fix(skill-mcp-manager): trust explicit skill MCP env vars (#3995)

Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)

Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>

src/features/skill-mcp-manager/env-cleaner.test.ts

@@ -142,24 +142,56 @@ describe("createCleanMcpEnvironment", () => {
       expect(cleanEnv.NODE_ENV).toBe("production")
     })
 
-    it("filters secret keys from customEnv that would bypass process.env filtering", () => {
+    it("passes through secret-named keys from customEnv without filtering", () => {
-      // given - customEnv tries to inject secrets that should be filtered
+      // given - custom env values are explicitly declared in skill config
       process.env.PATH = "/usr/bin"
+      process.env.MCP_API_KEY = "ambient-secret-from-process-env"
       const customEnv = {
-        MCP_API_KEY: "secret-key-that-should-be-filtered",
+        MCP_API_KEY: "skill-declared-api-key",
-        CUSTOM_SECRET: "another-secret",
+        TELEGRAM_BOT_TOKEN: "skill-configured-bot-token",
         SAFE_VAR: "safe-value",
       }
 
       // when
       const cleanEnv = createCleanMcpEnvironment(customEnv)
 
-      // then - secret keys from customEnv are filtered despite not being in process.env
+      // then - custom env overrides ambient values and is not filtered
-      expect(cleanEnv.MCP_API_KEY).toBeUndefined()
+      expect(cleanEnv.MCP_API_KEY).toBe("skill-declared-api-key")
-      expect(cleanEnv.CUSTOM_SECRET).toBeUndefined()
+      expect(cleanEnv.TELEGRAM_BOT_TOKEN).toBe("skill-configured-bot-token")
       expect(cleanEnv.SAFE_VAR).toBe("safe-value")
       expect(cleanEnv.PATH).toBe("/usr/bin")
     })
+
+    it("passes TELEGRAM_BOT_TOKEN through when declared in skill env (issue #3995)", () => {
+      // given - TELEGRAM_BOT_TOKEN matches /_TOKEN$/i but is explicitly declared
+      process.env.TELEGRAM_BOT_TOKEN = "ambient-bot-token"
+      const customEnv = {
+        TELEGRAM_BOT_TOKEN: "skill-bot-token",
+      }
+
+      // when
+      const cleanEnv = createCleanMcpEnvironment(customEnv)
+
+      // then
+      expect(cleanEnv.TELEGRAM_BOT_TOKEN).toBe("skill-bot-token")
+    })
+
+    it("still filters secret-named vars from process.env when customEnv is provided", () => {
+      // given
+      process.env.AMBIENT_API_KEY = "ambient-secret"
+      process.env.PATH = "/usr/bin"
+      const customEnv = {
+        SAFE_CUSTOM_VAR: "custom-value",
+      }
+
+      // when
+      const cleanEnv = createCleanMcpEnvironment(customEnv)
+
+      // then
+      expect(cleanEnv.AMBIENT_API_KEY).toBeUndefined()
+      expect(cleanEnv.PATH).toBe("/usr/bin")
+      expect(cleanEnv.SAFE_CUSTOM_VAR).toBe("custom-value")
+    })
   })
 
   describe("undefined value handling", () => {

src/features/skill-mcp-manager/env-cleaner.ts

@@ -35,25 +35,25 @@ export const EXCLUDED_ENV_PATTERNS: RegExp[] = [
   /_API_KEY$/i,
 ]
 
+function isExcludedEnvKey(key: string): boolean {
+  return EXCLUDED_ENV_PATTERNS.some((pattern) => pattern.test(key))
+}
+
 export function createCleanMcpEnvironment(
   customEnv: Record<string, string> = {}
 ): Record<string, string> {
-  const mergedEnv: Record<string, string> = {}
+  const cleanEnv: Record<string, string> = {}
 
+  // Apply the blacklist only to inherited ambient environment variables.
+  // Skill-configured env entries are explicitly declared and must be passed
+  // through as-is so stdio MCP servers can receive required credentials.
   for (const [key, value] of Object.entries(process.env)) {
     if (value === undefined) continue
-    mergedEnv[key] = value
+    if (isExcludedEnvKey(key)) continue
+    cleanEnv[key] = value
   }
 
-  Object.assign(mergedEnv, customEnv)
+  Object.assign(cleanEnv, customEnv)
-
-  const cleanEnv: Record<string, string> = {}
-  for (const [key, value] of Object.entries(mergedEnv)) {
-    const shouldExclude = EXCLUDED_ENV_PATTERNS.some((pattern) => pattern.test(key))
-    if (!shouldExclude) {
-      cleanEnv[key] = value
-    }
-  }
 
   return cleanEnv
 }