Added chall and some stuff

challs/cryptoMedium/aes.py

@@ -0,0 +1,249 @@
+"""
+This is a slightly modified version of BoppreH's AES implementation found at at https://github.com/boppreh/AES
+Follow the original disclaimer
+__________________________________
+This is an exercise in secure symmetric-key encryption, implemented in pure
+Python (no external libraries needed).
+Original AES-128 implementation by Bo Zhu (http://about.bozhu.me) at
+https://github.com/bozhu/AES-Python . PKCS#7 padding, CBC mode, PKBDF2, HMAC,
+byte array and string support added by me at https://github.com/boppreh/aes.
+Other block modes contributed by @righthandabacus.
+Although this is an exercise, the `encrypt` and `decrypt` functions should
+provide reasonable security to encrypted messages.
+"""
+
+
+s_box = (
+    0x63, 0x7C, 0x77, 0x7B, 0xF2, 0x6B, 0x6F, 0xC5, 0x30, 0x01, 0x67, 0x2B, 0xFE, 0xD7, 0xAB, 0x76,
+    0xCA, 0x82, 0xC9, 0x7D, 0xFA, 0x59, 0x47, 0xF0, 0xAD, 0xD4, 0xA2, 0xAF, 0x9C, 0xA4, 0x72, 0xC0,
+    0xB7, 0xFD, 0x93, 0x26, 0x36, 0x3F, 0xF7, 0xCC, 0x34, 0xA5, 0xE5, 0xF1, 0x71, 0xD8, 0x31, 0x15,
+    0x04, 0xC7, 0x23, 0xC3, 0x18, 0x96, 0x05, 0x9A, 0x07, 0x12, 0x80, 0xE2, 0xEB, 0x27, 0xB2, 0x75,
+    0x09, 0x83, 0x2C, 0x1A, 0x1B, 0x6E, 0x5A, 0xA0, 0x52, 0x3B, 0xD6, 0xB3, 0x29, 0xE3, 0x2F, 0x84,
+    0x53, 0xD1, 0x00, 0xED, 0x20, 0xFC, 0xB1, 0x5B, 0x6A, 0xCB, 0xBE, 0x39, 0x4A, 0x4C, 0x58, 0xCF,
+    0xD0, 0xEF, 0xAA, 0xFB, 0x43, 0x4D, 0x33, 0x85, 0x45, 0xF9, 0x02, 0x7F, 0x50, 0x3C, 0x9F, 0xA8,
+    0x51, 0xA3, 0x40, 0x8F, 0x92, 0x9D, 0x38, 0xF5, 0xBC, 0xB6, 0xDA, 0x21, 0x10, 0xFF, 0xF3, 0xD2,
+    0xCD, 0x0C, 0x13, 0xEC, 0x5F, 0x97, 0x44, 0x17, 0xC4, 0xA7, 0x7E, 0x3D, 0x64, 0x5D, 0x19, 0x73,
+    0x60, 0x81, 0x4F, 0xDC, 0x22, 0x2A, 0x90, 0x88, 0x46, 0xEE, 0xB8, 0x14, 0xDE, 0x5E, 0x0B, 0xDB,
+    0xE0, 0x32, 0x3A, 0x0A, 0x49, 0x06, 0x24, 0x5C, 0xC2, 0xD3, 0xAC, 0x62, 0x91, 0x95, 0xE4, 0x79,
+    0xE7, 0xC8, 0x37, 0x6D, 0x8D, 0xD5, 0x4E, 0xA9, 0x6C, 0x56, 0xF4, 0xEA, 0x65, 0x7A, 0xAE, 0x08,
+    0xBA, 0x78, 0x25, 0x2E, 0x1C, 0xA6, 0xB4, 0xC6, 0xE8, 0xDD, 0x74, 0x1F, 0x4B, 0xBD, 0x8B, 0x8A,
+    0x70, 0x3E, 0xB5, 0x66, 0x48, 0x03, 0xF6, 0x0E, 0x61, 0x35, 0x57, 0xB9, 0x86, 0xC1, 0x1D, 0x9E,
+    0xE1, 0xF8, 0x98, 0x11, 0x69, 0xD9, 0x8E, 0x94, 0x9B, 0x1E, 0x87, 0xE9, 0xCE, 0x55, 0x28, 0xDF,
+    0x8C, 0xA1, 0x89, 0x0D, 0xBF, 0xE6, 0x42, 0x68, 0x41, 0x99, 0x2D, 0x0F, 0xB0, 0x54, 0xBB, 0x16,
+)
+
+inv_s_box = (
+    0x52, 0x09, 0x6A, 0xD5, 0x30, 0x36, 0xA5, 0x38, 0xBF, 0x40, 0xA3, 0x9E, 0x81, 0xF3, 0xD7, 0xFB,
