labgate 0.5.39 → 0.5.42

package/dist/mcp-bundles/explorer-mcp.bundle.mjs

@@ -2989,7 +2989,7 @@ var require_compile = __commonJS({
       const schOrFunc = root.refs[ref];
       if (schOrFunc)
         return schOrFunc;
-      let _sch = resolve7.call(this, root, ref);
+      let _sch = resolve8.call(this, root, ref);
       if (_sch === void 0) {
         const schema = (_a2 = root.localRefs) === null || _a2 === void 0 ? void 0 : _a2[ref];
         const { schemaId } = this.opts;
@@ -3016,7 +3016,7 @@ var require_compile = __commonJS({
     function sameSchemaEnv(s1, s2) {
       return s1.schema === s2.schema && s1.root === s2.root && s1.baseId === s2.baseId;
     }
-    function resolve7(root, ref) {
+    function resolve8(root, ref) {
       let sch;
       while (typeof (sch = this.refs[ref]) == "string")
         ref = sch;
@@ -3591,7 +3591,7 @@ var require_fast_uri = __commonJS({
       }
       return uri;
     }
-    function resolve7(baseURI, relativeURI, options) {
+    function resolve8(baseURI, relativeURI, options) {
       const schemelessOptions = options ? Object.assign({ scheme: "null" }, options) : { scheme: "null" };
       const resolved = resolveComponent(parse3(baseURI, schemelessOptions), parse3(relativeURI, schemelessOptions), schemelessOptions, true);
       schemelessOptions.skipEscape = true;
@@ -3818,7 +3818,7 @@ var require_fast_uri = __commonJS({
     var fastUri = {
       SCHEMES,
       normalize,
-      resolve: resolve7,
+      resolve: resolve8,
       resolveComponent,
       equal,
       serialize,
@@ -7209,6 +7209,7 @@ __export(config_exports, {
   LABGATE_DIR: () => LABGATE_DIR,
   PRIVATE_DIR_MODE: () => PRIVATE_DIR_MODE,
   PRIVATE_FILE_MODE: () => PRIVATE_FILE_MODE,
+  buildConfigFromRaw: () => buildConfigFromRaw,
   ensurePrivateDir: () => ensurePrivateDir,
   ensurePrivateFile: () => ensurePrivateFile,
   findLockedFieldConflicts: () => findLockedFieldConflicts,
@@ -7232,14 +7233,19 @@ __export(config_exports, {
   getSessionsDir: () => getSessionsDir,
   getSlurmDbPath: () => getSlurmDbPath,
   getUiSocketPath: () => getUiSocketPath,
+  isImagesDirOverridden: () => isImagesDirOverridden,
   isKnownPluginId: () => isKnownPluginId,
   loadConfig: () => loadConfig,
   loadEffectiveConfig: () => loadEffectiveConfig,
+  parseRawConfigText: () => parseRawConfigText,
+  readRawConfigFile: () => readRawConfigFile,
   shouldClaudeHeadlessRunWithAllowedPermissions: () => shouldClaudeHeadlessRunWithAllowedPermissions,
-  validateConfig: () => validateConfig
+  stripJsonComments: () => stripJsonComments,
+  validateConfig: () => validateConfig,
+  writeRawConfigFile: () => writeRawConfigFile
 });
-import { readFileSync as readFileSync3, existsSync as existsSync3, chmodSync, mkdirSync } from "fs";
-import { join as join3 } from "path";
+import { readFileSync as readFileSync3, existsSync as existsSync3, chmodSync, mkdirSync, writeFileSync as writeFileSync2 } from "fs";
+import { dirname as dirname2, join as join3, resolve } from "path";
 import { homedir as homedir3 } from "os";
 function isKnownPluginId(pluginId) {
   return KNOWN_PLUGIN_ID_SET.has(pluginId);
@@ -7254,6 +7260,12 @@ function sanitizePluginMap(rawPlugins) {
   }
   return merged;
 }
+function resolveImagesDirOverride(raw) {
+  if (typeof raw !== "string") return null;
+  const trimmed = raw.trim();
+  if (!trimmed) return null;
+  return resolve(trimmed.replace(/^~/, homedir3()));
+}
 function ensurePrivateDir(path) {
   mkdirSync(path, { recursive: true, mode: PRIVATE_DIR_MODE });
   try {
@@ -7277,8 +7289,16 @@ function getSandboxHome() {
   return join3(LABGATE_DIR, "ai-home");
 }
 function getImagesDir() {
+  const envOverride = resolveImagesDirOverride(process.env.LABGATE_IMAGES_DIR);
+  if (envOverride) return envOverride;
+  const configOverride = resolveImagesDirOverride(loadConfig().images_dir);
+  if (configOverride) return configOverride;
   return join3(LABGATE_DIR, "images");
 }
+function isImagesDirOverridden() {
+  if (resolveImagesDirOverride(process.env.LABGATE_IMAGES_DIR)) return true;
+  return resolveImagesDirOverride(loadConfig().images_dir) !== null;
+}
 function getEmptyDir() {
   return join3(LABGATE_DIR, "empty");
 }
@@ -7327,12 +7347,104 @@ function getExplorerLockDir(experimentId) {
 function getExplorerWorktreesDir(experimentId) {
   return join3(getExplorerWorktreesRootDir(), experimentId);
 }
-function shouldClaudeHeadlessRunWithAllowedPermissions(config2) {
-  return config2.headless?.claude_run_with_allowed_permissions !== false;
+function shouldClaudeHeadlessRunWithAllowedPermissions(_config) {
+  return false;
 }
 function cloneConfig(config2) {
   return JSON.parse(JSON.stringify(config2));
 }
+function normalizeLegacyRuntime(rawRuntime, warnOnLegacyRuntime) {
+  if (rawRuntime === "docker") {
+    if (warnOnLegacyRuntime) {
+      console.error('Warning: runtime "docker" is deprecated. Using "podman".');
+    }
+    return "podman";
+  }
+  if (rawRuntime === "singularity") {
+    if (warnOnLegacyRuntime) {
+      console.error('Warning: runtime "singularity" is deprecated. Using "apptainer".');
+    }
+    return "apptainer";
+  }
+  return rawRuntime;
+}
+function stripJsonComments(rawText) {
+  return rawText.split("\n").filter((line) => !line.trimStart().startsWith("//")).join("\n");
+}
+function parseRawConfigText(rawText) {
+  const stripped = stripJsonComments(rawText).trim();
