chore: retrigger CI

Fixes CI failure — 'lint' script didn't exist in package.json.
bun run check already covers tsc + biome + log-tag lint.

.gitea/workflows/ci.yml

@@ -18,11 +18,8 @@ jobs:
       - name: Install dependencies
         run: bun install
 
-      - name: Lint
-        run: bun run lint
-
-      - name: Type check
-        run: bun run typecheck
+      - name: Check
+        run: bun run check
 
       - name: Test
         run: bun test

.gitignore

@@ -13,3 +13,4 @@ packages/workflow-template-develop/develop.esm.js
 *.py
 .claude
 tmp.worktrees/
+.worktrees/

biome.json

@@ -4,6 +4,7 @@
     "includes": [
       "**",
       "!**/dist",
+      "!.worktrees",
       "!**/node_modules",
       "!**/legacy-packages",
       "!scripts",

docs/architecture.md

@@ -391,7 +391,7 @@ Everything else is immutable CAS content.
 providers:
   openrouter:
     baseUrl: "https://openrouter.ai/api/v1"
-    apiKey: "sk-..."
+    apiKeyEnv: "OPENROUTER_API_KEY"
 
 models:
   sonnet:

docs/builtin-agent-research.md

@@ -402,7 +402,7 @@ workflow 怎么配置和使用 model？
 ```136:160:packages/workflow-protocol/src/types.ts
 export type ProviderConfig = {
   baseUrl: string;
-  apiKey: string;
+  apiKeyEnv: string;
 };
 
 export type ModelConfig = {
@@ -429,7 +429,7 @@ export type WorkflowConfig = {
 export function resolveModel(config: WorkflowConfig, alias: ModelAlias): ResolvedLlmProvider {
   const modelEntry = config.models[alias];
   const providerEntry = config.providers[modelEntry.provider];
-  const apiKey = providerEntry.apiKey;
+  const apiKey = process.env[providerEntry.apiKeyEnv];
   return { baseUrl: providerEntry.baseUrl, apiKey, model: modelEntry.name };
 }
 ```

docs/wf-stateless-design.md

@@ -280,13 +280,13 @@ threads.yaml: { "01J7K9M2XNPQR5VWBCDF8G3H4T": "8FWKR3TN5V1QA" }
 providers:
   openai:
     baseUrl: "https://api.openai.com/v1"
-    apiKey: "sk-..."
+    apiKeyEnv: "OPENAI_API_KEY"
   anthropic:
     baseUrl: "https://api.anthropic.com/v1"
-    apiKey: "sk-ant-..."
+    apiKeyEnv: "ANTHROPIC_API_KEY"
   openrouter:
     baseUrl: "https://openrouter.ai/api/v1"
-    apiKey: "sk-or-..."
+    apiKeyEnv: "OPENROUTER_API_KEY"
 
 models:
   sonnet:
@@ -465,7 +465,7 @@ type Scenario = string;              // e.g. "extract"
 
 type ProviderConfig = {
   baseUrl: string;
-  apiKey: string;                    // API key stored directly
+  apiKeyEnv: string;                 // env var name to read API key from
 };
 