+    0x7C, 0xE3, 0x39, 0x82, 0x9B, 0x2F, 0xFF, 0x87, 0x34, 0x8E, 0x43, 0x44, 0xC4, 0xDE, 0xE9, 0xCB,
+    0x54, 0x7B, 0x94, 0x32, 0xA6, 0xC2, 0x23, 0x3D, 0xEE, 0x4C, 0x95, 0x0B, 0x42, 0xFA, 0xC3, 0x4E,
+    0x08, 0x2E, 0xA1, 0x66, 0x28, 0xD9, 0x24, 0xB2, 0x76, 0x5B, 0xA2, 0x49, 0x6D, 0x8B, 0xD1, 0x25,
+    0x72, 0xF8, 0xF6, 0x64, 0x86, 0x68, 0x98, 0x16, 0xD4, 0xA4, 0x5C, 0xCC, 0x5D, 0x65, 0xB6, 0x92,
+    0x6C, 0x70, 0x48, 0x50, 0xFD, 0xED, 0xB9, 0xDA, 0x5E, 0x15, 0x46, 0x57, 0xA7, 0x8D, 0x9D, 0x84,
+    0x90, 0xD8, 0xAB, 0x00, 0x8C, 0xBC, 0xD3, 0x0A, 0xF7, 0xE4, 0x58, 0x05, 0xB8, 0xB3, 0x45, 0x06,
+    0xD0, 0x2C, 0x1E, 0x8F, 0xCA, 0x3F, 0x0F, 0x02, 0xC1, 0xAF, 0xBD, 0x03, 0x01, 0x13, 0x8A, 0x6B,
+    0x3A, 0x91, 0x11, 0x41, 0x4F, 0x67, 0xDC, 0xEA, 0x97, 0xF2, 0xCF, 0xCE, 0xF0, 0xB4, 0xE6, 0x73,
+    0x96, 0xAC, 0x74, 0x22, 0xE7, 0xAD, 0x35, 0x85, 0xE2, 0xF9, 0x37, 0xE8, 0x1C, 0x75, 0xDF, 0x6E,
+    0x47, 0xF1, 0x1A, 0x71, 0x1D, 0x29, 0xC5, 0x89, 0x6F, 0xB7, 0x62, 0x0E, 0xAA, 0x18, 0xBE, 0x1B,
+    0xFC, 0x56, 0x3E, 0x4B, 0xC6, 0xD2, 0x79, 0x20, 0x9A, 0xDB, 0xC0, 0xFE, 0x78, 0xCD, 0x5A, 0xF4,
+    0x1F, 0xDD, 0xA8, 0x33, 0x88, 0x07, 0xC7, 0x31, 0xB1, 0x12, 0x10, 0x59, 0x27, 0x80, 0xEC, 0x5F,
+    0x60, 0x51, 0x7F, 0xA9, 0x19, 0xB5, 0x4A, 0x0D, 0x2D, 0xE5, 0x7A, 0x9F, 0x93, 0xC9, 0x9C, 0xEF,
+    0xA0, 0xE0, 0x3B, 0x4D, 0xAE, 0x2A, 0xF5, 0xB0, 0xC8, 0xEB, 0xBB, 0x3C, 0x83, 0x53, 0x99, 0x61,
+    0x17, 0x2B, 0x04, 0x7E, 0xBA, 0x77, 0xD6, 0x26, 0xE1, 0x69, 0x14, 0x63, 0x55, 0x21, 0x0C, 0x7D,
+)
+
+
+def sub_bytes(s):
+    for i in range(4):
+        for j in range(4):
+            s[i][j] = s_box[s[i][j]]
+
+
+def inv_sub_bytes(s):
+    for i in range(4):
+        for j in range(4):
+            s[i][j] = inv_s_box[s[i][j]]
+
+
+def shift_rows(s):
+    s[0][1], s[1][1], s[2][1], s[3][1] = s[1][1], s[2][1], s[3][1], s[0][1]
+    s[0][2], s[1][2], s[2][2], s[3][2] = s[2][2], s[3][2], s[0][2], s[1][2]
+    s[0][3], s[1][3], s[2][3], s[3][3] = s[3][3], s[0][3], s[1][3], s[2][3]
+
+
+def inv_shift_rows(s):
+    s[0][1], s[1][1], s[2][1], s[3][1] = s[3][1], s[0][1], s[1][1], s[2][1]
+    s[0][2], s[1][2], s[2][2], s[3][2] = s[2][2], s[3][2], s[0][2], s[1][2]
+    s[0][3], s[1][3], s[2][3], s[3][3] = s[1][3], s[2][3], s[3][3], s[0][3]
+
+def add_round_key(s, k):
+
+    for i in range(4):
+        for j in range(4):
+            s[i][j] ^= k[i][j]
+
+
+# learned from http://cs.ucsb.edu/~koc/cs178/projects/JT/aes.c
+xtime = lambda a: (((a << 1) ^ 0x1B) & 0xFF) if (a & 0x80) else (a << 1)
+
+
+def mix_single_column(a):
+    # see Sec 4.1.2 in The Design of Rijndael
+    t = a[0] ^ a[1] ^ a[2] ^ a[3]
