       "teardown",
-    )}, ${chalk.cyan("setup-ci")}, ${chalk.cyan("help")}, ${chalk.cyan(
+    )}, ${chalk.cyan("setup-ci")}, ${chalk.cyan("get-install-dir")}, ${chalk.cyan("help")}, ${chalk.cyan(
       "--version",
     )}`,
   );
@@ -108,6 +120,11 @@ function writeHelp() {
       "safe-chain setup-ci",
     )}: This will setup safe-chain for CI environments by creating shims and modifying the PATH.`,
   );
+  ui.writeInformation(
+    `- ${chalk.cyan(
+      "safe-chain get-install-dir",
+    )}: Print the install directory for packaged safe-chain binaries.`,
+  );
   ui.writeInformation(
     `- ${chalk.cyan("safe-chain --version")} (or ${chalk.cyan(
       "-v",

packages/safe-chain/package.json

@@ -16,6 +16,7 @@
     "aikido-bun": "bin/aikido-bun.js",
     "aikido-bunx": "bin/aikido-bunx.js",
     "aikido-uv": "bin/aikido-uv.js",
+    "aikido-uvx": "bin/aikido-uvx.js",
     "aikido-pip": "bin/aikido-pip.js",
     "aikido-pip3": "bin/aikido-pip3.js",
     "aikido-python": "bin/aikido-python.js",
@@ -39,7 +40,6 @@
   "license": "AGPL-3.0-or-later",
   "description": "The Aikido Safe Chain wraps around the [npm cli](https://github.com/npm/cli), [npx](https://github.com/npm/cli/blob/latest/docs/content/commands/npx.md), [yarn](https://yarnpkg.com/), [pnpm](https://pnpm.io/), [pnpx](https://pnpm.io/cli/dlx), [bun](https://bun.sh/), [bunx](https://bun.sh/docs/cli/bunx), [uv](https://docs.astral.sh/uv/) (Python), [pip](https://pip.pypa.io/), and [pdm](https://pdm-project.org/) to provide extra checks before installing new packages. This tool will detect when a package contains malware and prompt you to exit, preventing npm, npx, yarn, pnpm, pnpx, bun, bunx, uv, pip/pip3, or pdm from downloading or running the malware.",
   "dependencies": {
-    "archiver": "^7.0.1",
     "certifi": "14.5.15",
     "chalk": "5.4.1",
     "https-proxy-agent": "7.0.6",
@@ -50,7 +50,6 @@
     "semver": "7.7.2"
   },
   "devDependencies": {
-    "@types/archiver": "^7.0.0",
     "@types/ini": "^4.1.1",
     "@types/make-fetch-happen": "^10.0.4",
     "@types/node": "^18.19.130",

packages/safe-chain/src/config/configFile.js

@@ -3,6 +3,7 @@ import path from "path";
 import os from "os";
 import { ui } from "../environment/userInteraction.js";
 import { getEcoSystem } from "./settings.js";
+import { getSafeChainBaseDir } from "./safeChainDir.js";
 
 /**
  * @typedef {Object} SafeChainConfig
@@ -304,8 +305,7 @@ function getConfigFilePath() {
  * @returns {string}
  */
 export function getSafeChainDirectory() {
-  const homeDir = os.homedir();
+  const safeChainDir = getSafeChainBaseDir();
-  const safeChainDir = path.join(homeDir, ".safe-chain");
 
   if (!fs.existsSync(safeChainDir)) {
     fs.mkdirSync(safeChainDir, { recursive: true });

packages/safe-chain/src/config/safeChainDir.js

@@ -0,0 +1,71 @@
+import os from "os";
+import path from "path";
+import { fileURLToPath } from "url";
+import { getInstalledSafeChainDir } from "../installLocation.js";
+
+/**
+ * @returns {string}
+ */
+export function getSafeChainBaseDir() {
+  return getInstalledSafeChainDir() ?? path.join(os.homedir(), ".safe-chain");
+}
+
+/**
+ * @returns {string}
+ */
+export function getBinDir() {
+  return path.join(getSafeChainBaseDir(), "bin");
+}
+
+/**
+ * @returns {string}
+ */
+export function getShimsDir() {
+  return path.join(getSafeChainBaseDir(), "shims");
+}
+
+/**
+ * @returns {string}
+ */
+export function getScriptsDir() {
+  return path.join(getSafeChainBaseDir(), "scripts");
+}
+
+/**
+ * @returns {string}
+ */
+export function getCertsDir() {
+  return path.join(getSafeChainBaseDir(), "certs");
+}
+
+/**
+ * Resolves the directory of the calling module.
+ * Falls back to __dirname when import.meta.url is unavailable (pkg CJS binary).
+ * @param {string | undefined} moduleUrl
+ * @returns {string}
+ */
+function resolveModuleDir(moduleUrl) {
+  if (moduleUrl) {
+    return path.dirname(fileURLToPath(moduleUrl));
+  }
+  // eslint-disable-next-line no-undef
+  return __dirname;
+}
+
+/**
+ * @param {string | undefined} moduleUrl
+ * @param {string} fileName
+ * @returns {string}
+ */
+export function getStartupScriptSourcePath(moduleUrl, fileName) {
+  return path.join(resolveModuleDir(moduleUrl), "startup-scripts", fileName);
+}
+
+/**
+ * @param {string | undefined} moduleUrl
+ * @param {string} fileName
+ * @returns {string}
+ */
+export function getPathWrapperTemplatePath(moduleUrl, fileName) {
+  return path.join(resolveModuleDir(moduleUrl), "path-wrappers", "templates", fileName);
+}

packages/safe-chain/src/installLocation.js

@@ -0,0 +1,42 @@
+import path from "path";
+
+/** @type {NodeJS.Process & { pkg?: unknown }} */
+const processWithPkg = process;
+
+/**
+ * @param {string} executablePath
+ * @returns {string | undefined}
+ */
+export function deriveInstallDirFromExecutablePath(executablePath) {
+  if (!executablePath) {
+    return undefined;
+  }
+
+  const pathLibrary = executablePath.includes("\\") ? path.win32 : path.posix;
+  const executableDir = pathLibrary.dirname(executablePath);
+  if (pathLibrary.basename(executableDir) !== "bin") {
+    return undefined;
+  }
+
+  return pathLibrary.dirname(executableDir);
+}
+
+/**
+ * Returns the install directory for a packaged safe-chain binary.
+ * Custom installation directories only apply to packaged binary installs.
+ * For npm/global/dev-script executions this intentionally returns undefined,
+ * which causes callers to fall back to the default ~/.safe-chain layout.
+ *
+ * @param {{ isPackaged?: boolean, executablePath?: string }} [options]
+ * @returns {string | undefined}
+ */
+export function getInstalledSafeChainDir(options = {}) {
+  const isPackaged = options.isPackaged ?? Boolean(processWithPkg.pkg);
+  if (!isPackaged) {
+    return undefined;
+  }
+
+  return deriveInstallDirFromExecutablePath(
+    options.executablePath ?? process.execPath,
+  );
+}

packages/safe-chain/src/installLocation.spec.js

@@ -0,0 +1,51 @@
+import { describe, it } from "node:test";
+import assert from "node:assert";
+import {
+  deriveInstallDirFromExecutablePath,
+  getInstalledSafeChainDir,
+} from "./installLocation.js";
+
+describe("deriveInstallDirFromExecutablePath", () => {
+  it("derives the install dir from a Unix binary path", () => {
+    assert.strictEqual(
+      deriveInstallDirFromExecutablePath("/usr/local/.safe-chain/bin/safe-chain"),
+      "/usr/local/.safe-chain",
+    );
+  });
+
+  it("derives the install dir from a Windows binary path", () => {
+    assert.strictEqual(
+      deriveInstallDirFromExecutablePath("C:\\ProgramData\\safe-chain\\bin\\safe-chain.exe"),
+      "C:\\ProgramData\\safe-chain",
+    );
+  });
+
+  it("returns undefined when the executable is not inside a bin directory", () => {
+    assert.strictEqual(
+      deriveInstallDirFromExecutablePath("/usr/local/.safe-chain/safe-chain"),
+      undefined,
+    );
+  });
+});
+
+describe("getInstalledSafeChainDir", () => {
+  it("returns undefined for non-packaged executions", () => {
+    assert.strictEqual(
+      getInstalledSafeChainDir({
+        isPackaged: false,
+        executablePath: "/usr/local/.safe-chain/bin/safe-chain",
+      }),
+      undefined,
+    );
+  });
+
+  it("returns the install dir for packaged executions", () => {
+    assert.strictEqual(
+      getInstalledSafeChainDir({
+        isPackaged: true,
+        executablePath: "/usr/local/.safe-chain/bin/safe-chain",
+      }),
+      "/usr/local/.safe-chain",
+    );
+  });
+});

packages/safe-chain/src/packagemanager/currentPackageManager.js

@@ -14,6 +14,7 @@ import { createUvPackageManager } from "./uv/createUvPackageManager.js";
 import { createPoetryPackageManager } from "./poetry/createPoetryPackageManager.js";
 import { createPipXPackageManager } from "./pipx/createPipXPackageManager.js";
 import { createPdmPackageManager } from "./pdm/createPdmPackageManager.js";
+import { createUvxPackageManager } from "./uvx/createUvxPackageManager.js";
 
