Improve handling of CA certificates (#518)

Instead of bundling Pkl's built-in CA certificates as a class path resource and loading them at runtime,
pass them to the native image compiler as the default SSL context's trust store.
This results in faster SSL initialization and is more consistent with how default certificates
are handled when running on the JVM.

Further related improvements:
- Remove HttpClientBuilder methods `addDefaultCliCertificates` and `addBuiltInCertificates`.
- Remove pkl-certs subproject and the optional dependencies on it.
- Move `PklCARoots.pem` to `pkl-cli/src/certs`.
- Fix certificate related error messages that were missing an argument.
- Prevent PklBugException if initialization of `CliBaseOptions.httpClient` fails.
- Add ability to set CA certificates as a byte array
- Add CA certificates option to message passing API

docs/modules/bindings-specification/pages/message-passing-api.adoc

@@ -121,7 +121,7 @@ outputFormat: String?
 /// The project dependency settings.
 project: Project?
 
-/// Configuration of outgoing HTTP requests.
+/// Configuration of outgoing HTTP(s) requests.
 http: Http?
 
 class ClientResourceReader {
@@ -178,8 +178,27 @@ class Project {
   dependencies: Mapping<String, Project|RemoteDependency>
 }
 
-/// Settings that control how Pkl talks to HTTP(S) servers.
+class RemoteDependency {
+  type: "remote"
+
+  /// The canonical URI of this dependency
+  packageUri: String?
+
+  /// The checksums of this remote dependency
+  checksums: Checksums?
+}
+
+class Checksums {
+  /// The sha-256 checksum of this dependency's metadata.
+  sha256: String
+}
+
 class Http {
+  /// PEM format certificates to trust when making HTTP requests.
+  ///
+  /// If [null], Pkl will trust its own built-in certificates.
+  caCertificates: Binary?
+
   /// Configuration of the HTTP proxy to use.
   ///
   /// If [null], uses the operating system's proxy configuration.
@@ -226,21 +245,9 @@ class Proxy {
   noProxy: Listing<String>(isDistinct)
 }
 
-class RemoteDependency {
-  type: "remote"
-
-  /// The canonical URI of this dependency
-  packageUri: String?
-
-  /// The checksums of this remote dependency
-  checksums: Checksums?
-}
-
-class Checksums {
-  /// The sha-256 checksum of this dependency's metadata.
-  sha256: String
-}
+typealias Binary = Any // <1>
 ----
+<1> link:{uri-messagepack-bin}[bin format] (not expressable in Pkl)
 
 Example:
 [source,json5]

pkl-certs/pkl-certs.gradle.kts

@@ -1,19 +0,0 @@
-plugins {
-  pklAllProjects
-  pklJavaLibrary
-  pklPublishLibrary
-}
-
-publishing {
-  publications {
-    named<MavenPublication>("library") {
-      pom {
-        url.set("https://github.com/apple/pkl/tree/main/pkl-certs")
-        description.set("""
-          Pkl's built-in CA certificates. 
-          Used by Pkl CLIs and optionally supported by pkl-core.")
-        """.trimIndent())
-      }
-    }
-  }
-}

pkl-cli/pkl-cli.gradle.kts

@@ -1,3 +1,6 @@
+import java.security.KeyStore
+import java.security.cert.CertificateFactory
+
 plugins {
   pklAllProjects
   pklKotlinLibrary
@@ -35,6 +38,8 @@ val stagedLinuxAarch64Executable: Configuration by configurations.creating
 val stagedAlpineLinuxAmd64Executable: Configuration by configurations.creating
 val stagedWindowsAmd64Executable: Configuration by configurations.creating
 
+val certs: SourceSet by sourceSets.creating
+
 dependencies {
   compileOnly(libs.svm)
 
