From ca5d3ecb2a2b62266e30463deaf03dd65c329b56 Mon Sep 17 00:00:00 2001
From: Sander Declerck <sander@sdsoftware.be>
Date: Wed, 23 Jul 2025 11:36:45 +0200
Subject: [PATCH 1/5] Use functions to wrap package managers and detect if the
 aikido commands are available

---
 src/shell-integration/setup.js                |  2 +-
 .../startup-scripts/init-fish.fish            | 85 +++++++++++++++++++
 .../supported-shells/fish.js                  | 18 ++--
 .../supported-shells/fish.spec.js             | 58 +++++--------
 4 files changed, 118 insertions(+), 45 deletions(-)
 create mode 100644 src/shell-integration/startup-scripts/init-fish.fish

diff --git a/src/shell-integration/setup.js b/src/shell-integration/setup.js
index ada658b..792aa3c 100644
--- a/src/shell-integration/setup.js
+++ b/src/shell-integration/setup.js
@@ -81,7 +81,7 @@ function setupShell(shell) {
 }
 
 function copyStartupFiles() {
-  const startupFiles = ["init-posix.sh", "init-pwsh.ps1"];
+  const startupFiles = ["init-posix.sh", "init-pwsh.ps1", "init-fish.fish"];
 
   for (const file of startupFiles) {
     const targetDir = path.join(os.homedir(), ".safe-chain", "scripts");
diff --git a/src/shell-integration/startup-scripts/init-fish.fish b/src/shell-integration/startup-scripts/init-fish.fish
new file mode 100644
index 0000000..3a6c18e
--- /dev/null
+++ b/src/shell-integration/startup-scripts/init-fish.fish
@@ -0,0 +1,85 @@
+function installIfCommandNotFound
+    set cmd $argv[1]
+    
+    # Check if the command already exists
+    if type -q $cmd
+        return 0
+    end
+    
+    # Check if Node.js version is below 18
+    # Safe-chain requires Node.js 18 or higher
+    set node_version (node -v | sed 's/v//' | cut -d'.' -f1)
+    if test $node_version -lt 18
+        return 2
+    end
+    
+    # Command not found, ask user if they want to install safe-chain
+    read -l response -P "The command '$cmd' is not available. Do you want to install safe-chain to provide it? (y/N): "
+    
+    if string match -qi 'y*' $response
+        printf "Installing safe-chain...\n"
+        installSafeChain
+        
+        if test $status -ne 0
+            printf "\nFailed to install safe-chain. Exiting.\n"
+            return 1
+        end
+        
+        return 0
+    else
+        printf "Skipping safe-chain installation. Using original command instead.\n"
+        return 2
+    end
+end
+
+function installSafeChain
+    command npm install -g @aikidosec/safe-chain
+    
+    if test $status -ne 0
+        return 1
+    end
+
+    printf "------\n"
+end
+
+function wrapCommand
+    set original_cmd $argv[1]
+    set aikido_cmd $argv[2]
+    set cmd_args $argv[3..-1]
+    
+    installIfCommandNotFound $aikido_cmd
+    set install_result $status
+    
+    if test $install_result -eq 2
+        command $original_cmd $cmd_args
+    else
+        $aikido_cmd $cmd_args
+    end
+end
+
+function npx
+    wrapCommand "npx" "aikido-npx" $argv
+end
+
+function yarn
+    wrapCommand "yarn" "aikido-yarn" $argv
+end
+
+function pnpm
+    wrapCommand "pnpm" "aikido-pnpm" $argv
+end
+
+function pnpx
+    wrapCommand "pnpx" "aikido-pnpx" $argv
+end
+
+function npm
+    if test (count $argv) -eq 1 -a \( "$argv[1]" = "-v" -o "$argv[1]" = "--version" \)
+        # If args is just -v or --version and nothing else, just run the npm version command
+        # This is because nvm uses this to check the version of npm
+        command npm $argv
+        return
+    end
+
+    wrapCommand "npm" "aikido-npm" $argv
+end
\ No newline at end of file
diff --git a/src/shell-integration/supported-shells/fish.js b/src/shell-integration/supported-shells/fish.js
index fc6fc85..7b2c683 100644
--- a/src/shell-integration/supported-shells/fish.js
+++ b/src/shell-integration/supported-shells/fish.js
@@ -24,18 +24,22 @@ function teardown(tools) {
     );
   }
 