+    u = a[0]
+    a[0] ^= t ^ xtime(a[0] ^ a[1])
+    a[1] ^= t ^ xtime(a[1] ^ a[2])
+    a[2] ^= t ^ xtime(a[2] ^ a[3])
+    a[3] ^= t ^ xtime(a[3] ^ u)
+
+
+def mix_columns(s):
+    for i in range(4):
+        mix_single_column(s[i])
+
+
+def inv_mix_columns(s):
+    # see Sec 4.1.3 in The Design of Rijndael
+    for i in range(4):
+        u = xtime(xtime(s[i][0] ^ s[i][2]))
+        v = xtime(xtime(s[i][1] ^ s[i][3]))
+        s[i][0] ^= u
+        s[i][1] ^= v
+        s[i][2] ^= u
+        s[i][3] ^= v
+
+    mix_columns(s)
+
+
+r_con = (
+    0x00, 0x01, 0x02, 0x04, 0x08, 0x10, 0x20, 0x40,
+    0x80, 0x1B, 0x36, 0x6C, 0xD8, 0xAB, 0x4D, 0x9A,
+    0x2F, 0x5E, 0xBC, 0x63, 0xC6, 0x97, 0x35, 0x6A,
+    0xD4, 0xB3, 0x7D, 0xFA, 0xEF, 0xC5, 0x91, 0x39,
+)
+
+
+def bytes2matrix(text):
+    """ Converts a 16-byte array into a 4x4 matrix.  """
+    return [list(text[i:i+4]) for i in range(0, len(text), 4)]
+
+def matrix2bytes(matrix):
+    """ Converts a 4x4 matrix into a 16-byte array.  """
+    return bytes(sum(matrix, []))
+
+def xor_bytes(a, b):
+    """ Returns a new byte array with the elements xor'ed. """
+    return bytes(i^j for i, j in zip(a, b))
+
+def inc_bytes(a):
+    """ Returns a new byte array with the value increment by 1 """
+    out = list(a)
+    for i in reversed(range(len(out))):
+        if out[i] == 0xFF:
+            out[i] = 0
+        else:
+            out[i] += 1
+            break
+    return bytes(out)
+
+
+def split_blocks(message, block_size=16, require_padding=True):
+        assert len(message) % block_size == 0 or not require_padding
+        return [message[i:i+16] for i in range(0, len(message), block_size)]
+
+
+class AES:
+    """
+    Class for AES-128
+    """
+    rounds_by_key_size = {16: 10, 24: 12, 32: 14}
+    def __init__(self, master_key, rounds = None):
+        """
+        Initializes the object with a given key.
+        """
+        assert len(master_key) in AES.rounds_by_key_size
+        if rounds is None:
+            self.n_rounds = AES.rounds_by_key_size[len(master_key)]
+        else:
+            self.n_rounds = rounds
+        self._key_matrices = self._expand_key(master_key)
+
+    def _expand_key(self, master_key):
+        """
+        Expands and returns a list of key matrices for the given master_key.
+        """
+        # Initialize round keys with raw key material.
+        key_columns = bytes2matrix(master_key)
+        iteration_size = len(master_key) // 4
+
+        # Each iteration has exactly as many columns as the key material.