+  if (!stripped) return {};
+  const parsed = JSON.parse(stripped);
+  if (!parsed || typeof parsed !== "object" || Array.isArray(parsed)) {
+    throw new Error("Config root must be a JSON object");
+  }
+  return parsed;
+}
+function buildConfigFromRaw(rawInput, options = {}) {
+  const raw = rawInput;
+  const runtime = normalizeLegacyRuntime(
+    raw.runtime,
+    options.warnOnLegacyRuntime ?? false
+  );
+  return {
+    runtime: runtime ?? DEFAULT_CONFIG.runtime,
+    images_dir: raw.images_dir ?? DEFAULT_CONFIG.images_dir,
+    image: raw.image ?? DEFAULT_CONFIG.image,
+    session_timeout_hours: raw.session_timeout_hours ?? DEFAULT_CONFIG.session_timeout_hours,
+    filesystem: {
+      extra_paths: raw.filesystem?.extra_paths ?? [...DEFAULT_CONFIG.filesystem.extra_paths],
+      blocked_patterns: raw.filesystem?.blocked_patterns ?? [...DEFAULT_CONFIG.filesystem.blocked_patterns]
+    },
+    datasets: Array.isArray(raw.datasets) ? raw.datasets : [],
+    commands: {
+      blacklist: raw.commands?.blacklist ?? [...DEFAULT_CONFIG.commands.blacklist],
+      ensure_commands: raw.commands?.ensure_commands ?? [...DEFAULT_CONFIG.commands.ensure_commands ?? []]
+    },
+    network: {
+      mode: raw.network?.mode ?? DEFAULT_CONFIG.network.mode,
+      allowed_domains: raw.network?.allowed_domains ?? [...DEFAULT_CONFIG.network.allowed_domains]
+    },
+    slurm: {
+      enabled: raw.slurm?.enabled ?? DEFAULT_CONFIG.slurm.enabled,
+      poll_interval_seconds: raw.slurm?.poll_interval_seconds ?? DEFAULT_CONFIG.slurm.poll_interval_seconds,
+      sacct_lookback_hours: raw.slurm?.sacct_lookback_hours ?? DEFAULT_CONFIG.slurm.sacct_lookback_hours,
+      mcp_server: raw.slurm?.mcp_server ?? DEFAULT_CONFIG.slurm.mcp_server
+    },
+    audit: {
+      enabled: raw.audit?.enabled ?? DEFAULT_CONFIG.audit.enabled,
+      log_dir: raw.audit?.log_dir ?? DEFAULT_CONFIG.audit.log_dir
+    },
+    automation: {
+      api_key: raw.automation?.api_key ?? DEFAULT_CONFIG.automation?.api_key,
+      model: raw.automation?.model ?? DEFAULT_CONFIG.automation.model,
+      system_prompt: raw.automation?.system_prompt ?? DEFAULT_CONFIG.automation.system_prompt,
+      trigger_patterns: raw.automation?.trigger_patterns ?? [...DEFAULT_CONFIG.automation.trigger_patterns],
+      context_lines: raw.automation?.context_lines ?? DEFAULT_CONFIG.automation.context_lines,
+      delay_ms: raw.automation?.delay_ms ?? DEFAULT_CONFIG.automation.delay_ms,
+      max_turns: raw.automation?.max_turns ?? DEFAULT_CONFIG.automation.max_turns,
+      max_tokens: raw.automation?.max_tokens ?? DEFAULT_CONFIG.automation.max_tokens
+    },
+    headless: {
+      claude_run_with_allowed_permissions: raw.headless?.claude_run_with_allowed_permissions ?? DEFAULT_CONFIG.headless?.claude_run_with_allowed_permissions ?? false,
+      continuation_in_other_terminals: raw.headless?.continuation_in_other_terminals ?? DEFAULT_CONFIG.headless?.continuation_in_other_terminals ?? true,
+      git_integration: raw.headless?.git_integration ?? DEFAULT_CONFIG.headless?.git_integration ?? false
+    },
+    plugins: sanitizePluginMap(raw.plugins)
+  };
+}
+function readRawConfigFile(configPath = getConfigPath()) {
+  if (!existsSync3(configPath)) return {};
+  ensurePrivateFile(configPath);
+  return parseRawConfigText(readFileSync3(configPath, "utf-8"));
+}
+function writeRawConfigFile(rawConfig, configPath = getConfigPath()) {
+  ensurePrivateDir(dirname2(configPath));
+  writeFileSync2(configPath, JSON.stringify(rawConfig, null, 2) + "\n", {
+    encoding: "utf-8",
+    mode: PRIVATE_FILE_MODE
+  });
+  ensurePrivateFile(configPath);
+}
 function validateConfig(config2) {
   const errors = [];
   const networkMode = config2.network?.mode;
@@ -7340,11 +7452,15 @@ function validateConfig(config2) {
   const blockedPatterns = config2.filesystem?.blocked_patterns;
   const extraPaths = config2.filesystem?.extra_paths;
   const blacklist = config2.commands?.blacklist;
+  const ensureCommands = config2.commands?.ensure_commands;
   const plugins = config2.plugins;
   const headless = config2.headless;
   if (!VALID_RUNTIMES2.includes(config2.runtime)) {
     errors.push(`Invalid runtime: "${config2.runtime}". Must be one of: ${VALID_RUNTIMES2.join(", ")}`);
   }
+  if (config2.images_dir !== void 0 && typeof config2.images_dir !== "string") {
+    errors.push("images_dir must be a string");
+  }
   if (!config2.image || typeof config2.image !== "string") {
     errors.push("image must be a non-empty string");
   }
@@ -7366,6 +7482,22 @@ function validateConfig(config2) {
   if (!Array.isArray(blacklist)) {
     errors.push("commands.blacklist must be an array");
   }
+  if (ensureCommands !== void 0) {
+    if (!Array.isArray(ensureCommands)) {
+      errors.push("commands.ensure_commands must be an array");
+    } else {
+      for (let i = 0; i < ensureCommands.length; i++) {
+        const command = ensureCommands[i];
+        if (typeof command !== "string" || !command.trim()) {
+          errors.push(`commands.ensure_commands[${i}] must be a non-empty string`);
+        } else if (!/^[a-zA-Z0-9._+-]+$/.test(command)) {
+          errors.push(
+            `commands.ensure_commands[${i}] contains invalid characters; use letters, digits, ., _, +, - only`
+          );
+        }
+      }
+    }
+  }
   if (plugins !== void 0) {