@@ -142,11 +147,38 @@ tasks.check {
   dependsOn(testStartJavaExecutable)
 }
 
+val trustStore = layout.buildDirectory.dir("generateTrustStore/PklCARoots.p12")
+val trustStorePassword = "password" // no sensitive data to protect
+
+// generate a trust store for Pkl's built-in CA certificates
+val generateTrustStore by tasks.registering {
+  inputs.file(certs.resources.singleFile)
+  outputs.file(trustStore)
+  doLast {
+    val certificates = certs.resources.singleFile.inputStream().use { stream ->
+      CertificateFactory.getInstance("X.509").generateCertificates(stream)
+    }
+    KeyStore.getInstance("PKCS12").apply {
+      load(null, trustStorePassword.toCharArray()) // initialize empty trust store
+      for ((index, certificate) in certificates.withIndex()) {
+        setCertificateEntry("cert-$index", certificate)
+      }
+      val trustStoreFile = trustStore.get().asFile
+      trustStoreFile.parentFile.mkdirs()
+      trustStoreFile.outputStream().use { stream ->
+        store(stream, trustStorePassword.toCharArray())
+      }
+    }
+  }
+}
+
 fun Exec.configureExecutable(
   graalVm: BuildInfo.GraalVm,
   outputFile: Provider<RegularFile>,
   extraArgs: List<String> = listOf()
 ) {
+  dependsOn(generateTrustStore)
+
   inputs.files(sourceSets.main.map { it.output })
     .withPropertyName("mainSourceSets")
     .withPathSensitivity(PathSensitivity.RELATIVE)
@@ -175,9 +207,13 @@ fun Exec.configureExecutable(
         // needed for messagepack-java (see https://github.com/msgpack/msgpack-java/issues/600)
         ,"--initialize-at-run-time=org.msgpack.core.buffer.DirectBufferAccess"
         ,"--no-fallback"
+        ,"-Djavax.net.ssl.trustStore=${trustStore.get().asFile}"
+        ,"-Djavax.net.ssl.trustStorePassword=$trustStorePassword"
+        ,"-Djavax.net.ssl.trustStoreType=PKCS12"
+        // security property "ocsp.enable=true" is set in Main.kt
+        ,"-Dcom.sun.net.ssl.checkRevocation=true"
         ,"-H:IncludeResources=org/pkl/core/stdlib/.*\\.pkl"
         ,"-H:IncludeResources=org/jline/utils/.*"
-        ,"-H:IncludeResources=org/pkl/certs/PklCARoots.pem"
         ,"-H:IncludeResourceBundles=org.pkl.core.errorMessages"
         ,"--macro:truffle"
         ,"-H:Class=org.pkl.cli.Main"

pkl-cli/src/test/kotlin/org/pkl/cli/CliEvaluatorTest.kt

@@ -1260,10 +1260,7 @@ result = someLib.x
 
   @Test
   fun `gives decent error message if CLI doesn't have the required CA certificate`() {
-    // provide SOME certs to prevent CliEvaluator from falling back to ~/.pkl/cacerts
-    val builtInCerts = FileTestUtils.writePklBuiltInCertificates(tempDir)
-    val err =
-      assertThrows<CliException> { evalModuleThatImportsPackage(builtInCerts, packageServer.port) }
+    val err = assertThrows<CliException> { evalModuleThatImportsPackage(null, packageServer.port) }
     assertThat(err)
       .hasMessageContaining("Error during SSL handshake with host `localhost`:")
       .hasMessageContaining("unable to find valid certification path to requested target")
@@ -1460,7 +1457,7 @@ result = someLib.x
     assertThat(output).isEqualTo("result = 1\n")
   }
 
-  private fun evalModuleThatImportsPackage(certsFile: Path, testPort: Int = -1) {
+  private fun evalModuleThatImportsPackage(certsFile: Path?, testPort: Int = -1) {
     val moduleUri =
       writePklFile(
         "test.pkl",
@@ -1475,7 +1472,7 @@ result = someLib.x
       CliEvaluatorOptions(
         CliBaseOptions(
           sourceModules = listOf(moduleUri),
-          caCertificates = listOf(certsFile),
+          caCertificates = buildList { if (certsFile != null) add(certsFile) },
           workingDir = tempDir,
           noCache = true,
           testPort = testPort

pkl-commons-cli/pkl-commons-cli.gradle.kts

@@ -14,7 +14,6 @@ dependencies {
 
   implementation(projects.pklCommons)
   testImplementation(projects.pklCommonsTest)
-  runtimeOnly(projects.pklCerts)
 }
 
 publishing {

pkl-commons-cli/src/main/kotlin/org/pkl/commons/cli/CliCommand.kt

@@ -15,8 +15,10 @@
  */
 package org.pkl.commons.cli
 
+import java.nio.file.Files
 import java.nio.file.Path
 import java.util.regex.Pattern
+import kotlin.io.path.isRegularFile
 import org.pkl.core.*
 import org.pkl.core.evaluatorSettings.PklEvaluatorSettings
 import org.pkl.core.http.HttpClient
@@ -166,6 +168,13 @@ abstract class CliCommand(protected val cliOptions: CliBaseOptions) {
     cliOptions.noProxy
       ?: project?.evaluatorSettings?.http?.proxy?.noProxy ?: settings.http?.proxy?.noProxy
 