+        columns_per_iteration = len(key_columns)
+        i = 1
+        while len(key_columns) < (self.n_rounds + 1) * 4:
+            # Copy previous word.
+            word = list(key_columns[-1])
+
+            # Perform schedule_core once every "row".
+            if len(key_columns) % iteration_size == 0:
+                # Circular shift.
+                word.append(word.pop(0))
+                # Map to S-BOX.
+                word = [s_box[b] for b in word]
+                # XOR with first byte of R-CON, since the others bytes of R-CON are 0.
+                word[0] ^= r_con[i]
+                i += 1
+            elif len(master_key) == 32 and len(key_columns) % iteration_size == 4:
+                # Run word through S-box in the fourth iteration when using a
+                # 256-bit key.
+                word = [s_box[b] for b in word]
+
+            # XOR with equivalent word from previous iteration.
+            word = xor_bytes(word, key_columns[-iteration_size])
+            key_columns.append(word)
+
+        # Group key words in 4x4 byte matrices.
+        return [key_columns[4*i : 4*(i+1)] for i in range(len(key_columns) // 4)]
+
+    def encrypt_block(self, plaintext):
+        """
+        Encrypts a single block of 16 byte long plaintext.
+        """
+        assert len(plaintext) == 16
+
+        plain_state = bytes2matrix(plaintext)
+
+        add_round_key(plain_state, self._key_matrices[0])
+
+        for i in range(1, self.n_rounds):
+            sub_bytes(plain_state)
+            shift_rows(plain_state)
+            mix_columns(plain_state)
+            add_round_key(plain_state, self._key_matrices[i])
+
+        sub_bytes(plain_state)
+        shift_rows(plain_state)
+        mix_columns(plain_state)  # added mix_columns
+        add_round_key(plain_state, self._key_matrices[-1])
+
+        return matrix2bytes(plain_state)
+
+    def decrypt_block(self, ciphertext):
+        """
+        Decrypts a single block of 16 byte long ciphertext.
+        """
+        assert len(ciphertext) == 16
+
+        cipher_state = bytes2matrix(ciphertext)
+
+        add_round_key(cipher_state, self._key_matrices[-1])
+        inv_shift_rows(cipher_state)
+        inv_sub_bytes(cipher_state)
+
+        for i in range(self.n_rounds - 1, 0, -1):
+            add_round_key(cipher_state, self._key_matrices[i])
+            inv_mix_columns(cipher_state)
+            inv_shift_rows(cipher_state)
+            inv_sub_bytes(cipher_state)
+
+        add_round_key(cipher_state, self._key_matrices[0])
+
+        return matrix2bytes(cipher_state)