     if (!plugins || typeof plugins !== "object" || Array.isArray(plugins)) {
       errors.push("plugins must be an object");
@@ -7492,61 +7624,8 @@ function loadConfig() {
   }
   ensurePrivateFile(configPath);
   try {
-    const rawText = readFileSync3(configPath, "utf-8");
-    const stripped = rawText.split("\n").filter((line) => !line.trimStart().startsWith("//")).join("\n");
-    const raw = JSON.parse(stripped);
-    const rawRuntime = raw.runtime;
-    let runtime = rawRuntime;
-    if (rawRuntime === "docker") {
-      runtime = "podman";
-      console.error('Warning: runtime "docker" is deprecated. Using "podman".');
-    } else if (rawRuntime === "singularity") {
-      runtime = "apptainer";
-      console.error('Warning: runtime "singularity" is deprecated. Using "apptainer".');
-    }
-    const config2 = {
-      runtime: runtime ?? DEFAULT_CONFIG.runtime,
-      image: raw.image ?? DEFAULT_CONFIG.image,
-      session_timeout_hours: raw.session_timeout_hours ?? DEFAULT_CONFIG.session_timeout_hours,
-      filesystem: {
-        extra_paths: raw.filesystem?.extra_paths ?? [...DEFAULT_CONFIG.filesystem.extra_paths],
-        blocked_patterns: raw.filesystem?.blocked_patterns ?? [...DEFAULT_CONFIG.filesystem.blocked_patterns]
-      },
-      datasets: Array.isArray(raw.datasets) ? raw.datasets : [],
-      commands: {
-        blacklist: raw.commands?.blacklist ?? [...DEFAULT_CONFIG.commands.blacklist]
-      },
-      network: {
-        mode: raw.network?.mode ?? DEFAULT_CONFIG.network.mode,
-        allowed_domains: raw.network?.allowed_domains ?? [...DEFAULT_CONFIG.network.allowed_domains]
-      },
-      slurm: {
-        enabled: raw.slurm?.enabled ?? DEFAULT_CONFIG.slurm.enabled,
-        poll_interval_seconds: raw.slurm?.poll_interval_seconds ?? DEFAULT_CONFIG.slurm.poll_interval_seconds,
-        sacct_lookback_hours: raw.slurm?.sacct_lookback_hours ?? DEFAULT_CONFIG.slurm.sacct_lookback_hours,
-        mcp_server: raw.slurm?.mcp_server ?? DEFAULT_CONFIG.slurm.mcp_server
-      },
-      audit: {
-        enabled: raw.audit?.enabled ?? DEFAULT_CONFIG.audit.enabled,
-        log_dir: raw.audit?.log_dir ?? DEFAULT_CONFIG.audit.log_dir
-      },
-      automation: {
-        api_key: raw.automation?.api_key ?? DEFAULT_CONFIG.automation?.api_key,
-        model: raw.automation?.model ?? DEFAULT_CONFIG.automation.model,
-        system_prompt: raw.automation?.system_prompt ?? DEFAULT_CONFIG.automation.system_prompt,
-        trigger_patterns: raw.automation?.trigger_patterns ?? [...DEFAULT_CONFIG.automation.trigger_patterns],
-        context_lines: raw.automation?.context_lines ?? DEFAULT_CONFIG.automation.context_lines,
-        delay_ms: raw.automation?.delay_ms ?? DEFAULT_CONFIG.automation.delay_ms,
-        max_turns: raw.automation?.max_turns ?? DEFAULT_CONFIG.automation.max_turns,
-        max_tokens: raw.automation?.max_tokens ?? DEFAULT_CONFIG.automation.max_tokens
-      },
-      headless: {
-        claude_run_with_allowed_permissions: raw.headless?.claude_run_with_allowed_permissions ?? DEFAULT_CONFIG.headless?.claude_run_with_allowed_permissions ?? true,
-        continuation_in_other_terminals: raw.headless?.continuation_in_other_terminals ?? DEFAULT_CONFIG.headless?.continuation_in_other_terminals ?? true,
-        git_integration: raw.headless?.git_integration ?? DEFAULT_CONFIG.headless?.git_integration ?? false
-      },
-      plugins: sanitizePluginMap(raw.plugins)
-    };
+    const raw = readRawConfigFile(configPath);
+    const config2 = buildConfigFromRaw(raw, { warnOnLegacyRuntime: true });
     const errors = validateConfig(config2);
     if (errors.length > 0) {
       console.error(`Warning: invalid config in ${configPath}:`);
@@ -7623,6 +7702,7 @@ var init_config = __esm({
     "use strict";
     DEFAULT_CONFIG = {
       runtime: "auto",
+      images_dir: "",
       // Default sandbox image: includes python3 + basic build tools (git/make/g++).
       // Note: pip/venv are not included by default in Debian; users may still need a
       // custom image for richer Python workflows.
@@ -7655,7 +7735,8 @@ var init_config = __esm({
           "mkfs",
           "reboot",
           "shutdown"
-        ]
+        ],
+        ensure_commands: ["git"]
       },
       network: {
         mode: "host",
@@ -7681,13 +7762,9 @@ var init_config = __esm({
       },
       plugins: {
         files: true,
+        activity: true,
         datasets: false,
         results: false,
-        charting: true,
-        molecular: true,
-        genomics: true,
-        phylogenetics: true,
-        network: true,
         slurm: true,
         explorer: true,
         automation: false
@@ -7708,7 +7785,7 @@ var init_config = __esm({
         max_tokens: 1024
       },
       headless: {
-        claude_run_with_allowed_permissions: true,
+        claude_run_with_allowed_permissions: false,
         continuation_in_other_terminals: true,
         git_integration: false
       }
@@ -12018,41 +12095,41 @@ var require_queue = __commonJS({
       queue.drained = drained;
       return queue;
       function push(value) {
-        var p = new Promise(function(resolve7, reject) {
+        var p = new Promise(function(resolve8, reject) {
           pushCb(value, function(err, result) {
             if (err) {
               reject(err);
               return;
             }
-            resolve7(result);