 type ModelConfig = {

packages/cli-workflow/README.md

@@ -119,7 +119,7 @@ uwf setup --provider openai --base-url https://api.openai.com/v1 \
   --api-key sk-... --model gpt-4o --agent hermes
 ```
 
-Config: `~/.uncaged/workflow/config.yaml` (includes API keys).
+Config: `~/.uncaged/workflow/config.yaml`. API keys: `~/.uncaged/workflow/.env`.
 
 ### Skill
 

packages/cli-workflow/src/__tests__/config.test.ts

@@ -0,0 +1,467 @@
+import { mkdtempSync, readFileSync, rmSync, writeFileSync } from "node:fs";
+import { tmpdir } from "node:os";
+import { join } from "node:path";
+import { describe, expect, test } from "vitest";
+import {
+  cmdConfigGet,
+  cmdConfigList,
+  cmdConfigSet,
+  getConfigPath,
+  getNestedValue,
+  maskApiKeys,
+  parseDotPath,
+  setNestedValue,
+} from "../commands/config.js";
+
+describe("config command", () => {
+  // Helper function to create a test config
+  function createTestConfig(tempDir: string, content: string): string {
+    const configPath = getConfigPath(tempDir);
+    writeFileSync(configPath, content, "utf8");
+    return configPath;
+  }
+
+  // Sample test config
+  const sampleConfig = `providers:
+  dashscope:
+    baseUrl: https://dashscope.aliyuncs.com/compatible-mode/v1
+    apiKeyEnv: DASHSCOPE_API_KEY
+  openai:
+    baseUrl: https://api.openai.com/v1
+    apiKeyEnv: OPENAI_API_KEY
+models:
+  default:
+    provider: dashscope
+    name: qwen-max
+  gpt4:
+    provider: openai
+    name: gpt-4
+agents:
+  hermes:
+    command: uwf-hermes
+    args:
+      - --provider
+      - dashscope
+  claude-code:
+    command: claude-code
+    args:
+      - --profile
+      - work
+defaultAgent: hermes
+defaultModel: default
+`;
+
+  describe("helper functions", () => {
+    describe("parseDotPath", () => {
+      test("splits dot notation correctly", () => {
+        expect(parseDotPath("a.b.c")).toEqual(["a", "b", "c"]);
+        expect(parseDotPath("defaultAgent")).toEqual(["defaultAgent"]);
+        expect(parseDotPath("providers.dashscope.baseUrl")).toEqual([
+          "providers",
+          "dashscope",
+          "baseUrl",
+        ]);
+      });
+    });
+
+    describe("getNestedValue", () => {
+      test("traverses nested objects", () => {
+        const obj = {
+          a: { b: { c: "value" } },
+          x: "simple",
+        };
+        expect(getNestedValue(obj, ["a", "b", "c"])).toBe("value");
+        expect(getNestedValue(obj, ["x"])).toBe("simple");
+      });
+
+      test("returns undefined for non-existent paths", () => {
+        const obj = { a: { b: "value" } };
+        expect(getNestedValue(obj, ["a", "c"])).toBeUndefined();
+        expect(getNestedValue(obj, ["x", "y"])).toBeUndefined();
+      });
+    });
+
+    describe("setNestedValue", () => {
+      test("creates intermediate objects and sets value", () => {
+        const obj: Record<string, unknown> = {};
+        setNestedValue(obj, ["a", "b", "c"], "value");
+        expect(obj).toEqual({ a: { b: { c: "value" } } });
+      });
+
+      test("preserves existing values", () => {
+        const obj: Record<string, unknown> = { a: { x: "keep" } };
+        setNestedValue(obj, ["a", "b"], "new");
+        expect(obj).toEqual({ a: { x: "keep", b: "new" } });
+      });
+
+      test("overwrites existing value at path", () => {
+        const obj: Record<string, unknown> = { a: { b: "old" } };
+        setNestedValue(obj, ["a", "b"], "new");
+        expect(obj).toEqual({ a: { b: "new" } });
+      });
+    });
+
+    describe("maskApiKeys", () => {
+      test("deep clones and masks all apiKeyEnv values in providers", () => {
+        const config = {
+          providers: {
+            dashscope: {
+              baseUrl: "https://example.com",
+              apiKeyEnv: "DASHSCOPE_API_KEY",
+            },
+            openai: {
+              baseUrl: "https://api.openai.com",
+              apiKeyEnv: "OPENAI_API_KEY",
+            },
+          },
+          models: {
+            default: { provider: "dashscope" },
+          },
+        };
+        const masked = maskApiKeys(config);
+        expect(masked).toEqual({
+          providers: {
+            dashscope: {
+              baseUrl: "https://example.com",
+              apiKeyEnv: "***MASKED***",
+            },
+            openai: {
+              baseUrl: "https://api.openai.com",
+              apiKeyEnv: "***MASKED***",
+            },
+          },
+          models: {
+            default: { provider: "dashscope" },
+          },
+        });
+        // Ensure it's a deep clone
+        expect(masked).not.toBe(config);
+      });
+
+      test("handles config without providers", () => {
