3 files changed, 251 insertions, 84 deletions

diff --git a/docs/tools/shell.md b/docs/tools/shell.md
index cc65b013..021cede1 100644
--- a/docs/tools/shell.md
+++ b/docs/tools/shell.md
@@ -64,96 +64,71 @@ run_shell_command(command="npm run dev &", description="Start development server
 
 You can restrict the commands that can be executed by the `run_shell_command` tool by using the `coreTools` and `excludeTools` settings in your configuration file.
 
-- `coreTools`: If you want to restrict the `run_shell_command` tool to a specific set of commands, you can add entries to the `coreTools` list in the format `ShellTool(<command>)`. For example, `"coreTools": ["ShellTool(ls -l)"]` will only allow the `ls -l` command to be executed. If you include `ShellTool` as a general entry in the `coreTools` list, it will act as a wildcard and allow any command to be executed, even if you have other specific commands in the list.
-- `excludeTools`: If you want to block specific commands, you can add entries to the `excludeTools` list in the format `ShellTool(<command>)`. For example, `"excludeTools": ["ShellTool(rm -rf /)"]` will block the `rm -rf /` command.
+- `coreTools`: To restrict `run_shell_command` to a specific set of commands, add entries to the `coreTools` list in the format `run_shell_command(<command>)`. For example, `"coreTools": ["run_shell_command(git)"]` will only allow `git` commands. Including the generic `run_shell_command` acts as a wildcard, allowing any command not explicitly blocked.
+- `excludeTools`: To block specific commands, add entries to the `excludeTools` list in the format `run_shell_command(<command>)`. For example, `"excludeTools": ["run_shell_command(rm)"]` will block `rm` commands.
 
-### Command Restriction Examples
-
-Here are some examples of how to use the `coreTools` and `excludeTools` settings to control which commands can be executed.
-
-**Allow only specific commands**
-
-To allow only `ls -l` and `git status`, and block all other commands:
-
-```json
-{
-  "coreTools": ["ShellTool(ls -l)", "ShellTool(git status)"]
-}
-```
-
-- `ls -l`: Allowed
-- `git status`: Allowed
-- `npm install`: Blocked
-
-**Block specific commands**
-
-To block `rm -rf /` and `npm install`, and allow all other commands:
+The validation logic is designed to be secure and flexible:
 
-```json
-{
-  "excludeTools": ["ShellTool(rm -rf /)", "ShellTool(npm install)"]
-}
-```
+1.  **Command Chaining Disabled**: The tool automatically splits commands chained with `&&`, `||`, or `;` and validates each part separately. If any part of the chain is disallowed, the entire command is blocked.
+2.  **Prefix Matching**: The tool uses prefix matching. For example, if you allow `git`, you can run `git status` or `git log`.
+3.  **Blocklist Precedence**: The `excludeTools` list is always checked first. If a command matches a blocked prefix, it will be denied, even if it also matches an allowed prefix in `coreTools`.
 
-- `rm -rf /`: Blocked
-- `npm install`: Blocked
-- `ls -l`: Allowed
+### Command Restriction Examples
 
-**Allow all commands**
+**Allow only specific command prefixes**
 
-To allow any command to be executed, you can use the `ShellTool` wildcard in `coreTools`:
+To allow only `git` and `npm` commands, and block all others:
 
 ```json
 {
-  "coreTools": ["ShellTool"]
+  "coreTools": ["run_shell_command(git)", "run_shell_command(npm)"]
 }
 ```
 
-- `ls -l`: Allowed
+- `git status`: Allowed
 - `npm install`: Allowed
-- `any other command`: Allowed
+- `ls -l`: Blocked
 
-**Wildcard with specific allowed commands**
+**Block specific command prefixes**
 
-If you include the `ShellTool` wildcard along with specific commands, the wildcard takes precedence, and all commands are allowed.
+To block `rm` and allow all other commands:
 
 ```json
 {
-  "coreTools": ["ShellTool", "ShellTool(ls -l)"]
+  "coreTools": ["run_shell_command"],
+  "excludeTools": ["run_shell_command(rm)"]
 }
 ```
 
-- `ls -l`: Allowed
+- `rm -rf /`: Blocked
+- `git status`: Allowed
 - `npm install`: Allowed
-- `any other command`: Allowed
 