 /**
  * @type {{packageManagerName: PackageManager | null}}
@@ -61,6 +62,8 @@ export function initializePackageManager(packageManagerName, context) {
     state.packageManagerName = createPipPackageManager(context);
   } else if (packageManagerName === "uv") {
     state.packageManagerName = createUvPackageManager();
+  } else if (packageManagerName === "uvx") {
+    state.packageManagerName = createUvxPackageManager();
   } else if (packageManagerName === "poetry") {
     state.packageManagerName = createPoetryPackageManager();
   } else if (packageManagerName === "pipx") {

packages/safe-chain/src/packagemanager/uvx/createUvxPackageManager.js

@@ -0,0 +1,18 @@
+import { runUv } from "../uv/runUvCommand.js";
+
+/**
+ * @returns {import("../currentPackageManager.js").PackageManager}
+ */
+export function createUvxPackageManager() {
+  return {
+    /**
+     * @param {string[]} args
+     */
+    runCommand: (args) => {
+      return runUv("uvx", args);
+    },
+    // For uvx, rely solely on MITM
+    isSupportedCommand: () => false,
+    getDependencyUpdatesForCommand: () => [],
+  };
+}

packages/safe-chain/src/packagemanager/uvx/createUvxPackageManager.spec.js

@@ -0,0 +1,14 @@
+import { test } from "node:test";
+import assert from "node:assert";
+import { createUvxPackageManager } from "./createUvxPackageManager.js";
+
+test("createUvxPackageManager returns valid package manager interface", () => {
+  const pm = createUvxPackageManager();
+
+  assert.ok(pm);
+  assert.strictEqual(typeof pm.runCommand, "function");
+  assert.strictEqual(typeof pm.isSupportedCommand, "function");
+  assert.strictEqual(typeof pm.getDependencyUpdatesForCommand, "function");
+  assert.strictEqual(pm.isSupportedCommand(), false);
+  assert.deepStrictEqual(pm.getDependencyUpdatesForCommand(), []);
+});

packages/safe-chain/src/registryProxy/certUtils.js

@@ -1,9 +1,8 @@
 import forge from "node-forge";
 import path from "path";
 import fs from "fs";
-import os from "os";
+import { getCertsDir } from "../config/safeChainDir.js";
 
-const certFolder = path.join(os.homedir(), ".safe-chain", "certs");
 const ca = loadCa();
 
 const certCache = new Map();
@@ -20,7 +19,7 @@ function createKeyIdentifier(publicKey) {
 }
 
 export function getCaCertPath() {
-  return path.join(certFolder, "ca-cert.pem");
+  return path.join(getCertsDir(), "ca-cert.pem");
 }
 
 /**
@@ -112,6 +111,7 @@ export function generateCertForHost(hostname) {
 }
 
 function loadCa() {
+  const certFolder = getCertsDir();
   const keyPath = path.join(certFolder, "ca-key.pem");
   const certPath = path.join(certFolder, "ca-cert.pem");
 

packages/safe-chain/src/registryProxy/certUtils.spec.js

@@ -0,0 +1,71 @@
+import { describe, it, beforeEach, afterEach, mock } from "node:test";
+import assert from "node:assert";
+
+describe("certUtils", () => {
+  let installedSafeChainDir;
+
+  beforeEach(() => {
+    installedSafeChainDir = undefined;
+    mock.module("../config/safeChainDir.js", {
+      namedExports: {
+        getSafeChainBaseDir: () => installedSafeChainDir ?? "/home/test/.safe-chain",
+        getCertsDir: () => `${installedSafeChainDir ?? "/home/test/.safe-chain"}/certs`,
+      },
+    });
+  });
+
+  afterEach(() => {
+    mock.reset();
+  });
+
+  it("stores CA certificates in the packaged install dir when available", async () => {
+    installedSafeChainDir = "/custom/safe-chain";
+
+    mock.module("fs", {
+      defaultExport: {
+        existsSync: () => false,
+        mkdirSync: () => {},
+        writeFileSync: () => {},
+      },
+    });
+
+    mock.module("node-forge", {
+      defaultExport: {
+        pki: {
+          getPublicKeyFingerprint: () => "fingerprint",
+          rsa: {
+            generateKeyPair: () => ({
+              publicKey: "public-key",
+              privateKey: "private-key",
+            }),
+          },
+          createCertificate: () => ({
+            publicKey: null,
+            serialNumber: "",
+            validity: {
+              notBefore: new Date(),
+              notAfter: new Date(),
+            },
+            setSubject: () => {},
+            setIssuer: () => {},
+            setExtensions: () => {},
+            sign: () => {},
+          }),
+          privateKeyToPem: () => "private-key-pem",
+          certificateToPem: () => "certificate-pem",
+        },
+        md: {
+          sha1: { create: () => "sha1" },
+          sha256: { create: () => "sha256" },
+        },
+      },
+    });
+
+    const { getCaCertPath } = await import("./certUtils.js");
+
+    assert.strictEqual(
+      getCaCertPath(),
+      "/custom/safe-chain/certs/ca-cert.pem",
+    );
+  });
+});

packages/safe-chain/src/registryProxy/interceptors/pip/modifyPipInfo.js

@@ -6,6 +6,23 @@ export { parsePipMetadataUrl, isPipPackageInfoUrl } from "./parsePipPackageUrl.j
 import { getPipMetadataContentType, logSuppressedVersion } from "./pipMetadataResponseUtils.js";
 import { modifyPipJsonResponse } from "./modifyPipJsonResponse.js";
 
+/**
+ * Strip conditional GET headers so PyPI always returns a full 200 response
+ * with a body we can rewrite. Without this, pip sends If-None-Match /
+ * If-Modified-Since, PyPI responds 304 Not Modified (empty body), and
+ * safe-chain cannot rewrite it — leaving pip with a cached index that still
+ * lists too-young versions. Those versions are then blocked at direct-download
+ * time with a hard 403, preventing dependency resolution from completing.
+ *
+ * @param {NodeJS.Dict<string | string[]>} headers
+ * @returns {NodeJS.Dict<string | string[]>}
+ */
+export function modifyPipInfoRequestHeaders(headers) {
+  delete headers["if-none-match"];
+  delete headers["if-modified-since"];
+  return headers;
+}
+
 // Match simple-index anchor tags and capture their href so we can suppress
 // individual distribution links from PyPI HTML metadata responses.
 const HTML_ANCHOR_HREF_RE =

packages/safe-chain/src/registryProxy/interceptors/pip/pipInterceptor.js

@@ -9,6 +9,7 @@ import { openNewPackagesDatabase } from "../../../scanning/newPackagesListCache.
 import { interceptRequests } from "../interceptorBuilder.js";
 import { isExcludedFromMinimumPackageAge } from "../minimumPackageAgeExclusions.js";
 import {
+  modifyPipInfoRequestHeaders,
   modifyPipInfoResponse,
   parsePipMetadataUrl,
 } from "./modifyPipInfo.js";
@@ -61,6 +62,7 @@ function createPipRequestHandler(registry) {
       !isExcludedFromMinimumPackageAge(metadataPackageName)
     ) {
       const newPackagesDatabase = await openNewPackagesDatabase();
+      reqContext.modifyRequestHeaders(modifyPipInfoRequestHeaders);
       reqContext.modifyBody((body, headers) =>
         modifyPipInfoResponse(
           body,

packages/safe-chain/src/registryProxy/interceptors/pip/pipInterceptor.minPackageAge.spec.js

@@ -129,6 +129,28 @@ describe("pipInterceptor minimum package age", async () => {
     newlyReleasedPackageResponse = false;
   });
 
+  it("strips If-None-Match and If-Modified-Since from metadata requests to prevent 304 cache bypass", async () => {
+    const url = "https://pypi.org/simple/foo-bar/";
+    newlyReleasedPackageResponse = true;
+
+    const interceptor = pipInterceptorForUrl(url);
+    const result = await interceptor.handleRequest(url);
+
+    const headers = {
+      "if-none-match": '"some-etag"',
+      "if-modified-since": "Thu, 01 Jan 2026 00:00:00 GMT",
+      accept: "*/*",
+    };
+
+    result.modifyRequestHeaders(headers);
+
+    assert.equal(headers["if-none-match"], undefined, "If-None-Match must be stripped");
+    assert.equal(headers["if-modified-since"], undefined, "If-Modified-Since must be stripped");
+    assert.equal(headers.accept, "*/*", "unrelated headers must be preserved");
+
+    newlyReleasedPackageResponse = false;
+  });
+
   it("should not block newly released package downloads when a dot-name package matches a hyphen exclusion", async () => {
     const url =
       "https://files.pythonhosted.org/packages/xx/yy/foo.bar-2.0.0.tar.gz";

packages/safe-chain/src/shell-integration/helpers.js

@@ -66,6 +66,12 @@ export const knownAikidoTools = [
     ecoSystem: ECOSYSTEM_PY,
     internalPackageManagerName: "uv",
   },
+  {
+    tool: "uvx",
+    aikidoCommand: "aikido-uvx",
+    ecoSystem: ECOSYSTEM_PY,
+    internalPackageManagerName: "uvx",
+  },
   {
     tool: "pip",
     aikidoCommand: "aikido-pip",
@@ -127,20 +133,6 @@ export function getPackageManagerList() {
   return `${tools.join(", ")}, and ${lastTool} commands`;
 }
 
-/**
- * @returns {string}
- */
-export function getShimsDir() {
-  return path.join(os.homedir(), ".safe-chain", "shims");
-}
-
-/**
- * @returns {string}
- */
-export function getScriptsDir() {
-  return path.join(os.homedir(), ".safe-chain", "scripts");
-}
-
 /**
  * @param {string} executableName
  *

packages/safe-chain/src/shell-integration/helpers.spec.js

@@ -1,6 +1,6 @@
 import { describe, it, beforeEach, afterEach, mock } from "node:test";
 import assert from "node:assert";
-import { tmpdir } from "node:os";
+import { tmpdir, homedir } from "node:os";
 import fs from "node:fs";
 import path from "path";
 
@@ -15,6 +15,7 @@ describe("removeLinesMatchingPatternTests", () => {
     mock.module("node:os", {
       namedExports: {
         EOL: "\r\n", // Simulate Windows line endings
+        homedir,
         tmpdir: tmpdir,
         platform: () => "linux",
       },
@@ -182,3 +183,30 @@ describe("removeLinesMatchingPatternTests", () => {
     assert.strictEqual(resultLines.length, 5, "Should have exactly 5 lines");
   });
 });
+
+describe("getSafeChainBaseDir / getBinDir / getShimsDir / getScriptsDir", () => {
+  it("defaults base dir to ~/.safe-chain when no packaged install dir is available", async () => {
+    const { getSafeChainBaseDir } = await import("../config/safeChainDir.js");
+    assert.strictEqual(getSafeChainBaseDir(), path.join(homedir(), ".safe-chain"));
+  });
+
+  it("getBinDir returns ~/.safe-chain/bin by default", async () => {
+    const { getBinDir } = await import("../config/safeChainDir.js");
+    assert.strictEqual(getBinDir(), path.join(homedir(), ".safe-chain", "bin"));
+  });
+
+  it("getShimsDir returns ~/.safe-chain/shims by default", async () => {
+    const { getShimsDir } = await import("../config/safeChainDir.js");
+    assert.strictEqual(getShimsDir(), path.join(homedir(), ".safe-chain", "shims"));
+  });
+
+  it("getScriptsDir returns ~/.safe-chain/scripts by default", async () => {
+    const { getScriptsDir } = await import("../config/safeChainDir.js");
+    assert.strictEqual(getScriptsDir(), path.join(homedir(), ".safe-chain", "scripts"));
+  });
+
+  it("getCertsDir returns ~/.safe-chain/certs by default", async () => {
+    const { getCertsDir } = await import("../config/safeChainDir.js");
+    assert.strictEqual(getCertsDir(), path.join(homedir(), ".safe-chain", "certs"));
+  });
+});

packages/safe-chain/src/shell-integration/path-wrappers/templates/unix-wrapper.template.sh