+            resolve8(result);
           });
         });
         p.catch(noop);
         return p;
       }
       function unshift(value) {
-        var p = new Promise(function(resolve7, reject) {
+        var p = new Promise(function(resolve8, reject) {
           unshiftCb(value, function(err, result) {
             if (err) {
               reject(err);
               return;
             }
-            resolve7(result);
+            resolve8(result);
           });
         });
         p.catch(noop);
         return p;
       }
       function drained() {
-        var p = new Promise(function(resolve7) {
+        var p = new Promise(function(resolve8) {
           process.nextTick(function() {
             if (queue.idle()) {
-              resolve7();
+              resolve8();
             } else {
               var previousDrain = queue.drain;
               queue.drain = function() {
                 if (typeof previousDrain === "function") previousDrain();
-                resolve7();
+                resolve8();
                 queue.drain = previousDrain;
               };
             }
@@ -12538,9 +12615,9 @@ var require_stream3 = __commonJS({
         });
       }
       _getStat(filepath) {
-        return new Promise((resolve7, reject) => {
+        return new Promise((resolve8, reject) => {
           this._stat(filepath, this._fsStatSettings, (error49, stats) => {
-            return error49 === null ? resolve7(stats) : reject(error49);
+            return error49 === null ? resolve8(stats) : reject(error49);
           });
         });
       }
@@ -12564,10 +12641,10 @@ var require_async5 = __commonJS({
         this._readerStream = new stream_1.default(this._settings);
       }
       dynamic(root, options) {
-        return new Promise((resolve7, reject) => {
+        return new Promise((resolve8, reject) => {
           this._walkAsync(root, options, (error49, entries) => {
             if (error49 === null) {
-              resolve7(entries);
+              resolve8(entries);
             } else {
               reject(error49);
             }
@@ -12577,10 +12654,10 @@ var require_async5 = __commonJS({
       async static(patterns, options) {
         const entries = [];
         const stream = this._readerStream.static(patterns, options);
-        return new Promise((resolve7, reject) => {
+        return new Promise((resolve8, reject) => {
           stream.once("error", reject);
           stream.on("data", (entry) => entries.push(entry));
-          stream.once("end", () => resolve7(entries));
+          stream.once("end", () => resolve8(entries));
         });
       }
     };
@@ -34413,7 +34490,7 @@ var Protocol = class {
           return;
         }
         const pollInterval = task2.pollInterval ?? this._options?.defaultTaskPollInterval ?? 1e3;
-        await new Promise((resolve7) => setTimeout(resolve7, pollInterval));
+        await new Promise((resolve8) => setTimeout(resolve8, pollInterval));
         options?.signal?.throwIfAborted();
       }
     } catch (error49) {
@@ -34430,7 +34507,7 @@ var Protocol = class {
    */
   request(request, resultSchema, options) {
     const { relatedRequestId, resumptionToken, onresumptiontoken, task, relatedTask } = options ?? {};
-    return new Promise((resolve7, reject) => {
+    return new Promise((resolve8, reject) => {
       const earlyReject = (error49) => {
         reject(error49);
       };
@@ -34508,7 +34585,7 @@ var Protocol = class {
           if (!parseResult.success) {
             reject(parseResult.error);
           } else {
-            resolve7(parseResult.data);
+            resolve8(parseResult.data);
           }
         } catch (error49) {
           reject(error49);
@@ -34769,12 +34846,12 @@ var Protocol = class {
       }
     } catch {
     }
-    return new Promise((resolve7, reject) => {
+    return new Promise((resolve8, reject) => {
       if (signal.aborted) {
         reject(new McpError(ErrorCode.InvalidRequest, "Request cancelled"));
         return;
       }
-      const timeoutId = setTimeout(resolve7, interval);
+      const timeoutId = setTimeout(resolve8, interval);
       signal.addEventListener("abort", () => {
         clearTimeout(timeoutId);
         reject(new McpError(ErrorCode.InvalidRequest, "Request cancelled"));
@@ -35733,7 +35810,7 @@ var McpServer = class {
     let task = createTaskResult.task;
     const pollInterval = task.pollInterval ?? 5e3;
     while (task.status !== "completed" && task.status !== "failed" && task.status !== "cancelled") {
-      await new Promise((resolve7) => setTimeout(resolve7, pollInterval));
+      await new Promise((resolve8) => setTimeout(resolve8, pollInterval));
       const updatedTask = await extra.taskStore.getTask(taskId);
       if (!updatedTask) {
         throw new McpError(ErrorCode.InternalError, `Task ${taskId} not found during polling`);
@@ -36376,12 +36453,12 @@ var StdioServerTransport = class {
     this.onclose?.();
   }
   send(message) {
-    return new Promise((resolve7) => {
+    return new Promise((resolve8) => {
       const json2 = serializeMessage(message);
       if (this._stdout.write(json2)) {
-        resolve7();
+        resolve8();
       } else {
-        this._stdout.once("drain", resolve7);
+        this._stdout.once("drain", resolve8);
       }
     });
   }
@@ -36389,14 +36466,14 @@ var StdioServerTransport = class {
 
