Merge pull request #166 from zevorn/fix/agent-defaults-permission-bypass

Author: SihaoLiu

src/config.ts

@@ -2,7 +2,7 @@ import { existsSync, mkdirSync, readFileSync, writeFileSync } from "node:fs";
 import { homedir } from "node:os";
 import { dirname, join } from "node:path";
 
-import type { AgentId } from "./agents/types.js";
+import type { AgentId, PermissionMode, SandboxMode } from "./agents/types.js";
 
 export const DEFAULT_RUN_TIMEOUT_MS = 6 * 60 * 60 * 1000;
 export const DEFAULT_DASHBOARD_THEME: DashboardTheme = "dark";
@@ -12,6 +12,9 @@ export type DashboardTheme = "light" | "dark";
 export interface AgentModelDefaults {
   model?: string;
   reasoningEffort?: string;
+  permissionMode?: PermissionMode;
+  sandbox?: SandboxMode;
+  extraArgs?: string[];
 }
 
 export type AgentModelDefaultsByAgent = Partial<Record<AgentId, AgentModelDefaults>>;
@@ -155,7 +158,7 @@ function parseSimpleYaml(
   const values: Partial<Pick<HumanizeConfig, "cacheDir" | "defaultRunTimeoutMs" | "defaultTheme" | "agentDefaults" | "workflow">> = {
     agentDefaults: {}
   };
-  let section: "agents" | "workflow" | "workflow.softEnforcement" | "workflow.scripts" | "workflow.scripts.allow" | undefined;
+  let section: "agents" | "workflow" | "workflow.softEnforcement" | "workflow.scripts" | "workflow.scripts.allow" | "agents.extraArgs" | undefined;
   let currentAgent: AgentId | undefined;
 
   for (const line of contents.split("\n")) {
@@ -176,6 +179,26 @@ function parseSimpleYaml(
       continue;
     }
 
+    // agent extraArgs list items (e.g., `  - --skip-git-repo-check`)
+    if (section === "agents.extraArgs" && indent >= 6 && currentAgent !== undefined && trimmed.startsWith("- ")) {
+      const item = trimmed.slice(2).trim().replace(/^["']|["']$/g, "");
+      if (item.length > 0) {
+        const defaults = values.agentDefaults?.[currentAgent] ?? {};
+        defaults.extraArgs = [...(defaults.extraArgs ?? []), item];
+        values.agentDefaults = {
+          ...values.agentDefaults,
+          [currentAgent]: defaults
+        };
+      }
+      continue;
+    }
+
+    // extraArgs list is done — reset section so sibling fields (model,
+    // permissionMode, sandbox) under the same agent are not silently ignored
+    if (section === "agents.extraArgs" && indent >= 4 && currentAgent !== undefined && !trimmed.startsWith("- ")) {
+      section = "agents";
+    }
+
     const separatorIndex = trimmed.indexOf(":");
     if (separatorIndex < 0) {
       continue;
@@ -233,8 +256,9 @@ function parseSimpleYaml(
       section = "workflow.scripts.allow";
       continue;
     }
-    if (section === "agents" && indent === 2) {
+    if ((section === "agents" || section === "agents.extraArgs") && indent === 2) {
       currentAgent = key === "codex" || key === "claude" ? key : undefined;
+      section = "agents";
       continue;
     }
     if (section === "agents" && indent >= 4 && currentAgent !== undefined && value.length > 0) {
@@ -245,6 +269,25 @@ function parseSimpleYaml(
       if (key === "reasoningEffort") {
         defaults.reasoningEffort = value;
       }
+      if (key === "permissionMode") {
+        defaults.permissionMode = value as PermissionMode;
+      }
+      if (key === "sandbox") {
+        defaults.sandbox = value as SandboxMode;
+      }
+      values.agentDefaults = {
+        ...values.agentDefaults,
+        [currentAgent]: defaults
+      };
+    }
+    if (section === "agents" && indent >= 4 && currentAgent !== undefined && key === "extraArgs") {
+      const defaults = values.agentDefaults?.[currentAgent] ?? {};
+      if (value === "[]" || value.length === 0) {
+        defaults.extraArgs = [];
+        section = "agents.extraArgs";
+      } else {
+        defaults.extraArgs = parseCommaList(value);
+      }
       values.agentDefaults = {
         ...values.agentDefaults,
         [currentAgent]: defaults
@@ -262,11 +305,13 @@ function mergeAgentDefaults(
   return {
     codex: {
       ...defaults.codex,
-      ...overrides?.codex
+      ...overrides?.codex,
+      extraArgs: overrides?.codex?.extraArgs ?? defaults.codex?.extraArgs
     },
     claude: {
       ...defaults.claude,
-      ...overrides?.claude
+      ...overrides?.claude,
+      extraArgs: overrides?.claude?.extraArgs ?? defaults.claude?.extraArgs
     }
   };
 }