@@ -4,13 +4,28 @@
 
 # Function to remove shim from PATH (POSIX-compliant)
 remove_shim_from_path() {
-    echo "$PATH" | sed "s|$HOME/.safe-chain/shims:||g"
+    _safe_chain_phys=$(CDPATH= cd -- "$(dirname -- "$0")" 2>/dev/null && pwd -P)
+    if [ -z "$_safe_chain_phys" ]; then
+        echo "$PATH"
+        return
+    fi
+    _path=$(echo "$PATH" | sed "s|${_safe_chain_phys}:||g")
+    # Also remove via dirname of $0 directly — on macOS /tmp is a symlink to /private/tmp,
+    # so pwd -P resolves to /private/tmp/… but PATH may still contain /tmp/….
+    _dir=$(dirname -- "$0")
+    case "$_dir" in
+        /*) [ "$_dir" != "$_safe_chain_phys" ] && _path=$(echo "$_path" | sed "s|${_dir}:||g") ;;
+    esac
+    echo "$_path"
 }
 
 if command -v safe-chain >/dev/null 2>&1; then
   # Remove shim directory from PATH when calling {{AIKIDO_COMMAND}} to prevent infinite loops
   PATH=$(remove_shim_from_path) exec safe-chain {{PACKAGE_MANAGER}} "$@"
 else
+  # safe-chain is not reachable — warn the user so they know protection is inactive
+  printf "\033[43;30mWarning:\033[0m safe-chain is not available to protect you from installing malware. {{PACKAGE_MANAGER}} will run without it.\n" >&2
+
   # Dynamically find original {{PACKAGE_MANAGER}} (excluding this shim directory)
   original_cmd=$(PATH=$(remove_shim_from_path) command -v {{PACKAGE_MANAGER}})
   if [ -n "$original_cmd" ]; then

packages/safe-chain/src/shell-integration/path-wrappers/templates/windows-wrapper.template.cmd

@@ -3,7 +3,8 @@ REM Generated wrapper for {{PACKAGE_MANAGER}} by safe-chain
 REM This wrapper intercepts {{PACKAGE_MANAGER}} calls for non-interactive environments
 
 REM Remove shim directory from PATH to prevent infinite loops
-set "SHIM_DIR=%USERPROFILE%\.safe-chain\shims"
+set "SHIM_DIR=%~dp0"
+if "%SHIM_DIR:~-1%"=="\" set "SHIM_DIR=%SHIM_DIR:~0,-1%"
 call set "CLEAN_PATH=%%PATH:%SHIM_DIR%;=%%"
 
 REM Check if aikido command is available with clean PATH

packages/safe-chain/src/shell-integration/setup-ci.js

@@ -1,24 +1,14 @@
 import chalk from "chalk";
 import { ui } from "../environment/userInteraction.js";
-import { getPackageManagerList, knownAikidoTools, getShimsDir } from "./helpers.js";
+import { getPackageManagerList, knownAikidoTools } from "./helpers.js";
+import {
+  getShimsDir,
+  getBinDir,
+  getPathWrapperTemplatePath,
+} from "../config/safeChainDir.js";
 import fs from "fs";
 import os from "os";
 import path from "path";
-import { fileURLToPath } from "url";
-
-/** @type {string} */
-// This checks the current file's dirname in a way that's compatible with:
-//  - Modulejs (import.meta.url)
-//  - ES modules (__dirname)
-// This is needed because safe-chain's npm package is built using ES modules,
-// but building the binaries requires commonjs.
-let dirname;
-if (import.meta.url) {
-  const filename = fileURLToPath(import.meta.url);
-  dirname = path.dirname(filename);
-} else {
-  dirname = __dirname;
-}
 
 /**
  * Loops over the detected shells and calls the setup function for each.
@@ -31,7 +21,7 @@ export async function setupCi() {
   ui.emptyLine();
 
   const shimsDir = getShimsDir();
-  const binDir = path.join(os.homedir(), ".safe-chain", "bin");
+  const binDir = getBinDir();
   // Create the shims directory if it doesn't exist
   if (!fs.existsSync(shimsDir)) {
     fs.mkdirSync(shimsDir, { recursive: true });
@@ -50,12 +40,7 @@ export async function setupCi() {
  */
 function createUnixShims(shimsDir) {
   // Read the template file
-  const templatePath = path.resolve(
+  const templatePath = getPathWrapperTemplatePath(import.meta.url, "unix-wrapper.template.sh");
-    dirname,
-    "path-wrappers",
-    "templates",
-    "unix-wrapper.template.sh"
-  );
 
   if (!fs.existsSync(templatePath)) {
     ui.writeError(`Template file not found: ${templatePath}`);
@@ -89,12 +74,7 @@ function createUnixShims(shimsDir) {
  */
 function createWindowsShims(shimsDir) {
   // Read the template file
-  const templatePath = path.resolve(
+  const templatePath = getPathWrapperTemplatePath(import.meta.url, "windows-wrapper.template.cmd");
-    dirname,
-    "path-wrappers",
-    "templates",
-    "windows-wrapper.template.cmd"
-  );
 
   if (!fs.existsSync(templatePath)) {
     ui.writeError(`Windows template file not found: ${templatePath}`);

packages/safe-chain/src/shell-integration/setup-ci.spec.js

@@ -22,12 +22,12 @@ describe("Setup CI shell integration", () => {
     fs.mkdirSync(path.join(mockTemplateDir, "path-wrappers", "templates"), { recursive: true });
     fs.writeFileSync(
       path.join(mockTemplateDir, "path-wrappers", "templates", "unix-wrapper.template.sh"),
-      "#!/bin/bash\n# Template for {{PACKAGE_MANAGER}}\nexec {{AIKIDO_COMMAND}} \"$@\"\n",
+      "#!/bin/bash\n# Template for {{PACKAGE_MANAGER}}\n_safe_chain_shims=$(CDPATH= cd -- \"$(dirname -- \"$0\")\" 2>/dev/null && pwd -P)\nexec {{AIKIDO_COMMAND}} \"$@\"\n",
       "utf-8"
     );
     fs.writeFileSync(
       path.join(mockTemplateDir, "path-wrappers", "templates", "windows-wrapper.template.cmd"),
-      "@echo off\nREM Template for {{PACKAGE_MANAGER}}\n{{AIKIDO_COMMAND}} %*\n",
+      "@echo off\nset \"SHIM_DIR=%~dp0\"\n{{AIKIDO_COMMAND}} %*\n",
       "utf-8"
     );
 
@@ -50,7 +50,15 @@ describe("Setup CI shell integration", () => {
           { tool: "yarn", aikidoCommand: "aikido-yarn" },
         ],
         getPackageManagerList: () => "npm, yarn",
+      },
+    });
+
+    mock.module("../config/safeChainDir.js", {
+      namedExports: {
         getShimsDir: () => mockShimsDir,
+        getBinDir: () => path.join(mockHomeDir, ".safe-chain", "bin"),
+        getPathWrapperTemplatePath: (_moduleUrl, fileName) =>
+          path.join(mockTemplateDir, "path-wrappers", "templates", fileName),
       },
     });
 
@@ -63,22 +71,6 @@ describe("Setup CI shell integration", () => {
       },
     });
 
-    // Mock path module to resolve templates correctly
-    mock.module("path", {
-      namedExports: {
-        join: path.join,
-        dirname: () => mockTemplateDir,
-        resolve: (...args) => path.resolve(mockTemplateDir, ...args.slice(1)),
-      },
-    });
-
-    // Mock fileURLToPath
-    mock.module("url", {
-      namedExports: {
-        fileURLToPath: () => path.join(mockTemplateDir, "setup-ci.js"),
-      },
-    });
-
     // Import setupCi module after mocking
     setupCi = (await import("./setup-ci.js")).setupCi;
   });
@@ -119,6 +111,10 @@ describe("Setup CI shell integration", () => {
       const npmShimContent = fs.readFileSync(npmShimPath, "utf-8");
       assert.ok(npmShimContent.includes("aikido-npm"), "npm shim should contain aikido-npm");
       assert.ok(npmShimContent.includes("#!/bin/bash"), "npm shim should have bash shebang");
+      assert.ok(
+        npmShimContent.includes("_safe_chain_shims=$(CDPATH= cd -- \"$(dirname -- \"$0\")\" 2>/dev/null && pwd -P)"),
+        "npm shim should derive the shims directory from its own location",
+      );
     });
 
     it("should create Windows .cmd shims on win32 platform", async () => {
@@ -142,6 +138,10 @@ describe("Setup CI shell integration", () => {
       assert.ok(npmShimContent.includes("aikido-npm"), "npm.cmd should contain aikido-npm");
       assert.ok(npmShimContent.includes("@echo off"), "npm.cmd should have Windows batch header");
       assert.ok(npmShimContent.includes("%*"), "npm.cmd should use Windows argument passing");
+      assert.ok(
+        npmShimContent.includes('set "SHIM_DIR=%~dp0"'),
+        "npm.cmd should derive the shims directory from its own location",
+      );
 