-**Wildcard with a blocklist**
+**Blocklist takes precedence**
 
-You can use the `ShellTool` wildcard to allow all commands, while still blocking specific commands using `excludeTools`.
+If a command prefix is in both `coreTools` and `excludeTools`, it will be blocked.
 
 ```json
 {
-  "coreTools": ["ShellTool"],
-  "excludeTools": ["ShellTool(rm -rf /)"]
+  "coreTools": ["run_shell_command(git)"],
+  "excludeTools": ["run_shell_command(git push)"]
 }
 ```
 
-- `rm -rf /`: Blocked
-- `ls -l`: Allowed
-- `npm install`: Allowed
+- `git push origin main`: Blocked
+- `git status`: Allowed
 
 **Block all shell commands**
 
-To block all shell commands, you can add the `ShellTool` wildcard to `excludeTools`:
+To block all shell commands, add the `run_shell_command` wildcard to `excludeTools`:
 
 ```json
 {
-  "excludeTools": ["ShellTool"]
+  "excludeTools": ["run_shell_command"]
 }
 ```
 
 - `ls -l`: Blocked
-- `npm install`: Blocked
 - `any other command`: Blocked
 
 ## Security Note for `excludeTools`
diff --git a/packages/core/src/tools/shell.test.ts b/packages/core/src/tools/shell.test.ts
index 2cbd0ff4..936c1f77 100644
--- a/packages/core/src/tools/shell.test.ts
+++ b/packages/core/src/tools/shell.test.ts
@@ -168,4 +168,171 @@ describe('ShellTool', () => {
     const isAllowed = shellTool.isCommandAllowed('rm -rf /');
     expect(isAllowed).toBe(false);
   });
+
+  it('should allow a command that starts with an allowed command prefix', async () => {
+    const config = {
+      getCoreTools: () => ['ShellTool(gh issue edit)'],
+      getExcludeTools: () => [],
+    } as unknown as Config;
+    const shellTool = new ShellTool(config);
+    const isAllowed = shellTool.isCommandAllowed(
+      'gh issue edit 1 --add-label "kind/feature"',
+    );
+    expect(isAllowed).toBe(true);
+  });
+
+  it('should allow a command that starts with an allowed command prefix using the public-facing name', async () => {
+    const config = {
+      getCoreTools: () => ['run_shell_command(gh issue edit)'],
+      getExcludeTools: () => [],
+    } as unknown as Config;
+    const shellTool = new ShellTool(config);
+    const isAllowed = shellTool.isCommandAllowed(
+      'gh issue edit 1 --add-label "kind/feature"',
+    );
+    expect(isAllowed).toBe(true);
+  });
+
+  it('should not allow a command that starts with an allowed command prefix but is chained with another command', async () => {
+    const config = {
+      getCoreTools: () => ['run_shell_command(gh issue edit)'],
+      getExcludeTools: () => [],
+    } as unknown as Config;
+    const shellTool = new ShellTool(config);
+    const isAllowed = shellTool.isCommandAllowed('gh issue edit&&rm -rf /');
+    expect(isAllowed).toBe(false);
+  });
+
+  it('should not allow a command that is a prefix of an allowed command', async () => {
+    const config = {
+      getCoreTools: () => ['run_shell_command(gh issue edit)'],
+      getExcludeTools: () => [],
+    } as unknown as Config;
+    const shellTool = new ShellTool(config);
+    const isAllowed = shellTool.isCommandAllowed('gh issue');
+    expect(isAllowed).toBe(false);
+  });
+
+  it('should not allow a command that is a prefix of a blocked command', async () => {
+    const config = {
+      getCoreTools: () => [],
+      getExcludeTools: () => ['run_shell_command(gh issue edit)'],
+    } as unknown as Config;
+    const shellTool = new ShellTool(config);
+    const isAllowed = shellTool.isCommandAllowed('gh issue');
+    expect(isAllowed).toBe(true);
+  });
+
+  it('should not allow a command that is chained with a pipe', async () => {
+    const config = {
+      getCoreTools: () => ['run_shell_command(gh issue list)'],
+      getExcludeTools: () => [],
+    } as unknown as Config;
+    const shellTool = new ShellTool(config);
+    const isAllowed = shellTool.isCommandAllowed('gh issue list | rm -rf /');
+    expect(isAllowed).toBe(false);
+  });
+
+  it('should not allow a command that is chained with a semicolon', async () => {
+    const config = {
+      getCoreTools: () => ['run_shell_command(gh issue list)'],
+      getExcludeTools: () => [],