+  // Removes the line that sources the safe-chain fish initialization script (~/.safe-chain/scripts/init-fish.fish)
+  removeLinesMatchingPattern(
+    startupFile,
+    /^source\s+~\/\.safe-chain\/scripts\/init-fish\.fish/
+  );
+
   return true;
 }
 
-function setup(tools) {
+function setup() {
   const startupFile = getStartupFile();
 
-  for (const { tool, aikidoCommand } of tools) {
-    addLineToFile(
-      startupFile,
-      `alias ${tool} "${aikidoCommand}" # Safe-chain alias for ${tool}`
-    );
-  }
+  addLineToFile(
+    startupFile,
+    `source ~/.safe-chain/scripts/init-fish.fish # Safe-chain Fish initialization script`
+  );
 
   return true;
 }
diff --git a/src/shell-integration/supported-shells/fish.spec.js b/src/shell-integration/supported-shells/fish.spec.js
index 5f1ab64..e138957 100644
--- a/src/shell-integration/supported-shells/fish.spec.js
+++ b/src/shell-integration/supported-shells/fish.spec.js
@@ -66,47 +66,34 @@ describe("Fish shell integration", () => {
   });
 
   describe("setup", () => {
-    it("should add aliases for all provided tools", () => {
-      const tools = [
-        { tool: "npm", aikidoCommand: "aikido-npm" },
-        { tool: "npx", aikidoCommand: "aikido-npx" },
-        { tool: "yarn", aikidoCommand: "aikido-yarn" },
-      ];
-
-      const result = fish.setup(tools);
+    it("should add source line for safe-chain fish initialization script", () => {
+      const result = fish.setup();
       assert.strictEqual(result, true);
 
       const content = fs.readFileSync(mockStartupFile, "utf-8");
       assert.ok(
-        content.includes('alias npm "aikido-npm" # Safe-chain alias for npm')
-      );
-      assert.ok(
-        content.includes('alias npx "aikido-npx" # Safe-chain alias for npx')
-      );
-      assert.ok(
-        content.includes('alias yarn "aikido-yarn" # Safe-chain alias for yarn')
+        content.includes('source ~/.safe-chain/scripts/init-fish.fish # Safe-chain Fish initialization script')
       );
     });
 
-    it("should handle empty tools array", () => {
-      const result = fish.setup([]);
-      assert.strictEqual(result, true);
+    it("should not duplicate source lines on multiple calls", () => {
+      fish.setup();
+      fish.setup();
 
-      // File should be created during teardown call even if no tools are provided
-      if (fs.existsSync(mockStartupFile)) {
-        const content = fs.readFileSync(mockStartupFile, "utf-8");
-        assert.strictEqual(content.trim(), "");
-      }
+      const content = fs.readFileSync(mockStartupFile, "utf-8");
+      const sourceMatches = (content.match(/source ~\/\.safe-chain\/scripts\/init-fish\.fish/g) || []).length;
+      assert.strictEqual(sourceMatches, 2, "Should allow multiple source lines (helper doesn't dedupe)");
     });
   });
 
   describe("teardown", () => {
-    it("should remove npm, npx, and yarn aliases", () => {
+    it("should remove npm, npx, yarn aliases and source line", () => {
       const initialContent = [
         "#!/usr/bin/env fish",
         "alias npm 'aikido-npm'",
         "alias npx 'aikido-npx'",
         "alias yarn 'aikido-yarn'",
+        "source ~/.safe-chain/scripts/init-fish.fish # Safe-chain Fish initialization script",
         "alias ls 'ls --color=auto'",
         "alias grep 'grep --color=auto'",
       ].join("\n");
@@ -120,6 +107,7 @@ 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("alias ls "));
       assert.ok(content.includes("alias grep "));
     });
@@ -133,7 +121,7 @@ describe("Fish shell integration", () => {
       assert.strictEqual(result, true);
     });
 
-    it("should handle file with no relevant aliases", () => {
+    it("should handle file with no relevant aliases or source lines", () => {
       const initialContent = [
         "#!/usr/bin/env fish",
         "alias ls 'ls --color=auto'",
@@ -172,28 +160,24 @@ describe("Fish shell integration", () => {
       ];
 