       // Verify Unix shims were NOT created
       const unixNpmShim = path.join(mockShimsDir, "npm");

packages/safe-chain/src/shell-integration/setup.js

@@ -1,28 +1,10 @@
 import chalk from "chalk";
 import { ui } from "../environment/userInteraction.js";
 import { detectShells } from "./shellDetection.js";
-import {
+import { knownAikidoTools, getPackageManagerList } from "./helpers.js";
-  knownAikidoTools,
+import { getScriptsDir, getStartupScriptSourcePath } from "../config/safeChainDir.js";
-  getPackageManagerList,
-  getScriptsDir,
-} from "./helpers.js";
 import fs from "fs";
 import path from "path";
-import { fileURLToPath } from "url";
-
-/** @type {string} */
-// This checks the current file's dirname in a way that's compatible with:
-//  - Modulejs (import.meta.url)
-//  - ES modules (__dirname)
-// This is needed because safe-chain's npm package is built using ES modules,
-// but building the binaries requires commonjs.
-let dirname;
-if (import.meta.url) {
-  const filename = fileURLToPath(import.meta.url);
-  dirname = path.dirname(filename);
-} else {
-  dirname = __dirname;
-}
 
 /**
  * Loops over the detected shells and calls the setup function for each.
@@ -122,8 +104,7 @@ function copyStartupFiles() {
       fs.mkdirSync(targetDir, { recursive: true });
     }
 
-    // Use absolute path for source
+    const sourcePath = getStartupScriptSourcePath(import.meta.url, file);
-    const sourcePath = path.join(dirname, "startup-scripts", file);
     fs.copyFileSync(sourcePath, targetPath);
   }
 }

packages/safe-chain/src/shell-integration/startup-scripts/init-fish.fish

@@ -1,4 +1,7 @@
-set -gx PATH $PATH $HOME/.safe-chain/bin
+set -l safe_chain_script (status filename)
+set -l safe_chain_scripts_dir (dirname $safe_chain_script)
+set -l safe_chain_base (dirname $safe_chain_scripts_dir)
+set -gx PATH $PATH $safe_chain_base/bin
 
 function npx
     wrapSafeChainCommand "npx" $argv
@@ -51,6 +54,10 @@ function uv
     wrapSafeChainCommand "uv" $argv
 end
 
+function uvx
+    wrapSafeChainCommand "uvx" $argv
+end
+
 function poetry
     wrapSafeChainCommand "poetry" $argv
 end

packages/safe-chain/src/shell-integration/startup-scripts/init-posix.sh

@@ -1,4 +1,16 @@
-export PATH="$PATH:$HOME/.safe-chain/bin"
+if [ -n "${BASH_SOURCE[0]:-}" ]; then
+    _sc_script_path="${BASH_SOURCE[0]}"
+elif [ -n "${ZSH_VERSION:-}" ]; then
+    # ${(%):-%x} uses Zsh prompt expansion to get the sourced file's path.
+    # eval is required so other shells don't try to parse the Zsh-specific syntax.
+    eval '_sc_script_path="${(%):-%x}"'
+else
+    _sc_script_path="$0"
+fi
+_sc_scripts_dir=$(CDPATH= cd -- "$(dirname -- "$_sc_script_path")" 2>/dev/null && pwd -P)
+_sc_base=$(dirname -- "$_sc_scripts_dir")
+export PATH="$PATH:${_sc_base}/bin"
+unset _sc_base _sc_script_path _sc_scripts_dir
 
 function npx() {
   wrapSafeChainCommand "npx" "$@"
@@ -47,6 +59,10 @@ function uv() {
   wrapSafeChainCommand "uv" "$@"
 }
 
+function uvx() {
+  wrapSafeChainCommand "uvx" "$@"
+}
+
 function poetry() {
   wrapSafeChainCommand "poetry" "$@"
 }

packages/safe-chain/src/shell-integration/startup-scripts/init-pwsh.ps1

@@ -2,7 +2,8 @@
 # $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 $HOME '.safe-chain') 'bin'
+$safeChainBase = Split-Path -Parent $PSScriptRoot
+$safeChainBin = Join-Path $safeChainBase 'bin'
 $env:PATH = "$env:PATH$pathSeparator$safeChainBin"
 
 function npx {
@@ -52,6 +53,10 @@ function uv {
     Invoke-WrappedCommand "uv" $args $MyInvocation.Line $MyInvocation.OffsetInLine
 }
 
+function uvx {
+    Invoke-WrappedCommand "uvx" $args $MyInvocation.Line $MyInvocation.OffsetInLine
+}
+
 function poetry {
     Invoke-WrappedCommand "poetry" $args $MyInvocation.Line $MyInvocation.OffsetInLine
 }

packages/safe-chain/src/shell-integration/supported-shells/bash.js

@@ -3,8 +3,10 @@ import {
   doesExecutableExistOnSystem,
   removeLinesMatchingPattern,
 } from "../helpers.js";
+import { getScriptsDir } from "../../config/safeChainDir.js";
 import { execSync, spawnSync } from "child_process";
 import * as os from "os";
+import path from "path";
 
 const shellName = "Bash";
 const executableName = "bash";
@@ -32,10 +34,10 @@ function teardown(tools) {
     );
   }
 
-  // Removes the line that sources the safe-chain bash initialization script (~/.safe-chain/scripts/init-posix.sh)
+  // Remove sourcing line to disable safe-chain shell integration
   removeLinesMatchingPattern(
     startupFile,
-    /^source\s+~\/\.safe-chain\/scripts\/init-posix\.sh/,
+    /^source\s+.*init-posix\.sh.*#\s*Safe-chain/,
     eol
   );
 
@@ -44,10 +46,11 @@ function teardown(tools) {
 
 function setup() {
   const startupFile = getStartupFile();
+  const scriptsDir = getShellScriptsDir();
 
   addLineToFile(
     startupFile,
-    `source ~/.safe-chain/scripts/init-posix.sh # Safe-chain bash initialization script`,
+    `source ${path.posix.join(scriptsDir, "init-posix.sh")} # Safe-chain bash initialization script`,
     eol
   );
 
@@ -94,6 +97,51 @@ function windowsFixPath(path) {
   }
 }
 
+function getShellScriptsDir() {
+  return toBashPath(getScriptsDir());
+}
+
+/**
+ * @param {string} path
+ *
+ * @returns {string}
+ */
+function toBashPath(path) {
+  try {
+    if (os.platform() !== "win32") {
+      return path.replace(/\\/g, "/");
+    }
+
+    const directWindowsPath = windowsPathToBashPath(path);
+    if (directWindowsPath) {
+      return directWindowsPath;
+    }
+
+    if (hasCygpath()) {
+      return convertCygwinPathToUnix(path);
+    }
+
+    return path.replace(/\\/g, "/");
+  } catch {
+    return path.replace(/\\/g, "/");
+  }
+}
+
+/**
+ * @param {string} path
+ *
+ * @returns {string | undefined}
+ */
+function windowsPathToBashPath(path) {
+  const match = /^([A-Za-z]):[\\/](.*)$/.exec(path);
+  if (!match) {
+    return undefined;
+  }
+
+  const [, driveLetter, rest] = match;
+  return `/${driveLetter.toLowerCase()}/${rest.replace(/\\/g, "/")}`;
+}
+
 function hasCygpath() {
   try {
     var result = spawnSync("where", ["cygpath"], { shell: executableName });
@@ -123,18 +171,40 @@ function cygpathw(path) {
   }
 }
 
+/**
+ * @param {string} path
+ *
+ * @returns {string}
+ */
+function convertCygwinPathToUnix(path) {
+  try {
+    var result = spawnSync("cygpath", ["-u", path], {
+      encoding: "utf8",
+      shell: executableName,
+    });
+    if (result.status === 0) {
+      return result.stdout.trim();
+    }
+    return path.replace(/\\/g, "/");
+  } catch {
+    return path.replace(/\\/g, "/");
+  }
+}
+
 function getManualTeardownInstructions() {
+  const scriptsDir = getShellScriptsDir();
   return [
     `Remove the following line from your ~/.bashrc file:`,
-    `  source ~/.safe-chain/scripts/init-posix.sh`,
+    `  source ${path.posix.join(scriptsDir, "init-posix.sh")}`,
     `Then restart your terminal or run: source ~/.bashrc`,
   ];
 }
 
 function getManualSetupInstructions() {
+  const scriptsDir = getShellScriptsDir();
   return [
     `Add the following line to your ~/.bashrc file:`,
-    `  source ~/.safe-chain/scripts/init-posix.sh`,
+    `  source ${path.posix.join(scriptsDir, "init-posix.sh")}`,
     `Then restart your terminal or run: source ~/.bashrc`,
   ];
 }

packages/safe-chain/src/shell-integration/supported-shells/bash.spec.js

@@ -9,6 +9,7 @@ describe("Bash shell integration", () => {
   let mockStartupFile;
   let bash;
   let windowsCygwinPath = "";
+  let mockScriptsDir = "/test-home/.safe-chain/scripts";
   let platform = "linux";
 
   beforeEach(async () => {
@@ -35,6 +36,12 @@ describe("Bash shell integration", () => {
       },
     });
 
+    mock.module("../../config/safeChainDir.js", {
+      namedExports: {
+        getScriptsDir: () => mockScriptsDir,
+      },
+    });
+
     // Mock child_process execSync
     mock.module("child_process", {
       namedExports: {
@@ -61,6 +68,17 @@ describe("Bash shell integration", () => {
               stdout: windowsCygwinPath + "\n",
             };
           }
+
+          if (
+            command === "cygpath" &&
+            args[0] === "-u" &&
+            args[1] === mockScriptsDir
+          ) {
+            return {
+              status: 0,
+              stdout: "/c/test-home/.safe-chain/scripts\n",
+            };
+          }
         },
       },
     });
@@ -87,6 +105,7 @@ describe("Bash shell integration", () => {
 
     // Reset mocks
     mock.reset();
+    mockScriptsDir = "/test-home/.safe-chain/scripts";
     platform = "linux";
   });
 