+    } as unknown as Config;
+    const shellTool = new ShellTool(config);
+    const isAllowed = shellTool.isCommandAllowed('gh issue list; rm -rf /');
+    expect(isAllowed).toBe(false);
+  });
+
+  it('should block a chained command if any part is blocked', async () => {
+    const config = {
+      getCoreTools: () => ['run_shell_command(echo "hello")'],
+      getExcludeTools: () => ['run_shell_command(rm)'],
+    } as unknown as Config;
+    const shellTool = new ShellTool(config);
+    const isAllowed = shellTool.isCommandAllowed('echo "hello" && rm -rf /');
+    expect(isAllowed).toBe(false);
+  });
+
+  it('should block a command if its prefix is on the blocklist, even if the command itself is on the allowlist', async () => {
+    const config = {
+      getCoreTools: () => ['run_shell_command(git push)'],
+      getExcludeTools: () => ['run_shell_command(git)'],
+    } as unknown as Config;
+    const shellTool = new ShellTool(config);
+    const isAllowed = shellTool.isCommandAllowed('git push');
+    expect(isAllowed).toBe(false);
+  });
+
+  it('should be case-sensitive in its matching', async () => {
+    const config = {
+      getCoreTools: () => ['run_shell_command(echo)'],
+      getExcludeTools: () => [],
+    } as unknown as Config;
+    const shellTool = new ShellTool(config);
+    const isAllowed = shellTool.isCommandAllowed('ECHO "hello"');
+    expect(isAllowed).toBe(false);
+  });
+
+  it('should correctly handle commands with extra whitespace around chaining operators', async () => {
+    const config = {
+      getCoreTools: () => ['run_shell_command(ls -l)'],
+      getExcludeTools: () => ['run_shell_command(rm)'],
+    } as unknown as Config;
+    const shellTool = new ShellTool(config);
+    const isAllowed = shellTool.isCommandAllowed('ls -l  ;  rm -rf /');
+    expect(isAllowed).toBe(false);
+  });
+
+  it('should allow a chained command if all parts are allowed', async () => {
+    const config = {
+      getCoreTools: () => [
+        'run_shell_command(echo)',
+        'run_shell_command(ls -l)',
+      ],
+      getExcludeTools: () => [],
+    } as unknown as Config;
+    const shellTool = new ShellTool(config);
+    const isAllowed = shellTool.isCommandAllowed('echo "hello" && ls -l');
+    expect(isAllowed).toBe(true);
+  });
+
+  it('should block a command with command substitution using backticks', async () => {
+    const config = {
+      getCoreTools: () => ['run_shell_command(echo)'],
+      getExcludeTools: () => [],
+    } as unknown as Config;
+    const shellTool = new ShellTool(config);
+    const isAllowed = shellTool.isCommandAllowed('echo `rm -rf /`');
+    expect(isAllowed).toBe(false);
+  });
+
+  it('should block a command with command substitution using $()', async () => {
+    const config = {
+      getCoreTools: () => ['run_shell_command(echo)'],
+      getExcludeTools: () => [],
+    } as unknown as Config;
+    const shellTool = new ShellTool(config);
+    const isAllowed = shellTool.isCommandAllowed('echo $(rm -rf /)');
+    expect(isAllowed).toBe(false);
+  });
+
+  it('should allow a command with I/O redirection', async () => {
+    const config = {
+      getCoreTools: () => ['run_shell_command(echo)'],
+      getExcludeTools: () => [],
+    } as unknown as Config;
+    const shellTool = new ShellTool(config);
+    const isAllowed = shellTool.isCommandAllowed('echo "hello" > file.txt');
+    expect(isAllowed).toBe(true);
+  });
+
+  it('should not allow a command that is chained with a double pipe', async () => {
+    const config = {
+      getCoreTools: () => ['run_shell_command(gh issue list)'],
+      getExcludeTools: () => [],
+    } as unknown as Config;
+    const shellTool = new ShellTool(config);
+    const isAllowed = shellTool.isCommandAllowed('gh issue list || rm -rf /');
+    expect(isAllowed).toBe(false);
+  });
 });
diff --git a/packages/core/src/tools/shell.ts b/packages/core/src/tools/shell.ts
index a2fa5ce4..bbb998d5 100644
--- a/packages/core/src/tools/shell.ts
+++ b/packages/core/src/tools/shell.ts
@@ -99,17 +99,39 @@ Process Group PGID: Process group started or \`(none)\``,
   }
 