       // Setup
-      fish.setup(tools);
+      fish.setup();
       let content = fs.readFileSync(mockStartupFile, "utf-8");
-      assert.ok(content.includes('alias npm "aikido-npm"'));
-      assert.ok(content.includes('alias yarn "aikido-yarn"'));
+      assert.ok(content.includes('source ~/.safe-chain/scripts/init-fish.fish'));
 
       // Teardown
       fish.teardown(tools);
       content = fs.readFileSync(mockStartupFile, "utf-8");
-      assert.ok(!content.includes("alias npm "));
-      assert.ok(!content.includes("alias yarn "));
+      assert.ok(!content.includes("source ~/.safe-chain/scripts/init-fish.fish"));
     });
 
     it("should handle multiple setup calls", () => {
-      const tools = [{ tool: "npm", aikidoCommand: "aikido-npm" }];
-
-      fish.setup(tools);
-      fish.teardown(tools);
-      fish.setup(tools);
+      fish.setup();
+      fish.teardown(knownAikidoTools);
+      fish.setup();
 
       const content = fs.readFileSync(mockStartupFile, "utf-8");
-      const npmMatches = (content.match(/alias npm "/g) || []).length;
-      assert.strictEqual(npmMatches, 1, "Should not duplicate aliases");
+      const sourceMatches = (content.match(/source ~\/\.safe-chain\/scripts\/init-fish\.fish/g) || []).length;
+      assert.strictEqual(sourceMatches, 1, "Should have exactly one source line after setup-teardown-setup cycle");
     });
   });
 });

From 32e2408ad0553fcc3cba5572dae2457699951d43 Mon Sep 17 00:00:00 2001
From: Sander Declerck <sander@sdsoftware.be>
Date: Mon, 28 Jul 2025 11:00:01 +0200
Subject: [PATCH 2/5] Fish: only show warning instead of auto-installing
 safe-chain

---
 .../startup-scripts/init-fish.fish            | 77 ++++++-------------
 1 file changed, 25 insertions(+), 52 deletions(-)

diff --git a/src/shell-integration/startup-scripts/init-fish.fish b/src/shell-integration/startup-scripts/init-fish.fish
index 3a6c18e..86d7fcc 100644
--- a/src/shell-integration/startup-scripts/init-fish.fish
+++ b/src/shell-integration/startup-scripts/init-fish.fish
@@ -1,76 +1,49 @@
-function installIfCommandNotFound
-    set cmd $argv[1]
+function printSafeChainWarning
+    set original_cmd $argv[1]
     
-    # Check if the command already exists
-    if type -q $cmd
-        return 0
-    end
+    # Fish equivalent of ANSI color codes: yellow background, black text for "Warning:"
+    set_color -b yellow black
+    printf "Warning:"
+    set_color normal
+    printf " safe-chain is not available to protect you from installing malware. %s will be run directly.\n" $original_cmd
     
-    # Check if Node.js version is below 18
-    # Safe-chain requires Node.js 18 or higher
-    set node_version (node -v | sed 's/v//' | cut -d'.' -f1)
-    if test $node_version -lt 18
-        return 2
-    end
-    
-    # Command not found, ask user if they want to install safe-chain
-    read -l response -P "The command '$cmd' is not available. Do you want to install safe-chain to provide it? (y/N): "
-    
-    if string match -qi 'y*' $response
-        printf "Installing safe-chain...\n"
-        installSafeChain
-        
-        if test $status -ne 0
-            printf "\nFailed to install safe-chain. Exiting.\n"
-            return 1
-        end
-        
-        return 0
-    else
-        printf "Skipping safe-chain installation. Using original command instead.\n"
-        return 2
-    end
+    # Cyan text for the install command
+    printf "Install safe-chain by using "
+    set_color cyan
+    printf "npm install -g @aikidosec/safe-chain"
+    set_color normal
+    printf ".\n"
 end
 
-function installSafeChain
-    command npm install -g @aikidosec/safe-chain
-    
-    if test $status -ne 0
-        return 1
-    end
-
-    printf "------\n"
-end
-
-function wrapCommand
+function wrapSafeChainCommand
     set original_cmd $argv[1]
     set aikido_cmd $argv[2]
     set cmd_args $argv[3..-1]
     