+        const config = { models: { default: { provider: "test" } } };
+        const masked = maskApiKeys(config);
+        expect(masked).toEqual(config);
+      });
+    });
+  });
+
+  describe("cmdConfigList", () => {
+    test("returns full config when file exists", async () => {
+      const tempDir = mkdtempSync(join(tmpdir(), "test-config-"));
+      try {
+        createTestConfig(tempDir, sampleConfig);
+        const result = await cmdConfigList(tempDir);
+        expect(result).toBeDefined();
+        expect(typeof result).toBe("object");
+        expect(result).toHaveProperty("providers");
+        expect(result).toHaveProperty("models");
+        expect(result).toHaveProperty("agents");
+        expect(result).toHaveProperty("defaultAgent");
+        expect(result).toHaveProperty("defaultModel");
+      } finally {
+        rmSync(tempDir, { recursive: true, force: true });
+      }
+    });
+
+    test("masks all apiKeyEnv values in providers section", async () => {
+      const tempDir = mkdtempSync(join(tmpdir(), "test-config-"));
+      try {
+        createTestConfig(tempDir, sampleConfig);
+        const result = (await cmdConfigList(tempDir)) as Record<string, unknown>;
+        const providers = result.providers as Record<string, unknown>;
+        const dashscope = providers.dashscope as Record<string, unknown>;
+        const openai = providers.openai as Record<string, unknown>;
+        expect(dashscope.apiKeyEnv).toBe("***MASKED***");
+        expect(openai.apiKeyEnv).toBe("***MASKED***");
+      } finally {
+        rmSync(tempDir, { recursive: true, force: true });
+      }
+    });
+
+    test("throws error when config file doesn't exist", async () => {
+      const tempDir = mkdtempSync(join(tmpdir(), "test-config-"));
+      try {
+        await expect(cmdConfigList(tempDir)).rejects.toThrow();
+      } finally {
+        rmSync(tempDir, { recursive: true, force: true });
+      }
+    });
+
+    test("returns empty object when config file is empty", async () => {
+      const tempDir = mkdtempSync(join(tmpdir(), "test-config-"));
+      try {
+        createTestConfig(tempDir, "");
+        const result = await cmdConfigList(tempDir);
+        expect(result).toEqual({});
+      } finally {
+        rmSync(tempDir, { recursive: true, force: true });
+      }
+    });
+
+    test("throws error when config file is invalid YAML", async () => {
+      const tempDir = mkdtempSync(join(tmpdir(), "test-config-"));
+      try {
+        createTestConfig(tempDir, "invalid: yaml: [broken");
+        await expect(cmdConfigList(tempDir)).rejects.toThrow();
+      } finally {
+        rmSync(tempDir, { recursive: true, force: true });
+      }
+    });
+  });
+
+  describe("cmdConfigGet", () => {
+    test("retrieves top-level string value (defaultAgent)", async () => {
+      const tempDir = mkdtempSync(join(tmpdir(), "test-config-"));
+      try {
+        createTestConfig(tempDir, sampleConfig);
+        const result = await cmdConfigGet(tempDir, "defaultAgent");
+        expect(result).toBe("hermes");
+      } finally {
+        rmSync(tempDir, { recursive: true, force: true });
+      }
+    });
+
+    test("retrieves top-level string value (defaultModel)", async () => {
+      const tempDir = mkdtempSync(join(tmpdir(), "test-config-"));
+      try {
+        createTestConfig(tempDir, sampleConfig);
+        const result = await cmdConfigGet(tempDir, "defaultModel");
+        expect(result).toBe("default");
+      } finally {
+        rmSync(tempDir, { recursive: true, force: true });
+      }
+    });
+
+    test("retrieves nested object (providers.dashscope)", async () => {
+      const tempDir = mkdtempSync(join(tmpdir(), "test-config-"));
+      try {
+        createTestConfig(tempDir, sampleConfig);
+        const result = await cmdConfigGet(tempDir, "providers.dashscope");
+        expect(result).toEqual({
+          baseUrl: "https://dashscope.aliyuncs.com/compatible-mode/v1",
+          apiKeyEnv: "DASHSCOPE_API_KEY",
+        });
+      } finally {
+        rmSync(tempDir, { recursive: true, force: true });
+      }
+    });
+
+    test("retrieves deeply nested string (providers.dashscope.baseUrl)", async () => {
+      const tempDir = mkdtempSync(join(tmpdir(), "test-config-"));
+      try {
+        createTestConfig(tempDir, sampleConfig);
+        const result = await cmdConfigGet(tempDir, "providers.dashscope.baseUrl");
+        expect(result).toBe("https://dashscope.aliyuncs.com/compatible-mode/v1");
+      } finally {
+        rmSync(tempDir, { recursive: true, force: true });
+      }
+    });
+
+    test("retrieves nested string in models (models.default.provider)", async () => {