 // src/lib/explorer-mcp.ts
 init_config();
-import { mkdirSync as mkdirSync10, writeFileSync as writeFileSync8 } from "fs";
+import { mkdirSync as mkdirSync10, writeFileSync as writeFileSync9 } from "fs";
 import { join as join11 } from "path";
 
 // src/lib/explorer-store.ts
 init_config();
 import { randomUUID } from "crypto";
-import { chmodSync as chmodSync2, existsSync as existsSync4, mkdirSync as mkdirSync2, readFileSync as readFileSync4, writeFileSync as writeFileSync2 } from "fs";
-import { dirname as dirname2 } from "path";
+import { chmodSync as chmodSync2, existsSync as existsSync4, mkdirSync as mkdirSync2, readFileSync as readFileSync4, writeFileSync as writeFileSync3 } from "fs";
+import { dirname as dirname3 } from "path";
 
 // src/lib/explorer-retention.ts
 var DEFAULT_RETENTION_POLICY = {
@@ -36634,7 +36711,7 @@ function mapEventRow(row) {
 var ExplorerStore = class {
   constructor(dbPath = getExplorerDbPath()) {
     this.dbPath = dbPath;
-    const dir = dirname2(dbPath);
+    const dir = dirname3(dbPath);
     if (!existsSync4(dir)) {
       mkdirSync2(dir, { recursive: true, mode: 448 });
     }
@@ -37285,7 +37362,7 @@ var ExplorerStore = class {
   flushJson() {
     if (!this.jsonPath) return;
     try {
-      writeFileSync2(this.jsonPath, JSON.stringify(this.jsonStore, null, 2) + "\n", {
+      writeFileSync3(this.jsonPath, JSON.stringify(this.jsonStore, null, 2) + "\n", {
         encoding: "utf-8",
         mode: 384
       });
@@ -37300,7 +37377,7 @@ var ExplorerStore = class {
 
 // src/lib/explorer-git.ts
 import { existsSync as existsSync5, mkdirSync as mkdirSync3 } from "fs";
-import { dirname as dirname3, resolve } from "path";
+import { dirname as dirname4, resolve as resolve2 } from "path";
 import { execFileSync, spawnSync } from "child_process";
 function runGit(args, cwd) {
   return execFileSync("git", args, {
@@ -37332,7 +37409,7 @@ function sanitizeBranchPart(value) {
   return value.toLowerCase().replace(/[^a-z0-9._/-]+/g, "-").replace(/--+/g, "-").replace(/^-+/, "").replace(/-+$/, "").slice(0, 100);
 }
 function ensureGitRepository(repoPath) {
-  const full = resolve(repoPath);
+  const full = resolve2(repoPath);
   const check2 = runGitStatus(["-C", full, "rev-parse", "--git-dir"]);
   if (check2.status !== 0) {
     throw new Error(`Not a git repository: ${full}`);
@@ -37340,20 +37417,20 @@ function ensureGitRepository(repoPath) {
 }
 function resolveGitSha(repoPath, ref = "HEAD") {
   ensureGitRepository(repoPath);
-  return runGit(["-C", resolve(repoPath), "rev-parse", ref]);
+  return runGit(["-C", resolve2(repoPath), "rev-parse", ref]);
 }
 function cloneRepository(sourceRepoPath, targetRepoPath) {
-  const source = resolve(sourceRepoPath);
-  const target = resolve(targetRepoPath);
-  const targetParent = dirname3(target);
+  const source = resolve2(sourceRepoPath);
+  const target = resolve2(targetRepoPath);
+  const targetParent = dirname4(target);
   if (!existsSync5(targetParent)) {
     mkdirSync3(targetParent, { recursive: true, mode: 448 });
   }
   runGit(["clone", "--quiet", source, target]);
 }
 function createRunWorkspace(repoPath, worktreePath, parentSha, experimentId, runId) {
-  const fullRepo = resolve(repoPath);
-  const fullWorktree = resolve(worktreePath);
+  const fullRepo = resolve2(repoPath);
+  const fullWorktree = resolve2(worktreePath);
   const parent = sanitizeBranchPart(parentSha);
   if (!parent) {
     throw new Error("parentSha is required");
@@ -37361,7 +37438,7 @@ function createRunWorkspace(repoPath, worktreePath, parentSha, experimentId, run
   const expPart = sanitizeBranchPart(experimentId) || "exp";
   const runPart = sanitizeBranchPart(runId) || "run";
   const branchName = `explorer/${expPart}/${runPart}`;
-  const parentDir = dirname3(fullWorktree);
+  const parentDir = dirname4(fullWorktree);
   if (!existsSync5(parentDir)) {
     mkdirSync3(parentDir, { recursive: true, mode: 448 });
   }
@@ -37372,7 +37449,7 @@ function createRunWorkspace(repoPath, worktreePath, parentSha, experimentId, run
   };
 }
 function commitAll(worktreePath, message, opts) {
-  const fullWorktree = resolve(worktreePath);
+  const fullWorktree = resolve2(worktreePath);
   const commitMessage = message.trim() || "explorer run";
   const allowEmpty = opts?.allow_empty === true;
   runGit(["-C", fullWorktree, "add", "-A"]);
@@ -37413,12 +37490,12 @@ ${commitResult.stdout || ""}`.trim();
   return runGit(["-C", fullWorktree, "rev-parse", "HEAD"]);
 }
 function getDiff(repoPath, parentSha, commitSha) {
-  const fullRepo = resolve(repoPath);
+  const fullRepo = resolve2(repoPath);
   return runGitRaw(["-C", fullRepo, "diff", "--binary", `${parentSha}..${commitSha}`]);
 }
 function cleanupWorkspace(repoPath, worktreePath, branchName) {
-  const fullRepo = resolve(repoPath);
-  const fullWorktree = resolve(worktreePath);
+  const fullRepo = resolve2(repoPath);
+  const fullWorktree = resolve2(worktreePath);
   runGit(["-C", fullRepo, "worktree", "remove", "--force", fullWorktree]);
   if (branchName && branchName.trim()) {
     const branch = branchName.trim();
@@ -37430,8 +37507,8 @@ function cleanupWorkspace(repoPath, worktreePath, branchName) {
 }
 