+  private fun HttpClient.Builder.addDefaultCliCertificates() {
+    val caCertsDir = IoUtils.getPklHomeDir().resolve("cacerts")
+    if (Files.isDirectory(caCertsDir)) {
+      Files.list(caCertsDir).filter { it.isRegularFile() }.forEach { addCertificates(it) }
+    }
+  }
+
   /**
    * The HTTP client used for this command.
    *

pkl-commons-cli/src/main/kotlin/org/pkl/commons/cli/CliMain.kt

@@ -16,6 +16,7 @@
 package org.pkl.commons.cli
 
 import java.io.PrintStream
+import java.security.Security
 import kotlin.system.exitProcess
 
 /** Building block for CLIs. Intended to be called from a `main` method. */
@@ -29,6 +30,8 @@ fun cliMain(block: () -> Unit) {
 
   // Force `native-image` to use system proxies (which does not happen with `-D`).
   System.setProperty("java.net.useSystemProxies", "true")
+  // enable OCSP for default SSL context
+  Security.setProperty("ocsp.enable", "true")
 
   try {
     block()

pkl-commons-test/pkl-commons-test.gradle.kts

@@ -13,7 +13,6 @@ dependencies {
   api(libs.junitParams)
   api(projects.pklCommons) // for convenience
   implementation(libs.assertj)
-  runtimeOnly(projects.pklCerts)
 }
 
 /**

pkl-commons-test/src/main/kotlin/org/pkl/commons/test/FileTestUtils.kt

@@ -38,11 +38,6 @@ object FileTestUtils {
     // drop some lines in the middle
     return dir.resolve("invalidCerts.pem").writeLines(lines.take(5) + lines.takeLast(5))
   }
-
-  fun writePklBuiltInCertificates(dir: Path): Path {
-    val text = javaClass.getResource("/org/pkl/certs/PklCARoots.pem")!!.readText()
-    return dir.resolve("PklCARoots.pem").apply { writeText(text) }
-  }
 }
 
 fun Path.listFilesRecursively(): List<Path> =

pkl-core/src/main/java/org/pkl/core/http/HttpClient.java

@@ -67,49 +67,22 @@ public interface HttpClient extends AutoCloseable {
      *
      * <p>The given file must contain <a href="https://en.wikipedia.org/wiki/X.509">X.509</a>
      * certificates in PEM format.
+     *
+     * <p>If no CA certificates are added via this method nor {@link #addCertificates(byte[])}, the
+     * built-in CA certificates of the Pkl native executable or JVM are used.
      */
-    Builder addCertificates(Path file);
+    Builder addCertificates(Path path);
 