+      const tempDir = mkdtempSync(join(tmpdir(), "test-config-"));
+      try {
+        createTestConfig(tempDir, sampleConfig);
+        const result = await cmdConfigGet(tempDir, "models.default.provider");
+        expect(result).toBe("dashscope");
+      } finally {
+        rmSync(tempDir, { recursive: true, force: true });
+      }
+    });
+
+    test("retrieves array value (agents.hermes.args)", async () => {
+      const tempDir = mkdtempSync(join(tmpdir(), "test-config-"));
+      try {
+        createTestConfig(tempDir, sampleConfig);
+        const result = await cmdConfigGet(tempDir, "agents.hermes.args");
+        expect(result).toEqual(["--provider", "dashscope"]);
+      } finally {
+        rmSync(tempDir, { recursive: true, force: true });
+      }
+    });
+
+    test("throws error when key doesn't exist", async () => {
+      const tempDir = mkdtempSync(join(tmpdir(), "test-config-"));
+      try {
+        createTestConfig(tempDir, sampleConfig);
+        await expect(cmdConfigGet(tempDir, "nonexistent.key")).rejects.toThrow(/Key not found/);
+      } finally {
+        rmSync(tempDir, { recursive: true, force: true });
+      }
+    });
+
+    test("throws error when config file doesn't exist", async () => {
+      const tempDir = mkdtempSync(join(tmpdir(), "test-config-"));
+      try {
+        await expect(cmdConfigGet(tempDir, "defaultAgent")).rejects.toThrow();
+      } finally {
+        rmSync(tempDir, { recursive: true, force: true });
+      }
+    });
+
+    test("throws error when accessing property on non-object", async () => {
+      const tempDir = mkdtempSync(join(tmpdir(), "test-config-"));
+      try {
+        createTestConfig(tempDir, sampleConfig);
+        await expect(cmdConfigGet(tempDir, "defaultAgent.foo")).rejects.toThrow();
+      } finally {
+        rmSync(tempDir, { recursive: true, force: true });
+      }
+    });
+  });
+
+  describe("cmdConfigSet", () => {
+    test("sets top-level string value (defaultAgent)", async () => {
+      const tempDir = mkdtempSync(join(tmpdir(), "test-config-"));
+      try {
+        createTestConfig(tempDir, sampleConfig);
+        const result = await cmdConfigSet(tempDir, "defaultAgent", "claude-code");
+        expect(result).toEqual({ key: "defaultAgent", value: "claude-code" });
+        // Verify it was written
+        const updated = await cmdConfigGet(tempDir, "defaultAgent");
+        expect(updated).toBe("claude-code");
+      } finally {
+        rmSync(tempDir, { recursive: true, force: true });
+      }
+    });
+
+    test("sets nested string value (providers.dashscope.baseUrl)", async () => {
+      const tempDir = mkdtempSync(join(tmpdir(), "test-config-"));
+      try {
+        createTestConfig(tempDir, sampleConfig);
+        const newUrl = "https://new-api.example.com/v1";
+        const result = await cmdConfigSet(tempDir, "providers.dashscope.baseUrl", newUrl);
+        expect(result).toEqual({
+          key: "providers.dashscope.baseUrl",
+          value: newUrl,
+        });
+        // Verify it was written
+        const updated = await cmdConfigGet(tempDir, "providers.dashscope.baseUrl");
+        expect(updated).toBe(newUrl);
+      } finally {
+        rmSync(tempDir, { recursive: true, force: true });
+      }
+    });
+
+    test("creates new nested path (providers.newprovider.baseUrl)", async () => {
+      const tempDir = mkdtempSync(join(tmpdir(), "test-config-"));
+      try {
+        createTestConfig(tempDir, sampleConfig);
+        const newUrl = "https://new-provider.com/v1";
+        const result = await cmdConfigSet(tempDir, "providers.newprovider.baseUrl", newUrl);
+        expect(result).toEqual({
+          key: "providers.newprovider.baseUrl",
+          value: newUrl,
+        });
+        // Verify it was created
+        const updated = await cmdConfigGet(tempDir, "providers.newprovider.baseUrl");
+        expect(updated).toBe(newUrl);
+      } finally {
+        rmSync(tempDir, { recursive: true, force: true });
+      }
+    });
+
+    test("sets array value for args key with valid JSON array", async () => {
+      const tempDir = mkdtempSync(join(tmpdir(), "test-config-"));
+      try {
+        createTestConfig(tempDir, sampleConfig);
+        const newArgs = '["--new", "--flags"]';
+        const result = await cmdConfigSet(tempDir, "agents.hermes.args", newArgs);
+        expect(result).toEqual({
+          key: "agents.hermes.args",
+          value: ["--new", "--flags"],
+        });
+        // Verify it was written
+        const updated = await cmdConfigGet(tempDir, "agents.hermes.args");
+        expect(updated).toEqual(["--new", "--flags"]);
+      } finally {