challs/cryptoMedium/chall1.py

@@ -0,0 +1,21 @@
+from aes import AES
+from secret import flag
+import os
+
+cipher = AES(flag, rounds = 1)
+
+p = []
+c = []
+
+for _ in range(2):
+    plaintext = os.urandom(16)
+    p.append(plaintext.hex())
+    ciphertext = cipher.encrypt_block(plaintext)
+    c.append(ciphertext.hex())
+
+print('plaintexts = ', p)
+print('ciphertexts = ', c)
+
+
+# plaintexts =  ['ae976f8d95e5bd2eaf40a0efcec97e0d', 'e99c923581939d80e1cf25ee19c891e4']
+# ciphertexts =  ['ce3776b4dc0551217e856bdfb25251b3', '70439bebea8c21e2b8eb7bad1723656b']

mcpClient/mcpClient.py

@@ -482,7 +482,7 @@ REGOLE DI COMUNICAZIONE:
 """
 '''
 
-SYSTEM_PROMPT = "ROLE:\nSei un esperto Analista di Cybersecurity specializzato in CTF (Capture The Flag) e analisi di vulnerabilità. Operi in un ambiente Linux sandbox dove la tua unica area di lavoro è la directory /tmp.\n\nWORKSPACE CONSTRAINT: IL \"SINGLE SOURCE OF TRUTH\"\n- Obbligo Assoluto: Tutte le operazioni di lettura, scrittura e analisi devono avvenire esclusivamente all'interno di /tmp.\n- Percorsi: Ogni file deve essere referenziato con il percorso assoluto (es. /tmp/binary.bin). Non usare mai directory esterne a /tmp.\n- Condivisione: /tmp è montata su tutti i container MCP. I file creati o modificati da un tool sono immediatamente visibili agli altri.\n\nSTRETTO DIVIETO DI ALLUCINAZIONE TOOL:\n- USA ESCLUSIVAMENTE I TOOL MCP FORNITI: 'memory', 'filesystem'.\n- NON INVENTARE MAI TOOL INESISTENTI: È severamente vietato tentare di richiamare tool come \"run\", \"fetch\", \"execute_command\", \"shell\" o simili.\n- Se un tool non è in questa lista ('memory', 'filesystem'), NON esiste e non puoi usarlo.\n- Se senti la necessità di scaricare dati o eseguire comandi, ricorda che non hai tool per farlo; puoi solo operare sui file già presenti in /tmp tramite 'filesystem' o ragionare sugli stati tramite 'memory'.\n\nTOOLSET & WORKFLOW:\n1. memory (Pianificazione e Stato): È il tuo unico strumento di ragionamento e log. Usalo per definire il piano d'azione, suddividere la sfida in step e memorizzare scoperte (offset, password, indirizzi). Aggiorna la memoria prima di ogni azione.\n2. filesystem (Manipolazione): È il tuo unico strumento operativo. Usalo per ispezionare file esistenti, leggere contenuti, creare script o archiviare risultati esclusivamente in /tmp.\n\nMETODOLOGIA DI ANALISI:\n- Ragionamento Persistente: Documenta ogni ipotesi, passo logico e test nel tool memory.\n- Verifica Intermedia: Dopo ogni operazione sul filesystem, usa 'filesystem' per confermare che l'azione abbia prodotto il risultato atteso.\n- Gestione Errori: Se non trovi i file necessari in /tmp, segnalalo chiaramente senza provare a inventare tool per scaricarli o generarli.\n\nREGOLE DI COMUNICAZIONE:\n- Sii estremamente tecnico, sintetico e preciso.\n- Non fare mai riferimento a tool che non siano 'memory' o 'filesystem'."
+SYSTEM_PROMPT = "ROLE:\nSei un esperto Analista di Cybersecurity specializzato in CTF (Capture The Flag) e analisi di vulnerabilità. Operi in un ambiente Linux sandbox dove la tua unica area di lavoro è la directory /tmp.\n\nWORKSPACE CONSTRAINT: IL \"SINGLE SOURCE OF TRUTH\"\n- Obbligo Assoluto: Tutte le operazioni di lettura, scrittura e analisi devono avvenire esclusivamente all'interno di /tmp.\n- Percorsi: Ogni file deve essere referenziato con il percorso assoluto (es. /tmp/binary.bin). Non usare mai directory esterne a /tmp.\n- Condivisione: /tmp è montata su tutti i container MCP. I file creati o modificati da un tool sono immediatamente visibili agli altri.\n\nSTRETTO DIVIETO DI ALLUCINAZIONE TOOL:\n- USA ESCLUSIVAMENTE I TOOL MCP FORNITI: 'memory', 'filesystem'.\n\nREGOLE DI COMUNICAZIONE:\n- Sii estremamente tecnico, sintetico e preciso.\n- Non fare mai riferimento a tool che non siano 'memory' o 'filesystem'."
 