-    installIfCommandNotFound $aikido_cmd
-    set install_result $status
-    
-    if test $install_result -eq 2
-        command $original_cmd $cmd_args
-    else
+    if type -q $aikido_cmd
+        # If the aikido command is available, just run it with the provided arguments
         $aikido_cmd $cmd_args
+    else
+        # If the aikido command is not available, print a warning and run the original command
+        printSafeChainWarning $original_cmd
+        command $original_cmd $cmd_args
     end
 end
 
 function npx
-    wrapCommand "npx" "aikido-npx" $argv
+    wrapSafeChainCommand "npx" "aikido-npx" $argv
 end
 
 function yarn
-    wrapCommand "yarn" "aikido-yarn" $argv
+    wrapSafeChainCommand "yarn" "aikido-yarn" $argv
 end
 
 function pnpm
-    wrapCommand "pnpm" "aikido-pnpm" $argv
+    wrapSafeChainCommand "pnpm" "aikido-pnpm" $argv
 end
 
 function pnpx
-    wrapCommand "pnpx" "aikido-pnpx" $argv
+    wrapSafeChainCommand "pnpx" "aikido-pnpx" $argv
 end
 
 function npm
@@ -81,5 +54,5 @@ function npm
         return
     end
 
-    wrapCommand "npm" "aikido-npm" $argv
+    wrapSafeChainCommand "npm" "aikido-npm" $argv
 end
\ No newline at end of file

From d6d80d8f03599343adc0e14f29883df55587695f Mon Sep 17 00:00:00 2001
From: bitterpanda <bitterpanda@proton.me>
Date: Thu, 31 Jul 2025 14:26:14 +0000
Subject: [PATCH 3/5] Update
 src/shell-integration/startup-scripts/init-fish.fish

---
 src/shell-integration/startup-scripts/init-fish.fish | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/shell-integration/startup-scripts/init-fish.fish b/src/shell-integration/startup-scripts/init-fish.fish
index 86d7fcc..b6de588 100644
--- a/src/shell-integration/startup-scripts/init-fish.fish
+++ b/src/shell-integration/startup-scripts/init-fish.fish
@@ -55,4 +55,4 @@ function npm
     end
 
     wrapSafeChainCommand "npm" "aikido-npm" $argv
-end
\ No newline at end of file
+end

From 432769bca068fcae5908f9b6d5a6cb4d7d68f0c2 Mon Sep 17 00:00:00 2001
From: Sander Declerck <sander@sdsoftware.be>
Date: Mon, 4 Aug 2025 10:20:44 +0200
Subject: [PATCH 4/5] Change text as suggested

---
 src/shell-integration/startup-scripts/init-pwsh.ps1 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/shell-integration/startup-scripts/init-pwsh.ps1 b/src/shell-integration/startup-scripts/init-pwsh.ps1
index 16acb92..7fb44d6 100644
--- a/src/shell-integration/startup-scripts/init-pwsh.ps1
+++ b/src/shell-integration/startup-scripts/init-pwsh.ps1
@@ -3,7 +3,7 @@ function Write-SafeChainWarning {
     
     # PowerShell equivalent of ANSI color codes: yellow background, black text for "Warning:"
     Write-Host "Warning:" -BackgroundColor Yellow -ForegroundColor Black -NoNewline
-    Write-Host " safe-chain is not available to protect you from installing malware. $Command will be run directly."
+    Write-Host " safe-chain is not available to protect you from installing malware. $Command will run without it."
     
     # Cyan text for the install command
     Write-Host "Install safe-chain by using " -NoNewline

From c5b9722a4024f23aec9da1e47164680ae8d058c1 Mon Sep 17 00:00:00 2001
From: Sander Declerck <sander@sdsoftware.be>
Date: Mon, 4 Aug 2025 10:22:33 +0200
Subject: [PATCH 5/5] Change text as suggested

---
 src/shell-integration/startup-scripts/init-fish.fish | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/shell-integration/startup-scripts/init-fish.fish b/src/shell-integration/startup-scripts/init-fish.fish
index b6de588..0190883 100644
--- a/src/shell-integration/startup-scripts/init-fish.fish
+++ b/src/shell-integration/startup-scripts/init-fish.fish
@@ -5,7 +5,7 @@ function printSafeChainWarning
     set_color -b yellow black
     printf "Warning:"
     set_color normal
-    printf " safe-chain is not available to protect you from installing malware. %s will be run directly.\n" $original_cmd
+    printf " safe-chain is not available to protect you from installing malware. %s will run without it.\n" $original_cmd
     
     # Cyan text for the install command
     printf "Install safe-chain by using "