fix(mcp): read pipe data before waitUntilExit to prevent deadlock

Core/PeekabooCore/Sources/PeekabooAgentRuntime/MCP/Tools/ShellTool.swift

@@ -65,10 +65,12 @@ public struct ShellTool: MCPTool {
 
         do {
             try process.run()
-            process.waitUntilExit()
 
-            let outputData = outputPipe.fileHandleForReading.readDataToEndOfFile()
-            let errorData = errorPipe.fileHandleForReading.readDataToEndOfFile()
+            // Either pipe can fill while the other waits for EOF, so drain both concurrently.
+            async let outputRead = outputPipe.fileHandleForReading.readDataToEndOfFile()
+            async let errorRead = errorPipe.fileHandleForReading.readDataToEndOfFile()
+            let (outputData, errorData) = await (outputRead, errorRead)
+            process.waitUntilExit()
 
             let output = String(data: outputData, encoding: .utf8) ?? ""
             let error = String(data: errorData, encoding: .utf8) ?? ""

Core/PeekabooCore/Tests/PeekabooTests/MCP/MCPSpecificToolTests.swift

@@ -429,6 +429,42 @@ struct MCPSpecificToolTests {
             try MCPAgentTool.validatedMaxSteps(101)
         }
     }
+
+    // MARK: - Shell Tool Tests
+
+    @Test(.timeLimit(.minutes(1)))
+    func `Shell tool does not deadlock on large output`() async throws {
+        let tool = makeTestTool(ShellTool.init)
+
+        // Generate output larger than the macOS pipe buffer (~64 KB)
+        // to trigger a deadlock if waitUntilExit() precedes pipe reads.
+        let result = try await tool.execute(arguments: ToolArguments(raw: [
+            "command": "head -c 131072 /dev/zero | base64",
+        ]))
+
+        #expect(result.isError == false)
+        if case let .text(text, _, _) = result.content.first {
+            #expect(text.count > 100_000)
+        } else {
+            Issue.record("Expected text content from shell output")
+        }
+    }
+
+    @Test(.timeLimit(.minutes(1)))
+    func `Shell tool does not deadlock when both pipes exceed their buffers`() async throws {
+        let tool = makeTestTool(ShellTool.init)
+
+        let result = try await tool.execute(arguments: ToolArguments(raw: [
+            "command": "head -c 131072 /dev/zero >&2; head -c 131072 /dev/zero",
+        ]))
+
+        #expect(result.isError == false)
+        if case let .text(text, _, _) = result.content.first {
+            #expect(text.count == 131_072)
+        } else {
+            Issue.record("Expected text content from shell output")
+        }
+    }
 }
 
 @MainActor