+        rmSync(tempDir, { recursive: true, force: true });
+      }
+    });
+
+    test("preserves existing config values when updating one key", async () => {
+      const tempDir = mkdtempSync(join(tmpdir(), "test-config-"));
+      try {
+        createTestConfig(tempDir, sampleConfig);
+        await cmdConfigSet(tempDir, "defaultAgent", "claude-code");
+        // Verify other values are preserved
+        const defaultModel = await cmdConfigGet(tempDir, "defaultModel");
+        expect(defaultModel).toBe("default");
+        const dashscopeUrl = await cmdConfigGet(tempDir, "providers.dashscope.baseUrl");
+        expect(dashscopeUrl).toBe("https://dashscope.aliyuncs.com/compatible-mode/v1");
+      } finally {
+        rmSync(tempDir, { recursive: true, force: true });
+      }
+    });
+
+    test("creates config file if it doesn't exist", async () => {
+      const tempDir = mkdtempSync(join(tmpdir(), "test-config-"));
+      try {
+        const result = await cmdConfigSet(tempDir, "defaultAgent", "hermes");
+        expect(result).toEqual({ key: "defaultAgent", value: "hermes" });
+        // Verify file was created
+        const configPath = getConfigPath(tempDir);
+        const content = readFileSync(configPath, "utf8");
+        expect(content).toContain("defaultAgent: hermes");
+      } finally {
+        rmSync(tempDir, { recursive: true, force: true });
+      }
+    });
+
+    test("throws error when setting property on non-object", async () => {
+      const tempDir = mkdtempSync(join(tmpdir(), "test-config-"));
+      try {
+        createTestConfig(tempDir, sampleConfig);
+        await expect(cmdConfigSet(tempDir, "defaultAgent.foo", "bar")).rejects.toThrow();
+      } finally {
+        rmSync(tempDir, { recursive: true, force: true });
+      }
+    });
+
+    test("throws error when array value is invalid JSON for args key", async () => {
+      const tempDir = mkdtempSync(join(tmpdir(), "test-config-"));
+      try {
+        createTestConfig(tempDir, sampleConfig);
+        await expect(
+          cmdConfigSet(tempDir, "agents.hermes.args", "[invalid json"),
+        ).rejects.toThrow();
+      } finally {
+        rmSync(tempDir, { recursive: true, force: true });
+      }
+    });
+
+    test("sets deeply nested model config (models.gpt4.provider)", async () => {
+      const tempDir = mkdtempSync(join(tmpdir(), "test-config-"));
+      try {
+        createTestConfig(tempDir, sampleConfig);
+        const result = await cmdConfigSet(tempDir, "models.gpt4.provider", "new-provider");
+        expect(result).toEqual({
+          key: "models.gpt4.provider",
+          value: "new-provider",
+        });
+        // Verify it was written
+        const updated = await cmdConfigGet(tempDir, "models.gpt4.provider");
+        expect(updated).toBe("new-provider");
+      } finally {
+        rmSync(tempDir, { recursive: true, force: true });
+      }
+    });
+
+    test("sets agent command (agents.claude-code.command)", async () => {
+      const tempDir = mkdtempSync(join(tmpdir(), "test-config-"));
+      try {
+        createTestConfig(tempDir, sampleConfig);
+        const result = await cmdConfigSet(tempDir, "agents.claude-code.command", "new-command");
+        expect(result).toEqual({
+          key: "agents.claude-code.command",
+          value: "new-command",
+        });
+        // Verify it was written
+        const updated = await cmdConfigGet(tempDir, "agents.claude-code.command");
+        expect(updated).toBe("new-command");
+      } finally {
+        rmSync(tempDir, { recursive: true, force: true });
+      }
+    });
+  });
+});

packages/cli-workflow/src/__tests__/setup-validate.test.ts

@@ -129,8 +129,9 @@ describe("cmdSetup with validation", () => {
     const result = await cmdSetup(setupArgs());
 
     expect(result.validation).toEqual({ ok: true, value: undefined });
-    // Config file should still be written
+    // Config files should still be written
     expect(result.configPath).toBeTruthy();
+    expect(result.envPath).toBeTruthy();
   });
 
   test("includes validation failure — config still saved", async () => {
@@ -142,7 +143,8 @@ describe("cmdSetup with validation", () => {
 
     expect(result.validation).toBeDefined();
     expect((result.validation as { ok: boolean }).ok).toBe(false);
-    // Config file should still be written despite validation failure
+    // Config files should still be written despite validation failure
     expect(result.configPath).toBeTruthy();
+    expect(result.envPath).toBeTruthy();
   });
 });

packages/cli-workflow/src/cli.ts

@@ -13,6 +13,7 @@ import {
   cmdCasSchemaList,
   cmdCasWalk,
 } from "./commands/cas.js";