     /**
-     * Adds a CA certificate file to the client's trust store.
+     * Adds CA certificate bytes to the client's trust store.
      *
-     * <p>The given file must contain <a href="https://en.wikipedia.org/wiki/X.509">X.509</a>
-     * certificates in PEM format.
+     * <p>The given cert must be an <a href="https://en.wikipedia.org/wiki/X.509">X.509</a>
+     * certificate in PEM format.
      *
-     * <p>This method is intended to be used for adding certificate files located on the class path.
-     * To add certificate files located on the file system, use {@link #addCertificates(Path)}.
-     *
-     * @throws HttpClientInitException if the given URI has a scheme other than {@code jar:} or
-     *     {@code file:}
+     * <p>If no CA certificates are added via this method nor {@link #addCertificates(Path)}, the
+     * built-in CA certificates of the Pkl native executable or JVM are used.
      */
-    Builder addCertificates(URI file);
-
-    /**
-     * Adds the CA certificate files in {@code ~/.pkl/cacerts/} to the client's trust store.
-     *
-     * <p>Each file must contain <a href="https://en.wikipedia.org/wiki/X.509">X.509</a>
-     * certificates in PEM format. If {@code ~/.pkl/cacerts/} does not exist or is empty, Pkl's
-     * {@link #addBuiltInCertificates() built-in certificates} are added instead.
-     *
-     * <p>This method implements the default behavior of Pkl CLIs.
-     *
-     * <p>NOTE: This method requires the optional {@code pkl-certs} JAR to be present on the class
-     * path.
-     *
-     * @throws HttpClientInitException if an I/O error occurs while scanning {@code ~/.pkl/cacerts/}
-     *     or the {@code pkl-certs} JAR is not found on the class path
-     */
-    Builder addDefaultCliCertificates();
-
-    /**
-     * Adds Pkl's built-in CA certificates to the client's trust store.
-     *
-     * <p>NOTE: This method requires the optional {@code pkl-certs} JAR to be present on the class
-     * path.
-     *
-     * @throws HttpClientInitException if the {@code pkl-certs} JAR is not found on the class path
-     */
-    Builder addBuiltInCertificates();
+    Builder addCertificates(byte[] certificateBytes);
 
     /**
      * Sets a test server's listening port.

pkl-core/src/main/java/org/pkl/core/http/HttpClientBuilder.java

@@ -15,11 +15,9 @@
  */
 package org.pkl.core.http;
 
-import java.io.IOException;
 import java.net.ProxySelector;
 import java.net.URI;
-import java.net.URISyntaxException;
-import java.nio.file.Files;
+import java.nio.ByteBuffer;
 import java.nio.file.Path;
 import java.time.Duration;
 import java.util.ArrayList;
@@ -27,27 +25,18 @@ import java.util.List;
 import java.util.function.Supplier;
 import org.pkl.core.Release;
 import org.pkl.core.http.HttpClient.Builder;
-import org.pkl.core.util.ErrorMessages;
-import org.pkl.core.util.IoUtils;
 
 final class HttpClientBuilder implements HttpClient.Builder {
   private String userAgent;
   private Duration connectTimeout = Duration.ofSeconds(60);
   private Duration requestTimeout = Duration.ofSeconds(60);
-  private final Path caCertsDir;
   private final List<Path> certificateFiles = new ArrayList<>();
-  private final List<URI> certificateUris = new ArrayList<>();
+  private final List<ByteBuffer> certificateBytes = new ArrayList<>();
   private int testPort = -1;
   private ProxySelector proxySelector;
 
   HttpClientBuilder() {
-    this(IoUtils.getPklHomeDir().resolve("cacerts"));
-  }
-
-  // only exists for testing
-  HttpClientBuilder(Path caCertsDir) {
     var release = Release.current();
-    this.caCertsDir = caCertsDir;
     this.userAgent =
         "Pkl/" + release.version() + " (" + release.os() + "; " + release.flavor() + ")";
   }
@@ -70,39 +59,14 @@ final class HttpClientBuilder implements HttpClient.Builder {
   }
 
   @Override
-  public HttpClient.Builder addCertificates(Path file) {
-    certificateFiles.add(file);
+  public HttpClient.Builder addCertificates(Path path) {
+    certificateFiles.add(path);
     return this;
   }
 
   @Override
-  public HttpClient.Builder addCertificates(URI url) {
-    var scheme = url.getScheme();
-    if (!"jar".equalsIgnoreCase(scheme) && !"file".equalsIgnoreCase(scheme)) {
-      throw new HttpClientInitException(ErrorMessages.create("expectedJarOrFileUrl", url));
-    }
-    certificateUris.add(url);
-    return this;
-  }
-
-  public HttpClient.Builder addDefaultCliCertificates() {
-    var fileCount = certificateFiles.size();
-    if (Files.isDirectory(caCertsDir)) {
-      try (var files = Files.list(caCertsDir)) {
-        files.filter(Files::isRegularFile).forEach(certificateFiles::add);
-      } catch (IOException e) {
-        throw new HttpClientInitException(e);
-      }
-    }
-    if (certificateFiles.size() == fileCount) {
-      addBuiltInCertificates();
-    }
-    return this;
-  }
-
-  @Override
-  public HttpClient.Builder addBuiltInCertificates() {
-    certificateUris.add(getBuiltInCertificates());
+  public Builder addCertificates(byte[] certificateBytes) {
+    this.certificateBytes.add(ByteBuffer.wrap(certificateBytes));
     return this;
   }
 