src/hub-server.ts

@@ -30,7 +30,8 @@ async function main(): Promise<void> {
     jsonRpcUrl,
     store,
     initialRuns,
-    defaultRunTimeoutMs: config.defaultRunTimeoutMs
+    defaultRunTimeoutMs: config.defaultRunTimeoutMs,
+    agentDefaults: config.agentDefaults
   });
   const workflowCoordinator = new WorkflowCoordinator(coordinator, {
     store: workflowStore,

src/hub/runs.ts

@@ -147,6 +147,9 @@ export class AgentRunCoordinator {
       ...input,
       model: input.model ?? defaults.model,
       reasoningEffort: input.reasoningEffort ?? defaults.reasoningEffort,
+      permissionMode: input.permissionMode ?? defaults.permissionMode,
+      sandbox: input.sandbox ?? defaults.sandbox,
+      extraArgs: input.extraArgs ?? defaults.extraArgs,
       cwd: input.cwd ?? parentRun?.cwd,
       workflowContext: input.workflowContext ?? inheritedWorkflowContext
     };

tests/config.test.ts

@@ -93,6 +93,69 @@ describe("humanize2 user config", () => {
     expect(config.defaultTheme).toBe("light");
   });
 
+  it("loads agent model fields after a prior agent's multiline extraArgs list", async () => {
+    const home = await tempDirectory();
+    const configPath = join(home, "multiline-extraargs-config.yaml");
+
+    const contents = [
+      "version: 1",
+      "cacheDir: /tmp/humanize2-cache",
+      "defaultRunTimeoutMs: 12345",
+      "defaultTheme: dark",
+      "agents:",
+      "  codex:",
+      "    model: gpt-5.4",
+      "    extraArgs:",
+      "      - --temperature",
+      "      - 0.7",
+      "      - --max-tokens",
+      "      - 4096",
+      "  claude:",
+      "    model: claude-opus-4-7",
+      "    reasoningEffort: xhigh",
+      ""
+    ].join("\n");
+    await writeFile(configPath, contents, "utf8");
+
+    const config = await loadHumanizeConfig({ HUMANIZE2_CONFIG: configPath }, home);
+
+    expect(config.agentDefaults.codex).toMatchObject({
+      model: "gpt-5.4",
+      extraArgs: ["--temperature", "0.7", "--max-tokens", "4096"]
+    });
+    expect(config.agentDefaults.claude).toMatchObject({
+      model: "claude-opus-4-7",
+      reasoningEffort: "xhigh"
+    });
+  });
+
+  it("loads sibling fields after empty extraArgs under the same agent", async () => {
+    const home = await tempDirectory();
+    const configPath = join(home, "sibling-after-extraargs-config.yaml");
+
+    const contents = [
+      "version: 1",
+      "cacheDir: /tmp/humanize2-cache",
+      "defaultRunTimeoutMs: 12345",
+      "defaultTheme: dark",
+      "agents:",
+      "  codex:",
+      "    extraArgs: []",
+      "    model: gpt-5.5",
+      "    reasoningEffort: xhigh",
+      ""
+    ].join("\n");
+    await writeFile(configPath, contents, "utf8");
+
+    const config = await loadHumanizeConfig({ HUMANIZE2_CONFIG: configPath }, home);
+
+    expect(config.agentDefaults.codex).toMatchObject({
+      model: "gpt-5.5",
+      reasoningEffort: "xhigh",
+      extraArgs: []
+    });
+  });
+
   it("loads workflow retry and script allowlist settings from the user config", async () => {
     const home = await tempDirectory();
     const configPath = join(home, "workflow-config.yaml");