@@ -109,7 +128,7 @@ describe("Bash shell integration", () => {
       const content = fs.readFileSync(mockStartupFile, "utf-8");
       assert.ok(
         content.includes(
-          "source ~/.safe-chain/scripts/init-posix.sh # Safe-chain bash initialization script"
+          "source /test-home/.safe-chain/scripts/init-posix.sh # Safe-chain bash initialization script"
         )
       );
     });
@@ -129,7 +148,24 @@ describe("Bash shell integration", () => {
       const content = fs.readFileSync(windowsCygwinPath, "utf-8");
       assert.ok(
         content.includes(
-          "source ~/.safe-chain/scripts/init-posix.sh # Safe-chain bash initialization script"
+          "source /c/test-home/.safe-chain/scripts/init-posix.sh # Safe-chain bash initialization script"
+        )
+      );
+    });
+
+    it("should write a bash-compatible scripts path on Windows", () => {
+      platform = "win32";
+      windowsCygwinPath = mockStartupFile;
+      mockScriptsDir = "C:\\test-home\\.safe-chain\\scripts";
+      mockStartupFile = "DUMMY";
+
+      const result = bash.setup();
+      assert.strictEqual(result, true);
+
+      const content = fs.readFileSync(windowsCygwinPath, "utf-8");
+      assert.ok(
+        content.includes(
+          "source /c/test-home/.safe-chain/scripts/init-posix.sh # Safe-chain bash initialization script"
         )
       );
     });
@@ -209,13 +245,13 @@ describe("Bash shell integration", () => {
       // Setup
       bash.setup(tools);
       let content = fs.readFileSync(mockStartupFile, "utf-8");
-      assert.ok(content.includes("source ~/.safe-chain/scripts/init-posix.sh"));
+      assert.ok(content.includes("source /test-home/.safe-chain/scripts/init-posix.sh"));
 
       // Teardown
       bash.teardown(tools);
       content = fs.readFileSync(mockStartupFile, "utf-8");
       assert.ok(
-        !content.includes("source ~/.safe-chain/scripts/init-posix.sh")
+        !content.includes("source /test-home/.safe-chain/scripts/init-posix.sh")
       );
     });
 
@@ -236,7 +272,7 @@ describe("Bash shell integration", () => {
       const initialContent = [
         "#!/bin/bash",
         "alias npm='old-npm'",
-        "source ~/.safe-chain/scripts/init-posix.sh",
+        "source /test-home/.safe-chain/scripts/init-posix.sh # Safe-chain bash initialization script",
         "alias ls='ls --color=auto'",
       ].join("\n");
 
@@ -247,7 +283,7 @@ describe("Bash shell integration", () => {
       const content = fs.readFileSync(mockStartupFile, "utf-8");
       assert.ok(!content.includes("alias npm="));
       assert.ok(
-        !content.includes("source ~/.safe-chain/scripts/init-posix.sh")
+        !content.includes("source /test-home/.safe-chain/scripts/init-posix.sh # Safe-chain bash initialization script")
       );
       assert.ok(content.includes("alias ls="));
     });

packages/safe-chain/src/shell-integration/supported-shells/fish.js

@@ -3,7 +3,9 @@ import {
   doesExecutableExistOnSystem,
   removeLinesMatchingPattern,
 } from "../helpers.js";
+import { getScriptsDir } from "../../config/safeChainDir.js";
 import { execSync } from "child_process";
+import path from "path";
 
 const shellName = "Fish";
 const executableName = "fish";
@@ -31,10 +33,10 @@ function teardown(tools) {
     );
   }
 
-  // Removes the line that sources the safe-chain fish initialization script (~/.safe-chain/scripts/init-fish.fish)
+  // Remove sourcing line to prevent safe-chain initialization in future shell sessions
   removeLinesMatchingPattern(
     startupFile,
-    /^source\s+~\/\.safe-chain\/scripts\/init-fish\.fish/,
+    /^source\s+.*init-fish\.fish.*#\s*Safe-chain/,
     eol
   );
 
@@ -46,7 +48,7 @@ function setup() {
 
   addLineToFile(
     startupFile,
-    `source ~/.safe-chain/scripts/init-fish.fish # Safe-chain Fish initialization script`,
+    `source ${path.join(getScriptsDir(), "init-fish.fish")} # Safe-chain Fish initialization script`,
     eol
   );
 
@@ -69,7 +71,7 @@ function getStartupFile() {
 function getManualTeardownInstructions() {
   return [
     `Remove the following line from your ~/.config/fish/config.fish file:`,
-    `  source ~/.safe-chain/scripts/init-fish.fish`,
+    `  source ${path.join(getScriptsDir(), "init-fish.fish")}`,
     `Then restart your terminal or run: source ~/.config/fish/config.fish`,
   ];
 }
@@ -77,7 +79,7 @@ function getManualTeardownInstructions() {
 function getManualSetupInstructions() {
   return [
     `Add the following line to your ~/.config/fish/config.fish file:`,
-    `  source ~/.safe-chain/scripts/init-fish.fish`,
+    `  source ${path.join(getScriptsDir(), "init-fish.fish")}`,
     `Then restart your terminal or run: source ~/.config/fish/config.fish`,
   ];
 }

packages/safe-chain/src/shell-integration/supported-shells/fish.spec.js

@@ -33,6 +33,12 @@ describe("Fish shell integration", () => {
       },
     });
 
+    mock.module("../../config/safeChainDir.js", {
+      namedExports: {
+        getScriptsDir: () => "/test-home/.safe-chain/scripts",
+      },
+    });
+
     // Mock child_process execSync
     mock.module("child_process", {
       namedExports: {
@@ -72,7 +78,7 @@ describe("Fish shell integration", () => {
 
       const content = fs.readFileSync(mockStartupFile, "utf-8");
       assert.ok(
-        content.includes('source ~/.safe-chain/scripts/init-fish.fish # Safe-chain Fish initialization script')
+        content.includes('source /test-home/.safe-chain/scripts/init-fish.fish # Safe-chain Fish initialization script')
       );
     });
 
@@ -81,7 +87,7 @@ describe("Fish shell integration", () => {
       fish.setup();
 
       const content = fs.readFileSync(mockStartupFile, "utf-8");
-      const sourceMatches = (content.match(/source ~\/\.safe-chain\/scripts\/init-fish\.fish/g) || []).length;
+      const sourceMatches = (content.match(/source \/test-home\/\.safe-chain\/scripts\/init-fish\.fish/g) || []).length;
       assert.strictEqual(sourceMatches, 2, "Should allow multiple source lines (helper doesn't dedupe)");
     });
   });
@@ -93,7 +99,7 @@ describe("Fish shell integration", () => {
         "alias npm 'aikido-npm'",
         "alias npx 'aikido-npx'",
         "alias yarn 'aikido-yarn'",
-        "source ~/.safe-chain/scripts/init-fish.fish # Safe-chain Fish initialization script",
+        "source /test-home/.safe-chain/scripts/init-fish.fish # Safe-chain Fish initialization script",
         "alias ls 'ls --color=auto'",
         "alias grep 'grep --color=auto'",
       ].join("\n");
@@ -107,7 +113,7 @@ describe("Fish shell integration", () => {
       assert.ok(!content.includes("alias npm "));
       assert.ok(!content.includes("alias npx "));
       assert.ok(!content.includes("alias yarn "));
-      assert.ok(!content.includes("source ~/.safe-chain/scripts/init-fish.fish"));
+      assert.ok(!content.includes("source /test-home/.safe-chain/scripts/init-fish.fish"));
       assert.ok(content.includes("alias ls "));
       assert.ok(content.includes("alias grep "));
     });
@@ -162,12 +168,12 @@ describe("Fish shell integration", () => {
       // Setup
       fish.setup();
       let content = fs.readFileSync(mockStartupFile, "utf-8");
-      assert.ok(content.includes('source ~/.safe-chain/scripts/init-fish.fish'));
+      assert.ok(content.includes('source /test-home/.safe-chain/scripts/init-fish.fish'));
 
       // Teardown
       fish.teardown(tools);
       content = fs.readFileSync(mockStartupFile, "utf-8");
-      assert.ok(!content.includes("source ~/.safe-chain/scripts/init-fish.fish"));
+      assert.ok(!content.includes("source /test-home/.safe-chain/scripts/init-fish.fish"));
     });
 
     it("should handle multiple setup calls", () => {
@@ -176,7 +182,7 @@ describe("Fish shell integration", () => {
       fish.setup();
 
       const content = fs.readFileSync(mockStartupFile, "utf-8");
-      const sourceMatches = (content.match(/source ~\/\.safe-chain\/scripts\/init-fish\.fish/g) || []).length;
+      const sourceMatches = (content.match(/source \/test-home\/\.safe-chain\/scripts\/init-fish\.fish/g) || []).length;
       assert.strictEqual(sourceMatches, 1, "Should have exactly one source line after setup-teardown-setup cycle");
     });
   });

packages/safe-chain/src/shell-integration/supported-shells/powershell.js

@@ -4,7 +4,9 @@ import {
   removeLinesMatchingPattern,
   validatePowerShellExecutionPolicy,
 } from "../helpers.js";
+import { getScriptsDir } from "../../config/safeChainDir.js";
 import { execSync } from "child_process";
+import path from "path";
 
 const shellName = "PowerShell Core";
 const executableName = "pwsh";
@@ -30,10 +32,10 @@ function teardown(tools) {
     );
   }
 
-  // Remove the line that sources the safe-chain PowerShell initialization script
+  // Remove sourcing line to prevent shell from loading safe-chain after uninstallation
   removeLinesMatchingPattern(
     startupFile,
-    /^\.\s+["']?\$HOME[/\\].safe-chain[/\\]scripts[/\\]init-pwsh\.ps1["']?/,
+    /^\.\s+["']?.*init-pwsh\.ps1["']?.*#\s*Safe-chain/,
   );
 
   return true;
@@ -52,7 +54,7 @@ async function setup() {
 
   addLineToFile(
     startupFile,
-    `. "$HOME\\.safe-chain\\scripts\\init-pwsh.ps1" # Safe-chain PowerShell initialization script`,
+    `. "${path.join(getScriptsDir(), "init-pwsh.ps1")}" # Safe-chain PowerShell initialization script`,
   );
 
   return true;
@@ -74,7 +76,7 @@ function getStartupFile() {
 function getManualTeardownInstructions() {
   return [
     `Remove the following line from your PowerShell profile (run "echo $PROFILE" to find its location):`,
-    `  . "$HOME\\.safe-chain\\scripts\\init-pwsh.ps1"`,
+    `  . "${path.join(getScriptsDir(), "init-pwsh.ps1")}"`,
     `Then restart your terminal or run: . $PROFILE`,
   ];
 }
@@ -82,7 +84,7 @@ function getManualTeardownInstructions() {
 function getManualSetupInstructions() {
   return [
     `Add the following line to your PowerShell profile (run "echo $PROFILE" to find its location):`,
-    `  . "$HOME\\.safe-chain\\scripts\\init-pwsh.ps1"`,
+    `  . "${path.join(getScriptsDir(), "init-pwsh.ps1")}"`,
     `Then restart your terminal or run: . $PROFILE`,
   ];
 }

packages/safe-chain/src/shell-integration/supported-shells/powershell.spec.js

@@ -43,6 +43,12 @@ describe("PowerShell Core shell integration", () => {
       },
     });
 