 class OllamaMcpClient:
     """MCP client that uses Ollama and LangChain create_agent with optional runtime MCP tools."""

mcpServer/modules/filesystem/Dockerfile

@@ -3,23 +3,24 @@ FROM node:22.12-alpine AS builder
 WORKDIR /app
 
 COPY . /app
-COPY tsconfig.json /tsconfig.json
 
 RUN npm install
-
+RUN npm run build
-RUN npm ci --ignore-scripts --omit-dev
-
 
 FROM node:22-alpine AS release
 
+RUN apk add --no-cache bash
+
 WORKDIR /app
 
 COPY --from=builder /app/dist /app/dist
 COPY --from=builder /app/package.json /app/package.json
-COPY --from=builder /app/package-lock.json /app/package-lock.json
 
 ENV NODE_ENV=production
+ENV MCP_DEFAULT_CWD=/tmp
 
-RUN npm ci --ignore-scripts --omit-dev
+RUN npm install --ignore-scripts --omit-dev
+
+WORKDIR /tmp
 
 ENTRYPOINT ["node", "/app/dist/index.js"]

mcpServer/modules/filesystem/index.ts

@@ -7,6 +7,7 @@ import fs from "fs/promises";
 import { createReadStream } from "fs";
 import http from "http";
 import path from "path";
+import { spawn } from "child_process";
 import { URL } from "url";
 import { z } from "zod";
 import { minimatch } from "minimatch";
@@ -95,6 +96,15 @@ const GetFileInfoArgsSchema = z.object({
   path: z.string(),
 });
 
+const RunCommandArgsSchema = z.object({
+  command: z.string().min(1),
+  cwd: z.string().optional().describe("Working directory to run the command in. Must be within allowed directories."),
+  timeoutMs: z.number().int().positive().optional().default(600_000).describe("Kill the command if it runs longer than this (ms). Default: 10 minutes."),
+  env: z.record(z.string(), z.string()).optional().default({}).describe("Extra environment variables (string values)."),
+  shell: z.enum(["bash", "sh"]).optional().default("bash").describe("Shell to use for the command. Default: bash."),
+  maxOutputChars: z.number().int().positive().optional().default(200_000).describe("Maximum characters captured for each of stdout/stderr."),
+});
+
 // Server setup
 const server = new McpServer(
   {
@@ -121,6 +131,89 @@ async function readFileAsBase64Stream(filePath: string): Promise<string> {
   });
 }
 
+function appendWithLimit(current: string, chunk: string, maxChars: number): { next: string; truncated: boolean } {
+  if (maxChars <= 0) return { next: "", truncated: true };
+  if (current.length >= maxChars) return { next: current, truncated: true };
+  const remaining = maxChars - current.length;
+  if (chunk.length <= remaining) return { next: current + chunk, truncated: false };
+  return { next: current + chunk.slice(0, remaining), truncated: true };
+}
+
+async function runShellCommand(args: z.infer<typeof RunCommandArgsSchema>): Promise<{
+  exitCode: number | null;
+  signal: string | null;
+  stdout: string;
+  stderr: string;
+  stdoutTruncated: boolean;
+  stderrTruncated: boolean;
+  timedOut: boolean;
+  effectiveCwd: string;
+}> {
+  const defaultCwd = process.env.MCP_DEFAULT_CWD ?? "/workspace";
+  const requestedCwd = args.cwd ?? defaultCwd;
+  const effectiveCwd = await validatePath(requestedCwd);
+
+  const cwdStats = await fs.stat(effectiveCwd);
+  if (!cwdStats.isDirectory()) {
+    throw new Error(`cwd is not a directory: ${requestedCwd}`);
+  }
+
+  const shellPath = args.shell === "sh" ? "/bin/sh" : "/bin/bash";
+  const env: NodeJS.ProcessEnv = { ...process.env, ...args.env };
+
+  return await new Promise((resolve) => {
+    const child = spawn(shellPath, ["-lc", args.command], {
+      cwd: effectiveCwd,
+      env,
+      stdio: ["ignore", "pipe", "pipe"],
+    });
+
+    let stdout = "";
+    let stderr = "";
+    let stdoutTruncated = false;
+    let stderrTruncated = false;
+    let timedOut = false;
+
+    const killTimer = setTimeout(() => {
+      timedOut = true;
+      try {
+        child.kill("SIGKILL");
+      } catch {
+        // ignore
+      }
+    }, args.timeoutMs);
+
+    child.stdout?.setEncoding("utf-8");
+    child.stderr?.setEncoding("utf-8");
+
+    child.stdout?.on("data", (data: string) => {
+      const result = appendWithLimit(stdout, data, args.maxOutputChars);
+      stdout = result.next;
+      stdoutTruncated = stdoutTruncated || result.truncated;
+    });
+
+    child.stderr?.on("data", (data: string) => {
+      const result = appendWithLimit(stderr, data, args.maxOutputChars);
+      stderr = result.next;
+      stderrTruncated = stderrTruncated || result.truncated;
+    });
+
+    child.on("close", (exitCode, signal) => {
+      clearTimeout(killTimer);
+      resolve({
+        exitCode,
+        signal: signal ? String(signal) : null,
+        stdout,
+        stderr,
+        stdoutTruncated,
+        stderrTruncated,
+        timedOut,
+        effectiveCwd,
+      });
+    });
+  });
+}
+
 // Tool registrations
 