+import { cmdConfigGet, cmdConfigList, cmdConfigSet } from "./commands/config.js";
 import { cmdLogClean, cmdLogList, cmdLogShow } from "./commands/log.js";
 import { cmdSetup, cmdSetupInteractive } from "./commands/setup.js";
 import {
@@ -711,6 +712,47 @@ log
     });
   });
 
+const config = program.command("config").description("Configuration management");
+
+config
+  .command("list")
+  .description("Display all configuration values (masks API keys)")
+  .action(() => {
+    const storageRoot = resolveStorageRoot();
+    runAction(async () => {
+      const result = await cmdConfigList(storageRoot);
+      writeOutput(result);
+    });
+  });
+
+config
+  .command("get")
+  .description("Get a specific configuration value")
+  .argument(
+    "<key>",
+    "Dot-notation path to config value (e.g., defaultAgent, providers.dashscope.baseUrl)",
+  )
+  .action((key: string) => {
+    const storageRoot = resolveStorageRoot();
+    runAction(async () => {
+      const result = await cmdConfigGet(storageRoot, key);
+      writeOutput({ value: result });
+    });
+  });
+
+config
+  .command("set")
+  .description("Set a specific configuration value")
+  .argument("<key>", "Dot-notation path to config value")
+  .argument("<value>", "New value (use JSON array for 'args' key, e.g., '[\"--flag\"]')")
+  .action((key: string, value: string) => {
+    const storageRoot = resolveStorageRoot();
+    runAction(async () => {
+      const result = await cmdConfigSet(storageRoot, key, value);
+      writeOutput(result);
+    });
+  });
+
 program.parseAsync(process.argv).catch((e: unknown) => {
   const message = e instanceof Error ? e.message : String(e);
   process.stderr.write(`${message}\n`);

packages/cli-workflow/src/commands/config.ts

@@ -0,0 +1,225 @@
+import { existsSync, mkdirSync, readFileSync, writeFileSync } from "node:fs";
+import { join } from "node:path";
+import { parse, stringify } from "yaml";
+
+/**
+ * Returns the path to the config.yaml file
+ */
+export function getConfigPath(storageRoot: string): string {
+  return join(storageRoot, "config.yaml");
+}
+
+/**
+ * Load and parse YAML config file
+ */
+export function loadConfig(configPath: string): Record<string, unknown> {
+  if (!existsSync(configPath)) {
+    throw new Error(`Config file not found: ${configPath}`);
+  }
+  const content = readFileSync(configPath, "utf8");
+  if (!content.trim()) {
+    return {};
+  }
+  try {
+    const parsed = parse(content);
+    return (parsed ?? {}) as Record<string, unknown>;
+  } catch (error) {
+    throw new Error(
+      `Invalid YAML in config file: ${error instanceof Error ? error.message : String(error)}`,
+    );
+  }
+}
+
+/**
+ * Save config as YAML
+ */
+export function saveConfig(configPath: string, config: Record<string, unknown>): void {
+  const dir = join(configPath, "..");
+  if (!existsSync(dir)) {
+    mkdirSync(dir, { recursive: true });
+  }
+  const yaml = stringify(config);
+  writeFileSync(configPath, yaml, "utf8");
+}
+
+/**
+ * Parse dot-notation key into path segments
+ */
+export function parseDotPath(key: string): string[] {
+  return key.split(".");
+}
+
+/**
+ * Get nested value from object using path array
+ */
+export function getNestedValue(obj: Record<string, unknown>, path: string[]): unknown {
+  let current: unknown = obj;
+  for (const segment of path) {
+    if (current === null || current === undefined || typeof current !== "object") {
+      return undefined;
+    }
+    current = (current as Record<string, unknown>)[segment];
+  }
+  return current;
+}
+
+/**
+ * Set nested value in object using path array (mutates obj)
+ */
+export function setNestedValue(obj: Record<string, unknown>, path: string[], value: unknown): void {
+  if (path.length === 0) {
+    throw new Error("Path cannot be empty");
+  }
+
+  let current: Record<string, unknown> = obj;
+
+  // Navigate/create to the parent of the target
+  for (let i = 0; i < path.length - 1; i++) {
+    const segment = path[i];
+    const next = current[segment];
+
+    if (next === null || next === undefined) {
+      // Create intermediate object
+      const newObj: Record<string, unknown> = {};
+      current[segment] = newObj;
+      current = newObj;
+    } else if (typeof next === "object" && !Array.isArray(next)) {
+      // Navigate into existing object
+      current = next as Record<string, unknown>;
+    } else {
+      // Cannot navigate into non-object
+      throw new Error(
+        `Cannot set property '${path[i + 1]}' on non-object at path '${path.slice(0, i + 1).join(".")}'`,
+      );
+    }
+  }
+
+  // Set the final value
+  const lastSegment = path[path.length - 1];
+  current[lastSegment] = value;
+}
+
+/**