+    mock.module("../../config/safeChainDir.js", {
+      namedExports: {
+        getScriptsDir: () => "/test-home/.safe-chain/scripts",
+      },
+    });
+
     // Mock child_process execSync
     mock.module("child_process", {
       namedExports: {
@@ -83,7 +89,7 @@ describe("PowerShell Core shell integration", () => {
       const content = fs.readFileSync(mockStartupFile, "utf-8");
       assert.ok(
         content.includes(
-          '. "$HOME\\.safe-chain\\scripts\\init-pwsh.ps1" # Safe-chain PowerShell initialization script',
+          '. "/test-home/.safe-chain/scripts/init-pwsh.ps1" # Safe-chain PowerShell initialization script',
         ),
       );
     });
@@ -93,7 +99,7 @@ describe("PowerShell Core shell integration", () => {
     it("should remove init-pwsh.ps1 source line", () => {
       const initialContent = [
         "# PowerShell profile",
-        '. "$HOME\\.safe-chain\\scripts\\init-pwsh.ps1" # Safe-chain PowerShell initialization script',
+        '. "/test-home/.safe-chain/scripts/init-pwsh.ps1" # Safe-chain PowerShell initialization script',
         "Set-Alias ls Get-ChildItem",
         "Set-Alias grep Select-String",
       ].join("\n");
@@ -105,7 +111,7 @@ describe("PowerShell Core shell integration", () => {
 
       const content = fs.readFileSync(mockStartupFile, "utf-8");
       assert.ok(
-        !content.includes('. "$HOME\\.safe-chain\\scripts\\init-pwsh.ps1"'),
+        !content.includes('. "/test-home/.safe-chain/scripts/init-pwsh.ps1"'),
       );
       assert.ok(content.includes("Set-Alias ls "));
       assert.ok(content.includes("Set-Alias grep "));
@@ -180,14 +186,14 @@ describe("PowerShell Core shell integration", () => {
       await powershell.setup();
       let content = fs.readFileSync(mockStartupFile, "utf-8");
       assert.ok(
-        content.includes('. "$HOME\\.safe-chain\\scripts\\init-pwsh.ps1"'),
+        content.includes('. "/test-home/.safe-chain/scripts/init-pwsh.ps1"'),
       );
 
       // Teardown
       powershell.teardown(knownAikidoTools);
       content = fs.readFileSync(mockStartupFile, "utf-8");
       assert.ok(
-        !content.includes('. "$HOME\\.safe-chain\\scripts\\init-pwsh.ps1"'),
+        !content.includes('. "/test-home/.safe-chain/scripts/init-pwsh.ps1"'),
       );
     });
 
@@ -198,7 +204,7 @@ describe("PowerShell Core shell integration", () => {
 
       const content = fs.readFileSync(mockStartupFile, "utf-8");
       const sourceMatches = (
-        content.match(/\. "\$HOME\\.safe-chain\\scripts\\init-pwsh\.ps1"/g) ||
+        content.match(/\. "\/test-home\/\.safe-chain\/scripts\/init-pwsh\.ps1"/g) ||
         []
       ).length;
       assert.strictEqual(sourceMatches, 1, "Should not duplicate source lines");

packages/safe-chain/src/shell-integration/supported-shells/windowsPowershell.js

@@ -4,7 +4,9 @@ import {
   removeLinesMatchingPattern,
   validatePowerShellExecutionPolicy,
 } from "../helpers.js";
+import { getScriptsDir } from "../../config/safeChainDir.js";
 import { execSync } from "child_process";
+import path from "path";
 
 const shellName = "Windows PowerShell";
 const executableName = "powershell";
@@ -30,10 +32,10 @@ function teardown(tools) {
     );
   }
 
-  // Remove the line that sources the safe-chain PowerShell initialization script
+  // Remove sourcing line to clean up safe-chain integration from the shell profile
   removeLinesMatchingPattern(
     startupFile,
-    /^\.\s+["']?\$HOME[/\\].safe-chain[/\\]scripts[/\\]init-pwsh\.ps1["']?/,
+    /^\.\s+["']?.*init-pwsh\.ps1["']?.*#\s*Safe-chain/,
   );
 
   return true;
@@ -52,7 +54,7 @@ async function setup() {
 
   addLineToFile(
     startupFile,
-    `. "$HOME\\.safe-chain\\scripts\\init-pwsh.ps1" # Safe-chain PowerShell initialization script`,
+    `. "${path.join(getScriptsDir(), "init-pwsh.ps1")}" # Safe-chain PowerShell initialization script`,
   );
 
   return true;
@@ -74,7 +76,7 @@ function getStartupFile() {
 function getManualTeardownInstructions() {
   return [
     `Remove the following line from your PowerShell profile (run "echo $PROFILE" to find its location):`,
-    `  . "$HOME\\.safe-chain\\scripts\\init-pwsh.ps1"`,
+    `  . "${path.join(getScriptsDir(), "init-pwsh.ps1")}"`,
     `Then restart your terminal or run: . $PROFILE`,
   ];
 }
@@ -82,7 +84,7 @@ function getManualTeardownInstructions() {
 function getManualSetupInstructions() {
   return [
     `Add the following line to your PowerShell profile (run "echo $PROFILE" to find its location):`,
-    `  . "$HOME\\.safe-chain\\scripts\\init-pwsh.ps1"`,
+    `  . "${path.join(getScriptsDir(), "init-pwsh.ps1")}"`,
     `Then restart your terminal or run: . $PROFILE`,
   ];
 }

packages/safe-chain/src/shell-integration/supported-shells/windowsPowershell.spec.js

@@ -43,6 +43,12 @@ describe("Windows PowerShell shell integration", () => {
       },
     });
 
+    mock.module("../../config/safeChainDir.js", {
+      namedExports: {
+        getScriptsDir: () => "/test-home/.safe-chain/scripts",
+      },
+    });
+
     // Mock child_process execSync
     mock.module("child_process", {
       namedExports: {
@@ -83,7 +89,7 @@ describe("Windows PowerShell shell integration", () => {
       const content = fs.readFileSync(mockStartupFile, "utf-8");
       assert.ok(
         content.includes(
-          '. "$HOME\\.safe-chain\\scripts\\init-pwsh.ps1" # Safe-chain PowerShell initialization script',
+          '. "/test-home/.safe-chain/scripts/init-pwsh.ps1" # Safe-chain PowerShell initialization script',
         ),
       );
     });
@@ -93,7 +99,7 @@ describe("Windows PowerShell shell integration", () => {
     it("should remove init-pwsh.ps1 source line", () => {
       const initialContent = [
         "# Windows PowerShell profile",
-        '. "$HOME\\.safe-chain\\scripts\\init-pwsh.ps1" # Safe-chain PowerShell initialization script',
+        '. "/test-home/.safe-chain/scripts/init-pwsh.ps1" # Safe-chain PowerShell initialization script',
         "Set-Alias ls Get-ChildItem",
         "Set-Alias grep Select-String",
       ].join("\n");
@@ -105,7 +111,7 @@ describe("Windows PowerShell shell integration", () => {
 
       const content = fs.readFileSync(mockStartupFile, "utf-8");
       assert.ok(
-        !content.includes('. "$HOME\\.safe-chain\\scripts\\init-pwsh.ps1"'),
+        !content.includes('. "/test-home/.safe-chain/scripts/init-pwsh.ps1"'),
       );
       assert.ok(content.includes("Set-Alias ls "));
       assert.ok(content.includes("Set-Alias grep "));
@@ -180,14 +186,14 @@ describe("Windows PowerShell shell integration", () => {
       await windowsPowershell.setup();
       let content = fs.readFileSync(mockStartupFile, "utf-8");
       assert.ok(
-        content.includes('. "$HOME\\.safe-chain\\scripts\\init-pwsh.ps1"'),
+        content.includes('. "/test-home/.safe-chain/scripts/init-pwsh.ps1"'),
       );
 
       // Teardown
       windowsPowershell.teardown(knownAikidoTools);
       content = fs.readFileSync(mockStartupFile, "utf-8");
       assert.ok(
-        !content.includes('. "$HOME\\.safe-chain\\scripts\\init-pwsh.ps1"'),
+        !content.includes('. "/test-home/.safe-chain/scripts/init-pwsh.ps1"'),
       );
     });
 
@@ -198,7 +204,7 @@ describe("Windows PowerShell shell integration", () => {
 
       const content = fs.readFileSync(mockStartupFile, "utf-8");
       const sourceMatches = (
-        content.match(/\. "\$HOME\\.safe-chain\\scripts\\init-pwsh\.ps1"/g) ||
+        content.match(/\. "\/test-home\/\.safe-chain\/scripts\/init-pwsh\.ps1"/g) ||
         []
       ).length;
       assert.strictEqual(sourceMatches, 1, "Should not duplicate source lines");

packages/safe-chain/src/shell-integration/supported-shells/zsh.js

@@ -3,7 +3,9 @@ import {
   doesExecutableExistOnSystem,
   removeLinesMatchingPattern,
 } from "../helpers.js";
+import { getScriptsDir } from "../../config/safeChainDir.js";
 import { execSync } from "child_process";
+import path from "path";
 
 const shellName = "Zsh";
 const executableName = "zsh";
@@ -31,10 +33,10 @@ function teardown(tools) {
     );
   }
 
-  // Removes the line that sources the safe-chain zsh initialization script (~/.safe-chain/scripts/init-posix.sh)
+  // Remove sourcing line to complete shell integration cleanup
   removeLinesMatchingPattern(
     startupFile,
-    /^source\s+~\/\.safe-chain\/scripts\/init-posix\.sh/,
+    /^source\s+.*init-posix\.sh.*#\s*Safe-chain/,
     eol
   );
 