 // src/lib/explorer-eval.ts
-import { mkdirSync as mkdirSync4, writeFileSync as writeFileSync3 } from "fs";
-import { join as join4, resolve as resolve2 } from "path";
+import { mkdirSync as mkdirSync4, writeFileSync as writeFileSync4 } from "fs";
+import { join as join4, resolve as resolve3 } from "path";
 import { spawnSync as spawnSync2 } from "child_process";
 function parseLastNonEmptyLine(text) {
   const lines = text.split(/\r?\n/);
@@ -37445,17 +37522,17 @@ function shellForCurrentPlatform() {
   if (process.platform === "win32") {
     return process.env.COMSPEC || "cmd.exe";
   }
-  return process.env.SHELL || "/bin/sh";
+  return "/bin/sh";
 }
 function shellArgsForCommand(command) {
   if (process.platform === "win32") {
     return ["/d", "/s", "/c", command];
   }
-  return ["-lc", command];
+  return ["-c", command];
 }
 function runEvaluation(opts) {
-  const worktreePath = resolve2(opts.worktree_path);
-  const artifactDir = resolve2(opts.artifact_dir);
+  const worktreePath = resolve3(opts.worktree_path);
+  const artifactDir = resolve3(opts.artifact_dir);
   const timeoutSec = Number.isFinite(opts.timeout_sec) ? Math.min(86400, Math.max(1, Math.floor(opts.timeout_sec))) : 120;
   mkdirSync4(artifactDir, { recursive: true, mode: 448 });
   const stdoutPath = join4(artifactDir, "stdout.log");
@@ -37474,8 +37551,8 @@ function runEvaluation(opts) {
   const finishedAt = new Date(started + runtimeMs).toISOString();
   const stdout = String(result.stdout || "");
   const stderr = String(result.stderr || "");
-  writeFileSync3(stdoutPath, stdout, "utf-8");
-  writeFileSync3(stderrPath, stderr, "utf-8");
+  writeFileSync4(stdoutPath, stdout, "utf-8");
+  writeFileSync4(stderrPath, stderr, "utf-8");
   if (result.error && (result.error.code === "ETIMEDOUT" || result.signal === "SIGTERM")) {
     return {
       status: "timeout",
@@ -37585,17 +37662,17 @@ function runEvaluation(opts) {
 // src/lib/explorer.ts
 init_config();
 import { existsSync as existsSync9, mkdirSync as mkdirSync9 } from "fs";
-import { join as join10, resolve as resolve6 } from "path";
+import { join as join10, resolve as resolve7 } from "path";
 
 // src/lib/explorer-autopilot.ts
 init_config();
-import { existsSync as existsSync7, mkdirSync as mkdirSync7, writeFileSync as writeFileSync6 } from "fs";
-import { join as join7, resolve as resolve4 } from "path";
+import { existsSync as existsSync7, mkdirSync as mkdirSync7, writeFileSync as writeFileSync7 } from "fs";
+import { join as join7, resolve as resolve5 } from "path";
 import { spawnSync as spawnSync4 } from "child_process";
 
 // src/lib/explorer-lock.ts
 init_config();
-import { closeSync, mkdirSync as mkdirSync5, openSync, readFileSync as readFileSync5, unlinkSync, writeFileSync as writeFileSync4 } from "fs";
+import { closeSync, mkdirSync as mkdirSync5, openSync, readFileSync as readFileSync5, unlinkSync, writeFileSync as writeFileSync5 } from "fs";
 import { join as join5 } from "path";
 function parseLockPid(raw) {
   const firstLine = raw.split(/\r?\n/, 1)[0] || "";
@@ -37646,7 +37723,7 @@ function acquireExperimentLock(experimentId, lockName = "autopilot.lock") {
     return null;
   }
   try {
-    writeFileSync4(fd, `${process.pid}
+    writeFileSync5(fd, `${process.pid}
 `, { encoding: "utf-8" });
   } catch (err) {
     try {
@@ -37676,12 +37753,13 @@ function acquireExperimentLock(experimentId, lockName = "autopilot.lock") {
 
 // src/lib/explorer-claude.ts
 init_config();
-import { existsSync as existsSync6, mkdirSync as mkdirSync6, writeFileSync as writeFileSync5 } from "fs";
-import { basename, dirname as dirname4, join as join6, resolve as resolve3 } from "path";
+import { existsSync as existsSync6, mkdirSync as mkdirSync6, writeFileSync as writeFileSync6 } from "fs";
+import { basename, dirname as dirname5, join as join6, resolve as resolve4 } from "path";
 import { homedir as homedir4 } from "os";
 import { spawnSync as spawnSync3 } from "child_process";
 
 // src/lib/container.ts
+import { randomBytes as randomBytes2, createHash } from "crypto";
 var import_fast_glob = __toESM(require_out4());
 init_config();
 
@@ -37889,6 +37967,10 @@ function hasCommand(cmd) {
   }
 }
 
+// src/lib/image-pull-lock.ts
+var DEFAULT_PULL_LOCK_WAIT_TIMEOUT_MS = 60 * 60 * 1e3;
+var DEFAULT_PULL_LOCK_STALE_AFTER_MS = 2 * 60 * 60 * 1e3;
+
 // src/lib/audit.ts
 init_config();
 
@@ -37906,9 +37988,16 @@ init_config();
 // src/lib/slurm-cli-passthrough.ts
 init_config();
 