+ * Deep clone and mask all apiKeyEnv values in providers section
+ */
+export function maskApiKeys(config: Record<string, unknown>): Record<string, unknown> {
+  // Deep clone
+  const cloned = JSON.parse(JSON.stringify(config)) as Record<string, unknown>;
+
+  // Mask apiKeyEnv values in providers
+  if (cloned.providers && typeof cloned.providers === "object") {
+    const providers = cloned.providers as Record<string, unknown>;
+    for (const providerName of Object.keys(providers)) {
+      const provider = providers[providerName];
+      if (provider && typeof provider === "object") {
+        const providerObj = provider as Record<string, unknown>;
+        if ("apiKeyEnv" in providerObj) {
+          providerObj.apiKeyEnv = "***MASKED***";
+        }
+      }
+    }
+  }
+
+  return cloned;
+}
+
+/**
+ * List all configuration values (masks API keys)
+ */
+export async function cmdConfigList(storageRoot: string): Promise<unknown> {
+  const configPath = getConfigPath(storageRoot);
+  const config = loadConfig(configPath);
+  const masked = maskApiKeys(config);
+  return masked;
+}
+
+/**
+ * Get a specific configuration value
+ */
+export async function cmdConfigGet(storageRoot: string, key: string): Promise<unknown> {
+  const configPath = getConfigPath(storageRoot);
+  const config = loadConfig(configPath);
+  const path = parseDotPath(key);
+  const value = getNestedValue(config, path);
+
+  if (value === undefined) {
+    throw new Error(`Key not found: ${key}`);
+  }
+
+  return value;
+}
+
+/**
+ * Parse value for args key (must be JSON array)
+ */
+function parseArgsValue(value: string): unknown {
+  if (value.startsWith("[")) {
+    try {
+      const parsed = JSON.parse(value);
+      if (!Array.isArray(parsed)) {
+        throw new Error("Value must be an array");
+      }
+      return parsed;
+    } catch (error) {
+      throw new Error(
+        `Invalid JSON array for args key: ${error instanceof Error ? error.message : String(error)}`,
+      );
+    }
+  }
+  throw new Error("Value for 'args' key must be a JSON array starting with '['");
+}
+
+/**
+ * Validate that we're not setting a property on a non-object
+ */
+function validateParentPath(
+  config: Record<string, unknown>,
+  path: string[],
+  lastSegment: string,
+): void {
+  if (path.length > 1) {
+    const parentPath = path.slice(0, -1);
+    const parent = getNestedValue(config, parentPath);
+    if (parent !== null && parent !== undefined && typeof parent !== "object") {
+      throw new Error(
+        `Cannot set property '${lastSegment}' on non-object at path '${parentPath.join(".")}'`,
+      );
+    }
+  }
+}
+
+/**
+ * Set a specific configuration value
+ */
+export async function cmdConfigSet(
+  storageRoot: string,
+  key: string,
+  value: string,
+): Promise<unknown> {
+  const configPath = getConfigPath(storageRoot);
+
+  // Load existing config or create empty one
+  let config: Record<string, unknown>;
+  if (existsSync(configPath)) {
+    config = loadConfig(configPath);
+  } else {
+    config = {};
+  }
+
+  const path = parseDotPath(key);
+  const lastSegment = path[path.length - 1];
+
+  // Parse value if it's for an array key (args)
+  let parsedValue: unknown = value;
+  if (lastSegment === "args") {
+    parsedValue = parseArgsValue(value);
+  }
+
+  // Validate we're not setting a property on a non-object
+  validateParentPath(config, path, lastSegment);
+
+  setNestedValue(config, path, parsedValue);
+  saveConfig(configPath, config);
+
+  return { key, value: parsedValue };
+}

packages/cli-workflow/src/commands/setup.ts

@@ -85,6 +85,10 @@ function getConfigPath(root: string): string {
   return join(root, "config.yaml");
 }
 
+function getEnvPath(root: string): string {
+  return join(root, ".env");
+}
+
 /**
  * Load existing config.yaml or return empty structure.
  */
@@ -102,6 +106,37 @@ function loadExistingConfig(configPath: string): Record<string, unknown> {
   return {};
 }
 
+/**
+ * Load existing .env as key=value map.
+ */
+function loadEnvFile(envPath: string): Record<string, string> {
+  const env: Record<string, string> = {};
+  try {
+    if (existsSync(envPath)) {
+      for (const line of readFileSync(envPath, "utf8").split("\n")) {
+        const trimmed = line.trim();
+        if (trimmed === "" || trimmed.startsWith("#")) continue;
+        const eq = trimmed.indexOf("=");
+        if (eq > 0) {
+          env[trimmed.slice(0, eq)] = trimmed.slice(eq + 1);
+        }
+      }
+    }
+  } catch {
+    // ignore
+  }
+  return env;
+}
+
+function saveEnvFile(envPath: string, env: Record<string, string>): void {
+  const lines = Object.entries(env).map(([k, v]) => `${k}=${v}`);