@@ -134,27 +98,14 @@ final class HttpClientBuilder implements HttpClient.Builder {
   }
 
   private Supplier<HttpClient> doBuild() {
-    // make defensive copies because Supplier may get called after builder was mutated
+    // make defensive copy because Supplier may get called after builder was mutated
     var certificateFiles = List.copyOf(this.certificateFiles);
-    var certificateUris = List.copyOf(this.certificateUris);
     var proxySelector =
         this.proxySelector != null ? this.proxySelector : java.net.ProxySelector.getDefault();
     return () -> {
       var jdkClient =
-          new JdkHttpClient(certificateFiles, certificateUris, connectTimeout, proxySelector);
+          new JdkHttpClient(certificateFiles, certificateBytes, connectTimeout, proxySelector);
       return new RequestRewritingClient(userAgent, requestTimeout, testPort, jdkClient);
     };
   }
-
-  private static URI getBuiltInCertificates() {
-    var resource = HttpClientBuilder.class.getResource("/org/pkl/certs/PklCARoots.pem");
-    if (resource == null) {
-      throw new HttpClientInitException(ErrorMessages.create("cannotFindBuiltInCertificates"));
-    }
-    try {
-      return resource.toURI();
-    } catch (URISyntaxException e) {
-      throw new AssertionError("unreachable");
-    }
-  }
 }

pkl-core/src/main/java/org/pkl/core/http/JdkHttpClient.java

@@ -15,17 +15,18 @@
  */
 package org.pkl.core.http;
 
+import java.io.ByteArrayInputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.lang.invoke.MethodHandle;
 import java.lang.invoke.MethodHandles;
 import java.lang.invoke.MethodType;
 import java.net.ConnectException;
-import java.net.URI;
 import java.net.http.HttpClient.Redirect;
 import java.net.http.HttpRequest;
 import java.net.http.HttpResponse;
 import java.net.http.HttpResponse.BodyHandler;
+import java.nio.ByteBuffer;
 import java.nio.file.Files;
 import java.nio.file.NoSuchFileException;
 import java.nio.file.Path;
@@ -79,12 +80,12 @@ final class JdkHttpClient implements HttpClient {
 
   JdkHttpClient(
       List<Path> certificateFiles,
-      List<URI> certificateUris,
+      List<ByteBuffer> certificateBytes,
       Duration connectTimeout,
       java.net.ProxySelector proxySelector) {
     underlying =
         java.net.http.HttpClient.newBuilder()
-            .sslContext(createSslContext(certificateFiles, certificateUris))
+            .sslContext(createSslContext(certificateFiles, certificateBytes))
             .connectTimeout(connectTimeout)
             .proxy(proxySelector)
             .followRedirects(Redirect.NORMAL)
@@ -126,10 +127,10 @@ final class JdkHttpClient implements HttpClient {
 
   // https://docs.oracle.com/en/java/javase/11/docs/specs/security/standard-names.html#security-algorithm-implementation-requirements
   private static SSLContext createSslContext(
-      List<Path> certificateFiles, List<URI> certificateUris) {
+      List<Path> certificateFiles, List<ByteBuffer> certificateBytes) {
     try {
-      if (certificateFiles.isEmpty() && certificateUris.isEmpty()) {
-        // fall back to JVM defaults (not Pkl built-in certs)
+      if (certificateFiles.isEmpty() && certificateBytes.isEmpty()) {
+        // use Pkl native executable's or JVM's built-in CA certificates
         return SSLContext.getDefault();
       }
 