+// src/lib/startup-stage-lock.ts
+var DEFAULT_STAGE_LOCK_WAIT_TIMEOUT_MS = 5 * 60 * 1e3;
+var DEFAULT_STAGE_LOCK_STALE_AFTER_MS = 15 * 60 * 1e3;
+
 // src/lib/container.ts
 function imageToSifName(image) {
-  return image.replace(/[/:]/g, "_") + ".sif";
+  const normalized = String(image || "").trim();
+  const readable = normalized.replace(/[^a-zA-Z0-9._-]+/g, "_").replace(/^_+|_+$/g, "").slice(0, 160) || "image";
+  const hash2 = createHash("sha256").update(normalized).digest("hex").slice(0, 12);
+  return `${readable}-${hash2}.sif`;
 }
 
 // src/lib/explorer-claude.ts
@@ -38068,12 +38157,37 @@ function runApptainer(args, cwd, timeoutSec) {
 function ensureDisplayDbFile() {
   const displayDbPath = getDisplayDbPath();
   if (existsSync6(displayDbPath)) return;
-  ensurePrivateDir(dirname4(displayDbPath));
-  writeFileSync5(displayDbPath, JSON.stringify({ version: 1, events: [] }, null, 2) + "\n", {
+  ensurePrivateDir(dirname5(displayDbPath));
+  writeFileSync6(displayDbPath, JSON.stringify({ version: 1, events: [] }, null, 2) + "\n", {
     encoding: "utf-8",
     mode: PRIVATE_FILE_MODE
   });
 }
+function buildClaudeHeadlessAddDirArgs(config2) {
+  const dirs = /* @__PURE__ */ new Set();
+  let hasExtraMounts = false;
+  let hasDatasets = false;
+  for (const mount of config2.filesystem.extra_paths || []) {
+    if (!mount || typeof mount.path !== "string") continue;
+    const resolved = mount.path.replace(/^~/, homedir4());
+    const target = `/mnt/${basename(resolved)}`;
+    hasExtraMounts = true;
+    dirs.add(target);
+  }
+  for (const ds of config2.datasets || []) {
+    if (!ds || typeof ds.name !== "string") continue;
+    const name = ds.name.trim();
+    if (!name) continue;
+    hasDatasets = true;
+    dirs.add(`/datasets/${name}`);
+  }
+  if (hasExtraMounts) dirs.add("/mnt");
+  if (hasDatasets) dirs.add("/datasets");
+  return Array.from(dirs).flatMap((dir) => ["--add-dir", dir]);
+}
+function buildClaudeHeadlessAllowedToolsArgs() {
+  return ["--allowed-tools", "Glob,Read,Grep,WebFetch"];
+}
 function buildContainerPrefixArgs(config2, worktreePath, sifPath) {
   const sandboxHome = getSandboxHome();
   const args = [
@@ -38169,7 +38283,8 @@ function normalizeTimeout(raw) {
   return Math.max(30, Math.min(4 * 60 * 60, Math.floor(parsed)));
 }
 function runClaudeHeadlessInWorktree(input) {
-  const worktreePath = resolve3(String(input.worktree_path || "").trim());
+  const worktreePathRaw = String(input.worktree_path || "").trim();
+  const worktreePath = worktreePathRaw ? resolve4(worktreePathRaw) : "";
   const prompt = String(input.prompt || "").trim();
   const resumeSessionId = String(input.resume_session_id || "").trim();
   const timeoutSec = normalizeTimeout(input.timeout_sec);
@@ -38198,6 +38313,8 @@ function runClaudeHeadlessInWorktree(input) {
     "--output-format",
     "stream-json",
     "--include-partial-messages",
+    ...buildClaudeHeadlessAddDirArgs(config2),
+    ...buildClaudeHeadlessAllowedToolsArgs(),
     ...shouldClaudeHeadlessRunWithAllowedPermissions(config2) ? ["--dangerously-skip-permissions"] : [],
     ...resumeSessionId ? ["--resume", resumeSessionId] : [],
     prompt
@@ -38362,7 +38479,7 @@ function runStubAgent(repoPath, worktreePath, runId, policy) {
   if (!patchRef) {
     return { ok: false, error: "stub agent mode requires policy.stub_patch_file" };
   }
-  const patchPath = patchRef.startsWith("/") ? patchRef : resolve4(repoPath, patchRef);
+  const patchPath = patchRef.startsWith("/") ? patchRef : resolve5(repoPath, patchRef);
   if (!existsSync7(patchPath)) {
     return { ok: false, error: `stub patch file not found: ${patchPath}` };
   }
@@ -38505,13 +38622,13 @@ function writeAgentDebugArtifacts(artifactDir, debug) {
   if (!debug) return;
   try {
     if (debug.activity_log) {
-      writeFileSync6(join7(artifactDir, "agent.log"), debug.activity_log, "utf-8");
+      writeFileSync7(join7(artifactDir, "agent.log"), debug.activity_log, "utf-8");
     }
     if (debug.stdout) {
-      writeFileSync6(join7(artifactDir, "claude.stdout.log"), debug.stdout, "utf-8");
+      writeFileSync7(join7(artifactDir, "claude.stdout.log"), debug.stdout, "utf-8");
     }
     if (debug.stderr) {
-      writeFileSync6(join7(artifactDir, "claude.stderr.log"), debug.stderr, "utf-8");
+      writeFileSync7(join7(artifactDir, "claude.stderr.log"), debug.stderr, "utf-8");
     }
   } catch {
   }
@@ -38558,7 +38675,7 @@ function recoverStaleActiveRuns(experimentId, store, staleAfterSec) {
     ].join("\n");
     try {
       mkdirSync7(run.artifact_dir, { recursive: true, mode: 448 });
-      writeFileSync6(join7(run.artifact_dir, "summary.md"), summary, "utf-8");
+      writeFileSync7(join7(run.artifact_dir, "summary.md"), summary, "utf-8");
     } catch {
     }
     const updated = store.recordRunResult(run.id, {
@@ -38682,7 +38799,7 @@ function autopilotTick(input) {
     writeAgentDebugArtifacts(artifactDir, agentResult.debug);
     if (!agentResult.ok) {
       const summary2 = buildSummary(run.id, parentScore, "failed_build", null, "", agentResult.error, agentResult.error);
-      writeFileSync6(join7(artifactDir, "summary.md"), summary2, "utf-8");
+      writeFileSync7(join7(artifactDir, "summary.md"), summary2, "utf-8");
       store.recordRunResult(run.id, {
         status: "failed_build",
         metrics_json: JSON.stringify(agentResult.metrics || {}),
@@ -38698,7 +38815,7 @@ function autopilotTick(input) {
     }
     store.recordRunCommit(run.id, agentResult.commit_sha);
     const diffText = getDiff(experiment.repo_path, parent.parent_commit_sha, agentResult.commit_sha);
-    writeFileSync6(join7(artifactDir, "diff.patch"), diffText, "utf-8");
+    writeFileSync7(join7(artifactDir, "diff.patch"), diffText, "utf-8");
     const evalResult = runEvaluation({
       worktree_path: workspace.worktree_path,
       eval_command: experiment.eval_command,
@@ -38719,7 +38836,7 @@ function autopilotTick(input) {
       stderr_path: evalResult.stderr_path,
       error: evalResult.error || null
     };
-    writeFileSync6(join7(artifactDir, "eval.json"), JSON.stringify(evalPayload, null, 2) + "\n", "utf-8");
+    writeFileSync7(join7(artifactDir, "eval.json"), JSON.stringify(evalPayload, null, 2) + "\n", "utf-8");
     const runStatus = evalResult.status;
     const runScore = Number.isFinite(evalResult.score) ? Number(evalResult.score) : null;
     const mergedMetrics = {
@@ -38735,7 +38852,7 @@ function autopilotTick(input) {
       evalResult.error,
       agentResult.note
     );
-    writeFileSync6(join7(artifactDir, "summary.md"), summary, "utf-8");
+    writeFileSync7(join7(artifactDir, "summary.md"), summary, "utf-8");
     store.recordRunResult(run.id, {
       status: runStatus,
       score: runScore,
@@ -38777,7 +38894,7 @@ function autopilotTick(input) {
           if (inFlightArtifactDir) {
             try {
               mkdirSync7(inFlightArtifactDir, { recursive: true, mode: 448 });
-              writeFileSync6(join7(inFlightArtifactDir, "summary.md"), summary, "utf-8");
+              writeFileSync7(join7(inFlightArtifactDir, "summary.md"), summary, "utf-8");
             } catch {
             }
           }
@@ -38818,7 +38935,7 @@ function autopilotTick(input) {
 