+  writeFileSync(envPath, `${lines.join("\n")}\n`, "utf8");
+}
+
+function apiKeyEnvName(providerName: string): string {
+  return `${providerName.toUpperCase().replace(/[^A-Z0-9]/g, "_")}_API_KEY`;
+}
+
 // ──────────────────────────────────────────────────────────────────────────────
 // Extracted helpers — _discoverAgents
 // ──────────────────────────────────────────────────────────────────────────────
@@ -362,7 +397,8 @@ function mergeConfig(existing: Record<string, unknown>, args: SetupArgs): Record
       : {}
   ) as Record<string, unknown>;
 
-  providers[args.provider] = { baseUrl: args.baseUrl, apiKey: args.apiKey };
+  const envName = apiKeyEnvName(args.provider);
+  providers[args.provider] = { baseUrl: args.baseUrl, apiKeyEnv: envName };
 
   const models = (
     typeof existing.models === "object" && existing.models !== null
@@ -401,17 +437,25 @@ export async function cmdSetup(args: SetupArgs): Promise<Record<string, unknown>
   mkdirSync(storageRoot, { recursive: true });
 
   const configPath = getConfigPath(storageRoot);
+  const envPath = getEnvPath(storageRoot);
 
   const existing = loadExistingConfig(configPath);
   const merged = mergeConfig(existing, args);
 
   writeFileSync(configPath, stringify(merged, { indent: 2 }), "utf8");
 
+  // Write API key to .env
+  const envName = apiKeyEnvName(args.provider);
+  const envData = loadEnvFile(envPath);
+  envData[envName] = args.apiKey;
+  saveEnvFile(envPath, envData);
+
   // Validate model connectivity
   const validation = await validateModel(args.baseUrl, args.apiKey, args.model);
 
   return {
     configPath,
+    envPath,
     provider: args.provider,
     model: args.model,
     defaultAgent: merged.defaultAgent,

packages/workflow-protocol/README.md

@@ -100,7 +100,7 @@ type ProviderAlias = string;
 type ModelAlias = string;
 type AgentAlias = string;
 
-type ProviderConfig = { baseUrl: string; apiKey: string };
+type ProviderConfig = { baseUrl: string; apiKeyEnv: string };
 type ModelConfig = {
   provider: ProviderAlias;
   name: string;

packages/workflow-protocol/src/types.ts

@@ -151,7 +151,7 @@ export type Scenario = string;
 
 export type ProviderConfig = {
   baseUrl: string;
-  apiKey: string;
+  apiKeyEnv: string;
 };
 
 export type ModelConfig = {

packages/workflow-util-agent/src/extract.ts

@@ -1,7 +1,8 @@
 import { getSchema, validate } from "@uncaged/json-cas";
 
 import type { CasRef, ModelAlias, WorkflowConfig } from "@uncaged/workflow-protocol";
-import { createAgentStore, resolveStorageRoot } from "./storage.js";
+import { config as loadDotenv } from "dotenv";
+import { createAgentStore, getEnvPath, resolveStorageRoot } from "./storage.js";
 
 export type ResolvedLlmProvider = {
   baseUrl: string;
@@ -37,9 +38,9 @@ export function resolveModel(config: WorkflowConfig, alias: ModelAlias): Resolve
   if (providerEntry === undefined) {
     throw new Error(`unknown provider "${modelEntry.provider}" for model "${alias}"`);
   }
-  const apiKey = providerEntry.apiKey;
+  const apiKey = process.env[providerEntry.apiKeyEnv];
   if (apiKey === undefined || apiKey === "") {
-    throw new Error(`missing API key for provider: ${modelEntry.provider}`);
+    throw new Error(`missing API key env var: ${providerEntry.apiKeyEnv}`);
   }
   return {
     baseUrl: providerEntry.baseUrl,
@@ -129,7 +130,7 @@ export type ExtractResult = {
 
 /**
  * Call an OpenAI-compatible LLM to extract structured output matching outputSchema.
- * Loads config.yaml from the workflow storage root.
+ * Loads config.yaml and .env from the workflow storage root.
  */
 export async function extract(
   rawOutput: string,
@@ -137,6 +138,7 @@ export async function extract(
   config: WorkflowConfig,
 ): Promise<ExtractResult> {
   const storageRoot = resolveStorageRoot();
+  loadDotenv({ path: getEnvPath(storageRoot) });
 
   const { store } = await createAgentStore(storageRoot);
   const schema = getSchema(store, outputSchema);

packages/workflow-util-agent/src/storage.ts

@@ -84,11 +84,11 @@ function normalizeProviders(raw: unknown): Record<ProviderAlias, ProviderConfig>
       throw new Error(`config.providers.${name} must be a mapping`);
     }
     const baseUrl = entry.baseUrl;
-    const apiKey = entry.apiKey;
-    if (typeof baseUrl !== "string" || typeof apiKey !== "string") {
-      throw new Error(`config.providers.${name} requires baseUrl and apiKey`);
+    const apiKeyEnv = entry.apiKeyEnv;
+    if (typeof baseUrl !== "string" || typeof apiKeyEnv !== "string") {
+      throw new Error(`config.providers.${name} requires baseUrl and apiKeyEnv`);
     }
-    providers[name] = { baseUrl, apiKey };
+    providers[name] = { baseUrl, apiKeyEnv };
   }
   return providers;
 }