@@ -46,7 +48,7 @@ function setup() {
 
   addLineToFile(
     startupFile,
-    `source ~/.safe-chain/scripts/init-posix.sh # Safe-chain Zsh initialization script`,
+    `source ${path.join(getScriptsDir(), "init-posix.sh")} # Safe-chain Zsh initialization script`,
     eol
   );
 
@@ -69,7 +71,7 @@ function getStartupFile() {
 function getManualTeardownInstructions() {
   return [
     `Remove the following line from your ~/.zshrc file:`,
-    `  source ~/.safe-chain/scripts/init-posix.sh`,
+    `  source ${path.join(getScriptsDir(), "init-posix.sh")}`,
     `Then restart your terminal or run: source ~/.zshrc`,
   ];
 }
@@ -77,7 +79,7 @@ function getManualTeardownInstructions() {
 function getManualSetupInstructions() {
   return [
     `Add the following line to your ~/.zshrc file:`,
-    `  source ~/.safe-chain/scripts/init-posix.sh`,
+    `  source ${path.join(getScriptsDir(), "init-posix.sh")}`,
     `Then restart your terminal or run: source ~/.zshrc`,
   ];
 }

packages/safe-chain/src/shell-integration/supported-shells/zsh.spec.js

@@ -33,6 +33,12 @@ describe("Zsh shell integration", () => {
       },
     });
 
+    mock.module("../../config/safeChainDir.js", {
+      namedExports: {
+        getScriptsDir: () => "/test-home/.safe-chain/scripts",
+      },
+    });
+
     // Mock child_process execSync
     mock.module("child_process", {
       namedExports: {
@@ -73,7 +79,7 @@ describe("Zsh shell integration", () => {
       const content = fs.readFileSync(mockStartupFile, "utf-8");
       assert.ok(
         content.includes(
-          "source ~/.safe-chain/scripts/init-posix.sh # Safe-chain Zsh initialization script"
+          "source /test-home/.safe-chain/scripts/init-posix.sh # Safe-chain Zsh initialization script"
         )
       );
     });
@@ -83,7 +89,7 @@ describe("Zsh shell integration", () => {
       assert.strictEqual(result, true);
 
       const content = fs.readFileSync(mockStartupFile, "utf-8");
-      assert.ok(content.includes("source ~/.safe-chain/scripts/init-posix.sh"));
+      assert.ok(content.includes("source /test-home/.safe-chain/scripts/init-posix.sh"));
     });
   });
 
@@ -114,7 +120,7 @@ describe("Zsh shell integration", () => {
     it("should remove zsh initialization script source line", () => {
       const initialContent = [
         "#!/bin/zsh",
-        "source ~/.safe-chain/scripts/init-posix.sh",
+        "source /test-home/.safe-chain/scripts/init-posix.sh # Safe-chain Zsh initialization script",
         "alias ls='ls --color=auto'",
       ].join("\n");
 
@@ -125,7 +131,7 @@ describe("Zsh shell integration", () => {
 
       const content = fs.readFileSync(mockStartupFile, "utf-8");
       assert.ok(
-        !content.includes("source ~/.safe-chain/scripts/init-posix.sh")
+        !content.includes("source /test-home/.safe-chain/scripts/init-posix.sh # Safe-chain Zsh initialization script")
       );
       assert.ok(content.includes("alias ls="));
     });
@@ -180,13 +186,13 @@ describe("Zsh shell integration", () => {
       // Setup
       zsh.setup();
       let content = fs.readFileSync(mockStartupFile, "utf-8");
-      assert.ok(content.includes("source ~/.safe-chain/scripts/init-posix.sh"));
+      assert.ok(content.includes("source /test-home/.safe-chain/scripts/init-posix.sh"));
 
       // Teardown
       zsh.teardown(tools);
       content = fs.readFileSync(mockStartupFile, "utf-8");
       assert.ok(
-        !content.includes("source ~/.safe-chain/scripts/init-posix.sh")
+        !content.includes("source /test-home/.safe-chain/scripts/init-posix.sh")
       );
     });
 
@@ -207,7 +213,7 @@ describe("Zsh shell integration", () => {
       const initialContent = [
         "#!/bin/zsh",
         "alias npm='old-npm'",
-        "source ~/.safe-chain/scripts/init-posix.sh",
+        "source /test-home/.safe-chain/scripts/init-posix.sh # Safe-chain Zsh initialization script",
         "alias ls='ls --color=auto'",
       ].join("\n");
 
@@ -218,7 +224,7 @@ describe("Zsh shell integration", () => {
       const content = fs.readFileSync(mockStartupFile, "utf-8");
       assert.ok(!content.includes("alias npm="));
       assert.ok(
-        !content.includes("source ~/.safe-chain/scripts/init-posix.sh")
+        !content.includes("source /test-home/.safe-chain/scripts/init-posix.sh # Safe-chain Zsh initialization script")
       );
       assert.ok(content.includes("alias ls="));
     });

packages/safe-chain/src/shell-integration/teardown.js

@@ -1,7 +1,8 @@
 import chalk from "chalk";
 import { ui } from "../environment/userInteraction.js";
 import { detectShells } from "./shellDetection.js";
-import { knownAikidoTools, getPackageManagerList, getShimsDir, getScriptsDir } from "./helpers.js";
+import { knownAikidoTools, getPackageManagerList } from "./helpers.js";
+import { getShimsDir, getScriptsDir } from "../config/safeChainDir.js";
 import fs from "fs";
 
 /**
@@ -109,4 +110,5 @@ export async function teardownDirectories() {
       );
     }
   }
+
 }

packages/safe-chain/src/ultimate/ultimateTroubleshooting.js

@@ -1,111 +0,0 @@
-import { platform } from 'os';
-import { ui } from "../environment/userInteraction.js";
-import { readFileSync, existsSync } from "node:fs";
-import {randomUUID} from "node:crypto";
-import {createWriteStream} from "fs";
-import archiver from 'archiver';
-import path from "node:path";
-
-export async function printUltimateLogs() {
-  const { proxyLogPath, ultimateLogPath, proxyErrLogPath, ultimateErrLogPath } = getPathsPerPlatform();
-
-  await printLogs(
-    "SafeChain Proxy",
-    proxyLogPath,
-    proxyErrLogPath
-  );
-
-  await printLogs(
-    "SafeChain Ultimate",
-    ultimateLogPath,
-    ultimateErrLogPath
-  );
-}
-
-export async function troubleshootingExport() {
-  const { logDir } = getPathsPerPlatform();
-  return new Promise((resolve, reject) => {
-    if (!existsSync(logDir)) {
-      ui.writeError(`Log directory not found: ${logDir}`);
-      reject(new Error(`Log directory not found: ${logDir}`));
-      return;
-    }
-
-    const date = new Date().toISOString().split('T')[0];
-    const uuid = randomUUID();
-    const zipFileName = `safechain-ultimate-${date}-${uuid}.zip`;
-    const output = createWriteStream(zipFileName);
-    const archive = archiver('zip', { zlib: { level: 9 } });
-
-    output.on('close', () => {
-      ui.writeInformation(`Logs collected and zipped as: ${path.resolve(zipFileName)}`);
-      resolve(zipFileName);
-    });
-
-    archive.on('error', (/** @type {Error} */ err) => {
-      ui.writeError(`Failed to zip logs: ${err.message}`);
-      reject(err);
-    });
-
-    archive.pipe(output);
-    archive.directory(logDir, false);
-    archive.finalize();
-  });
-}
-
-
-function getPathsPerPlatform() {
-  const os = platform();
-  if (os === 'win32') {
-    const logDir = `C:\\ProgramData\\AikidoSecurity\\SafeChainUltimate\\logs`;
-    return {
-      logDir,
-      proxyLogPath: `${logDir}\\SafeChainProxy.log`,
-      ultimateLogPath: `${logDir}\\SafeChainUltimate.log`,
-      proxyErrLogPath: `${logDir}\\SafeChainProxy.err`,
-      ultimateErrLogPath: `${logDir}\\SafeChainUltimate.err`,
-    };
-  } else if (os === 'darwin') {
-    const logDir = `/Library/Logs/AikidoSecurity/SafeChainUltimate`;
-    return {
-      logDir,
-      proxyLogPath: `${logDir}/safechain-proxy.log`,
-      ultimateLogPath: `${logDir}/safechain-ultimate.log`,
-      proxyErrLogPath: `${logDir}/safechain-proxy.error.log`,
-      ultimateErrLogPath: `${logDir}/safechain-ultimate.error.log`,
-    };
-  } else {
-    throw new Error('Unsupported platform for log printing.');
-  }
-}
-
-/**
- * @param {string} appName
- * @param {string} logPath
- * @param {string} errLogPath
- */
-async function printLogs(appName, logPath, errLogPath) {
-  ui.writeInformation(`=== ${appName} Logs ===`);
-  try {
-    if (existsSync(logPath)) {
-      const logs = readFileSync(logPath, "utf-8");
-      ui.writeInformation(logs);
-    } else {
-      ui.writeWarning(`${appName} log file not found: ${logPath}`);
-    }
-  } catch (error) {
-    ui.writeError(`Failed to read ${appName} logs: ${error}`);
-  }
-
-  ui.writeInformation(`=== ${appName} Error Logs ===`);
-  try {
-    if (existsSync(errLogPath)) {
-      const errLogs = readFileSync(errLogPath, "utf-8");
-      ui.writeInformation(errLogs);
-    } else {
-      ui.writeInformation(`No error log file found for ${appName}.`);
-    }
-  } catch (error) {
-    ui.writeError(`Failed to read ${appName} error logs: ${error}`);
-  }
-}

test/e2e/DockerTestContainer.js

@@ -84,10 +84,14 @@ export class DockerTestContainer {
     }
   }
 
-  async openShell(shell) {
+  async openShell(shell, { user } = {}) {
+    const execArgs = user
+      ? ["exec", "-it", "-u", user, this.containerName, shell]
+      : ["exec", "-it", this.containerName, shell];
+
     let ptyProcess = pty.spawn(
       "docker",
-      ["exec", "-it", this.containerName, shell],
+      execArgs,
       {
         name: "xterm-color",
         cols: 80,