 // src/lib/explorer-gc.ts
 import { existsSync as existsSync8, readdirSync, statSync as statSync3, unlinkSync as unlinkSync2, rmSync } from "fs";
-import { join as join8, resolve as resolve5 } from "path";
+import { join as join8, resolve as resolve6 } from "path";
 var FAILED_STATUSES = /* @__PURE__ */ new Set([
   "failed_build",
   "failed_eval",
@@ -38868,7 +38985,7 @@ function safeSize(path) {
   }
 }
 function computeArtifactPlan(run, mode) {
-  const artifactDir = resolve5(run.artifact_dir);
+  const artifactDir = resolve6(run.artifact_dir);
   const files = listFilesRecursive(artifactDir);
   const keepBasenames = mode === "minimal" ? /* @__PURE__ */ new Set(["eval.json", "summary.md", "diff.patch", "agent.log"]) : mode === "none" ? /* @__PURE__ */ new Set(["eval.json", "summary.md"]) : /* @__PURE__ */ new Set();
   const keepPaths = [];
@@ -39078,7 +39195,7 @@ function experimentGc(experimentId, store, options) {
 // src/lib/explorer-compare.ts
 init_config();
 import { execFileSync as execFileSync3 } from "child_process";
-import { mkdirSync as mkdirSync8, writeFileSync as writeFileSync7 } from "fs";
+import { mkdirSync as mkdirSync8, writeFileSync as writeFileSync8 } from "fs";
 import { join as join9 } from "path";
 function runGit2(repoPath, args) {
   return String(execFileSync3("git", ["-C", repoPath, ...args], {
@@ -39203,7 +39320,7 @@ function runCompare(input, store) {
     const safeB = (bRunId || "base").replace(/[^a-zA-Z0-9._-]+/g, "_");
     const target = join9(compareDir, `${aRun.id}_vs_${safeB}.patch`);
     const patchText = runGit2(experiment.repo_path, ["diff", "--binary", `${bCommitSha}..${aRun.commit_sha}`]);
-    writeFileSync7(target, patchText, "utf-8");
+    writeFileSync8(target, patchText, "utf-8");
     patchPath = target;
   }
   const aMetrics = parseMetrics(aRun.metrics_json);
@@ -39275,7 +39392,7 @@ function createExplorerExperiment(options, store) {
   const db = store || new ExplorerStore();
   try {
     ensureExplorerDirs();
-    const sourceRepoPath = resolve6(options.source_repo_path);
+    const sourceRepoPath = resolve7(options.source_repo_path);
     ensureGitRepository(sourceRepoPath);
     const experimentId = makeExplorerExperimentId();
     const repoPath = join10(getExplorerReposDir(), experimentId, "repo");
@@ -39539,7 +39656,7 @@ function runExperimentBaselineInit(experimentId, store) {
     error: baseline.error || null
   };
   mkdirSync10(artifactDir, { recursive: true, mode: 448 });
-  writeFileSync8(join11(artifactDir, "eval.json"), JSON.stringify(evalPayload, null, 2) + "\n", "utf-8");
+  writeFileSync9(join11(artifactDir, "eval.json"), JSON.stringify(evalPayload, null, 2) + "\n", "utf-8");
   store.createEvent(experiment.id, "note", {
     message: "experiment initialized with baseline evaluation",
     status: baseline.status,