   isCommandAllowed(command: string): boolean {
-    const normalize = (cmd: string) => cmd.trim().replace(/\s+/g, ' ');
+    // 0. Disallow command substitution
+    if (command.includes('$(') || command.includes('`')) {
+      return false;
+    }
+
+    const SHELL_TOOL_NAMES = [ShellTool.name, ShellTool.Name];
+
+    const normalize = (cmd: string): string => cmd.trim().replace(/\s+/g, ' ');
+
+    /**
+     * Checks if a command string starts with a given prefix, ensuring it's a
+     * whole word match (i.e., followed by a space or it's an exact match).
+     * e.g., `isPrefixedBy('npm install', 'npm')` -> true
+     * e.g., `isPrefixedBy('npm', 'npm')` -> true
+     * e.g., `isPrefixedBy('npminstall', 'npm')` -> false
+     */
+    const isPrefixedBy = (cmd: string, prefix: string): boolean => {
+      if (!cmd.startsWith(prefix)) {
+        return false;
+      }
+      return cmd.length === prefix.length || cmd[prefix.length] === ' ';
+    };
 
+    /**
+     * Extracts and normalizes shell commands from a list of tool strings.
+     * e.g., 'ShellTool("ls -l")' becomes 'ls -l'
+     */
     const extractCommands = (tools: string[]): string[] =>
       tools.flatMap((tool) => {
-        if (tool.startsWith(`${ShellTool.name}(`) && tool.endsWith(')')) {
-          return [normalize(tool.slice(ShellTool.name.length + 1, -1))];
-        } else if (
-          tool.startsWith(`${ShellTool.Name}(`) &&
-          tool.endsWith(')')
-        ) {
-          return [normalize(tool.slice(ShellTool.Name.length + 1, -1))];
+        for (const toolName of SHELL_TOOL_NAMES) {
+          if (tool.startsWith(`${toolName}(`) && tool.endsWith(')')) {
+            return [normalize(tool.slice(toolName.length + 1, -1))];
+          }
         }
         return [];
       });
@@ -117,41 +139,44 @@ Process Group PGID: Process group started or \`(none)\``,
     const coreTools = this.config.getCoreTools() || [];
     const excludeTools = this.config.getExcludeTools() || [];
 
-    if (
-      excludeTools.includes(ShellTool.name) ||
-      excludeTools.includes(ShellTool.Name)
-    ) {
+    // 1. Check if the shell tool is globally disabled.
+    if (SHELL_TOOL_NAMES.some((name) => excludeTools.includes(name))) {
       return false;
     }
 
-    const blockedCommands = extractCommands(excludeTools);
-    const normalizedCommand = normalize(command);
+    const blockedCommands = new Set(extractCommands(excludeTools));
+    const allowedCommands = new Set(extractCommands(coreTools));
 
-    if (blockedCommands.includes(normalizedCommand)) {
-      return false;
-    }
-
-    const hasSpecificCommands = coreTools.some(
-      (tool) =>
-        (tool.startsWith(`${ShellTool.name}(`) && tool.endsWith(')')) ||
-        (tool.startsWith(`${ShellTool.Name}(`) && tool.endsWith(')')),
+    const hasSpecificAllowedCommands = allowedCommands.size > 0;
+    const isWildcardAllowed = SHELL_TOOL_NAMES.some((name) =>
+      coreTools.includes(name),
     );
 
-    if (hasSpecificCommands) {
-      // If the generic `ShellTool` is also present, it acts as a wildcard,
-      // allowing all commands (that are not explicitly blocked).
-      if (
-        coreTools.includes(ShellTool.name) ||
-        coreTools.includes(ShellTool.Name)
-      ) {
-        return true;
+    const commandsToValidate = command.split(/&&|\|\||\||;/).map(normalize);
+
+    for (const cmd of commandsToValidate) {
+      // 2. Check if the command is on the blocklist.
+      const isBlocked = [...blockedCommands].some((blocked) =>
+        isPrefixedBy(cmd, blocked),
+      );
+      if (isBlocked) {
+        return false;
       }
 
-      // Otherwise, we are in strict allow-list mode.
-      const allowedCommands = extractCommands(coreTools);
-      return allowedCommands.includes(normalizedCommand);
+      // 3. If in strict allow-list mode, check if the command is permitted.
+      const isStrictAllowlist =
+        hasSpecificAllowedCommands && !isWildcardAllowed;
+      if (isStrictAllowlist) {
+        const isAllowed = [...allowedCommands].some((allowed) =>
+          isPrefixedBy(cmd, allowed),
+        );
+        if (!isAllowed) {
+          return false;
+        }
+      }
     }
 
+    // 4. If all checks pass, the command is allowed.
     return true;
   }