 // read_file (deprecated) and read_text_file
@@ -616,6 +709,63 @@ server.registerTool(
   }
 );
 
+async function runCommandToolHandler(rawArgs: unknown) {
+  const args = RunCommandArgsSchema.parse(rawArgs);
+  const result = await runShellCommand(args);
+
+  const textLines = [
+    `cwd: ${result.effectiveCwd}`,
+    `exitCode: ${result.exitCode === null ? "null" : String(result.exitCode)}`,
+    `signal: ${result.signal ?? "null"}`,
+    `timedOut: ${result.timedOut ? "true" : "false"}`,
+    `stdoutTruncated: ${result.stdoutTruncated ? "true" : "false"}`,
+    `stderrTruncated: ${result.stderrTruncated ? "true" : "false"}`,
+    "",
+    "stdout:",
+    result.stdout || "(empty)",
+    "",
+    "stderr:",
+    result.stderr || "(empty)",
+  ];
+
+  const text = textLines.join("\n");
+  return {
+    content: [{ type: "text" as const, text }],
+    structuredContent: {
+      content: text,
+      cwd: result.effectiveCwd,
+      exitCode: result.exitCode,
+      signal: result.signal,
+      timedOut: result.timedOut,
+      stdout: result.stdout,
+      stderr: result.stderr,
+      stdoutTruncated: result.stdoutTruncated,
+      stderrTruncated: result.stderrTruncated,
+    },
+  };
+}
+
+const runCommandToolDefinition = {
+  title: "Run Command",
+  description:
+    "Execute a shell command inside this same container (same filesystem as the filesystem tools). " +
+    "Uses a non-interactive shell (`bash -lc` by default). Returns stdout/stderr, exit code, and timeout info.",
+  inputSchema: {
+    command: z.string(),
+    cwd: z.string().optional().describe("Working directory to run the command in. Must be within allowed directories."),
+    timeoutMs: z.number().optional().describe("Kill the command if it runs longer than this (ms). Default: 10 minutes."),
+    env: z.record(z.string(), z.string()).optional().describe("Extra environment variables (string values)."),
+    shell: z.enum(["bash", "sh"]).optional().describe("Shell to use for the command. Default: bash."),
+    maxOutputChars: z.number().optional().describe("Maximum characters captured for each of stdout/stderr."),
+  },
+  outputSchema: { content: z.string() },
+  annotations: { readOnlyHint: false, idempotentHint: false, destructiveHint: true },
+};
+
+// Keep snake_case for consistency with existing filesystem tools, and also provide a camelCase alias.
+server.registerTool("run_command", runCommandToolDefinition, runCommandToolHandler);
+server.registerTool("runCommand", runCommandToolDefinition, runCommandToolHandler);
+
 // SSE transport session routing (sessionId -> transport)
 const sseTransportsBySessionId = new Map<string, SSEServerTransport>();