test/e2e/pip-minimum-age.e2e.spec.js

@@ -0,0 +1,168 @@
+import { describe, it, before, beforeEach, afterEach } from "node:test";
+import assert from "node:assert";
+import { DockerTestContainer } from "./DockerTestContainer.js";
+
+describe("E2E: pip minimum package age", () => {
+  let container;
+
+  before(async () => {
+    DockerTestContainer.buildImage();
+  });
+
+  beforeEach(async () => {
+    container = new DockerTestContainer();
+    await container.start();
+
+    const installationShell = await container.openShell("zsh");
+    await installationShell.runCommand("safe-chain setup");
+    await installationShell.runCommand("pip3 cache purge");
+  });
+
+  afterEach(async () => {
+    if (container) {
+      await container.stop();
+      container = null;
+    }
+  });
+
+  it("falls back to an older PyPI version for flexible constraints", async () => {
+    const shell = await container.openShell("zsh");
+    const latestVersion = await getLatestPackageVersion(shell, "openai");
+    const tooYoungTimestamps = getTooYoungReleaseTimestamps();
+
+    await startFeedServer(container, [
+      {
+        source: "pypi",
+        package_name: "openai",
+        version: latestVersion,
+        ...tooYoungTimestamps,
+      },
+    ]);
+
+    const installResult = await shell.runCommand(
+      'SAFE_CHAIN_MALWARE_LIST_BASE_URL=http://127.0.0.1:8123 pip3 install --break-system-packages "openai>=2.8.0,<3" --safe-chain-logging=verbose'
+    );
+
+    assert.ok(
+      installResult.output.includes(`openai@${latestVersion} is newer than 48 hours and was removed`),
+      `Expected Safe Chain to suppress the latest openai version. Output was:\n${installResult.output}`
+    );
+    assert.ok(
+      !installResult.output.includes("blocked by safe-chain direct download minimum package age"),
+      `Expected fallback during resolution, not a direct-download block. Output was:\n${installResult.output}`
+    );
+    assert.ok(
+      installResult.output.includes("Successfully installed"),
+      `Expected pip install to succeed after fallback. Output was:\n${installResult.output}`
+    );
+
+    const installedVersion = await getInstalledVersion(shell, "openai");
+    assert.notEqual(
+      installedVersion,
+      latestVersion,
+      `Expected fallback to an older openai version, but installed ${latestVersion}.`
+    );
+  });
+
+  it("fails cleanly for exact pinned too-young PyPI versions", async () => {
+    const shell = await container.openShell("zsh");
+    const latestVersion = await getLatestPackageVersion(shell, "openai");
+    const tooYoungTimestamps = getTooYoungReleaseTimestamps();
+
+    await startFeedServer(container, [
+      {
+        source: "pypi",
+        package_name: "openai",
+        version: latestVersion,
+        ...tooYoungTimestamps,
+      },
+    ]);
+
+    const installResult = await shell.runCommand(
+      `SAFE_CHAIN_MALWARE_LIST_BASE_URL=http://127.0.0.1:8123 pip3 install --break-system-packages openai==${latestVersion} --safe-chain-logging=verbose`
+    );
+
+    assert.ok(
+      installResult.output.includes(`openai@${latestVersion} is newer than 48 hours and was removed`),
+      `Expected Safe Chain to suppress the pinned openai version. Output was:\n${installResult.output}`
+    );
+    assert.ok(
+      installResult.output.includes(`No matching distribution found for openai==${latestVersion}`) ||
+        installResult.output.includes(`Could not find a version that satisfies the requirement openai==${latestVersion}`),
+      `Expected pip to fail because the exact version was suppressed. Output was:\n${installResult.output}`
+    );
+    assert.ok(
+      !installResult.output.includes("blocked by safe-chain direct download minimum package age"),
+      `Expected resolver failure for an exact pin, not a direct-download block. Output was:\n${installResult.output}`
+    );
+  });
+});
+
+async function getLatestPackageVersion(shell, packageName) {
+  const result = await shell.runCommand(`/usr/bin/pip3 index versions ${packageName}`);
+  const version = result.output.match(new RegExp(`${packageName} \\(([^)]+)\\)`))?.[1];
+
+  assert.ok(
+    version,
+    `Could not determine latest ${packageName} version from pip output:\n${result.output}`
+  );
+
+  return version;
+}
+
+async function getInstalledVersion(shell, packageName) {
+  const result = await shell.runCommand(
+    `python3 - <<'PY'
+import importlib.metadata
+print(importlib.metadata.version("${packageName}"))
+PY`
+  );
+
+  return result.output.trim();
+}
+
+async function startFeedServer(container, releases) {
+  const shell = await container.openShell("bash");
+  const releasesJson = JSON.stringify(releases, null, 2);
+
+  await shell.runCommand(`mkdir -p /tmp/safe-chain-feed/releases
+cat > /tmp/safe-chain-feed/malware_pypi.json <<'EOF'
+[]
+EOF
+cat > /tmp/safe-chain-feed/releases/pypi.json <<'EOF'
+${releasesJson}
+EOF`);
+
+  container.dockerExec(
+    "nohup python3 -m http.server 8123 -d /tmp/safe-chain-feed >/tmp/safe-chain-feed.log 2>&1 </dev/null &",
+    true
+  );
+
+  const readinessResult = await shell.runCommand(`i=0
+while [ "$i" -lt 100 ]; do
+  if curl -fsS http://127.0.0.1:8123/releases/pypi.json >/dev/null; then
+    break
+  fi
+  sleep 0.1
+  i=$((i + 1))
+done
+if [ "$i" -ge 100 ]; then
+  echo "feed server did not become ready" >&2
+  cat /tmp/safe-chain-feed.log >&2 || true
+fi`);
+
+  assert.equal(
+    readinessResult.output.includes("feed server did not become ready"),
+    false,
+    `Expected local feed server to become ready. Output was:\n${readinessResult.output}`
+  );
+}
+
+function getTooYoungReleaseTimestamps() {
+  const now = Math.floor(Date.now() / 1000);
+
+  return {
+    released_on: now,
+    scraped_on: now,
+  };
+}

test/e2e/uvx.e2e.spec.js

@@ -0,0 +1,132 @@
+import { describe, it, before, beforeEach, afterEach } from "node:test";
+import { DockerTestContainer } from "./DockerTestContainer.js";
+import assert from "node:assert";
+
+describe("E2E: uvx coverage", () => {
+  let container;
+
+  before(async () => {
+    DockerTestContainer.buildImage();
+  });
+
+  beforeEach(async () => {
+    container = new DockerTestContainer();
+    await container.start();
+
+    const installationShell = await container.openShell("zsh");
+    await installationShell.runCommand("safe-chain setup");
+
+    // Clear uv cache
+    await installationShell.runCommand("uv cache clean");
+  });
+
+  afterEach(async () => {
+    if (container) {
+      await container.stop();
+      container = null;
+    }
+  });
+
+  it(`successfully runs a known safe tool with uvx`, async () => {
+    const shell = await container.openShell("zsh");
+
+    const result = await shell.runCommand(
+      "uvx ruff --version --safe-chain-logging=verbose"
+    );
+
+    assert.ok(
+      result.output.includes("no malware found.") || /ruff/i.test(result.output),
+      `Expected safe tool to run successfully. Output was:\n${result.output}`
+    );
+  });
+
+  it(`safe-chain blocks malicious packages via uvx`, async () => {
+    const shell = await container.openShell("zsh");
+
+    const result = await shell.runCommand(
+      "uvx safe-chain-pi-test"
+    );
+
+    assert.ok(
+      result.output.includes("blocked by safe-chain"),
+      `Expected malicious package to be blocked. Output was:\n${result.output}`
+    );
+    assert.ok(
+      result.output.includes("Exiting without installing malicious packages."),
+      `Expected exit message. Output was:\n${result.output}`
+    );
+  });
+
+  it(`uvx with --from flag runs a safe tool`, async () => {
+    const shell = await container.openShell("zsh");
+
+    const result = await shell.runCommand(
+      "uvx --from ruff ruff --version --safe-chain-logging=verbose"
+    );
+
+    assert.ok(
+      result.output.includes("no malware found.") || /ruff/i.test(result.output),
+      `Expected safe tool to run successfully with --from. Output was:\n${result.output}`
+    );
+  });
+
+  it(`uvx with --from flag blocks malicious packages`, async () => {
+    const shell = await container.openShell("zsh");
+
+    const result = await shell.runCommand(
+      "uvx --from safe-chain-pi-test some-command"
+    );
+
+    assert.ok(
+      result.output.includes("blocked by safe-chain"),
+      `Expected malicious package to be blocked with --from. Output was:\n${result.output}`
+    );
+    assert.ok(
+      result.output.includes("Exiting without installing malicious packages."),
+      `Expected exit message. Output was:\n${result.output}`
+    );
+  });
+
+  it(`uvx with specific version runs successfully`, async () => {
+    const shell = await container.openShell("zsh");
+
+    const result = await shell.runCommand(
+      "uvx ruff@0.4.0 --version --safe-chain-logging=verbose"
+    );
+
+    assert.ok(
+      result.output.includes("no malware found.") || /ruff/i.test(result.output),
+      `Expected safe tool with version to run. Output was:\n${result.output}`
+    );
+  });
+
+  it(`uvx with --with flag for additional dependencies`, async () => {
+    const shell = await container.openShell("zsh");
+
+    const result = await shell.runCommand(
+      "uvx --with requests ruff --version --safe-chain-logging=verbose"
+    );
+
+    assert.ok(
+      result.output.includes("no malware found.") || /ruff/i.test(result.output),
+      `Expected safe tool with --with dependency to run. Output was:\n${result.output}`
+    );
+  });
+
+  it(`uvx with --with flag blocks malicious additional dependencies`, async () => {
+    const shell = await container.openShell("zsh");
+
+    const result = await shell.runCommand(
+      "uvx --with safe-chain-pi-test ruff --version"
+    );
+
+    assert.ok(
+      result.output.includes("blocked by safe-chain"),
+      `Expected malicious --with dependency to be blocked. Output was:\n${result.output}`
+    );
+    assert.ok(
+      result.output.includes("Exiting without installing malicious packages."),
+      `Expected exit message. Output was:\n${result.output}`
+    );
+  });
+});