@@ -141,7 +142,7 @@ final class JdkHttpClient implements HttpClient {
 
       var certFactory = CertificateFactory.getInstance("X.509");
       Set<TrustAnchor> trustAnchors =
-          createTrustAnchors(certFactory, certificateFiles, certificateUris);
+          createTrustAnchors(certFactory, certificateFiles, certificateBytes);
       var pkixParameters = new PKIXBuilderParameters(trustAnchors, new X509CertSelector());
       // equivalent of "com.sun.net.ssl.checkRevocation=true"
       pkixParameters.setRevocationEnabled(true);
@@ -161,9 +162,8 @@ final class JdkHttpClient implements HttpClient {
   }
 
   private static Set<TrustAnchor> createTrustAnchors(
-      CertificateFactory factory, List<Path> certificateFiles, List<URI> certificateUris) {
+      CertificateFactory factory, List<Path> certificateFiles, List<ByteBuffer> certificateBytes) {
     var anchors = new HashSet<TrustAnchor>();
-
     for (var file : certificateFiles) {
       try (var stream = Files.newInputStream(file)) {
         collectTrustAnchors(anchors, factory, stream, file);
@@ -174,16 +174,10 @@ final class JdkHttpClient implements HttpClient {
             ErrorMessages.create("cannotReadCertFile", Exceptions.getRootReason(e)));
       }
     }
-
-    for (var uri : certificateUris) {
-      try (var stream = uri.toURL().openStream()) {
-        collectTrustAnchors(anchors, factory, stream, uri);
-      } catch (IOException e) {
-        throw new HttpClientInitException(
-            ErrorMessages.create("cannotReadCertFile", Exceptions.getRootReason(e)));
-      }
+    for (var byteBuffer : certificateBytes) {
+      var stream = new ByteArrayInputStream(byteBuffer.array());
+      collectTrustAnchors(anchors, factory, stream, "<unavailable>");
     }
-
     return anchors;
   }
 

pkl-core/src/main/java/org/pkl/core/service/ExecutorSpiImpl.java

@@ -17,7 +17,6 @@ package org.pkl.core.service;
 
 import static org.pkl.core.module.ProjectDependenciesManager.PKL_PROJECT_FILENAME;
 
-import java.net.URI;
 import java.nio.file.Path;
 import java.util.Collections;
 import java.util.LinkedHashMap;
@@ -132,35 +131,35 @@ public final class ExecutorSpiImpl implements ExecutorSpi {
 
   private HttpClient getOrCreateHttpClient(ExecutorSpiOptions options) {
     List<Path> certificateFiles;
-    List<URI> certificateUris;
+    List<byte[]> certificateBytes;
     int testPort;
     try {
       if (options instanceof ExecutorSpiOptions2 options2) {
         certificateFiles = options2.getCertificateFiles();
-        certificateUris = options2.getCertificateUris();
+        certificateBytes = options2.getCertificateBytes();
         testPort = options2.getTestPort();
       } else {
         certificateFiles = List.of();
-        certificateUris = List.of();
+        certificateBytes = List.of();
         testPort = -1;
       }
       // host pkl-executor does not have class ExecutorOptions2 defined.
       // this will happen if the pkl-executor distribution is too old.
     } catch (NoClassDefFoundError e) {
       certificateFiles = List.of();
-      certificateUris = List.of();
+      certificateBytes = List.of();
       testPort = -1;
     }
-    var clientKey = new HttpClientKey(certificateFiles, certificateUris, testPort);
+    var clientKey = new HttpClientKey(certificateFiles, certificateBytes, testPort);
     return httpClients.computeIfAbsent(
         clientKey,
         (key) -> {
           var builder = HttpClient.builder();
-          for (var file : key.certificateFiles) {
-            builder.addCertificates(file);
+          for (var path : key.certificateFiles) {
+            builder.addCertificates(path);
           }
-          for (var uri : key.certificateUris) {
-            builder.addCertificates(uri);
+          for (var bytes : key.certificateBytes) {
+            builder.addCertificates(bytes);
           }
           builder.setTestPort(key.testPort);
           // If the above didn't add any certificates,
@@ -171,13 +170,13 @@ public final class ExecutorSpiImpl implements ExecutorSpi {
 
   private static final class HttpClientKey {
     final Set<Path> certificateFiles;
-    final Set<URI> certificateUris;
+    final Set<byte[]> certificateBytes;
     final int testPort;
 
-    HttpClientKey(List<Path> certificateFiles, List<URI> certificateUris, int testPort) {
-      // also serve as defensive copies
+    HttpClientKey(List<Path> certificateFiles, List<byte[]> certificateBytes, int testPort) {
+      // also serves as defensive copy
       this.certificateFiles = Set.copyOf(certificateFiles);
-      this.certificateUris = Set.copyOf(certificateUris);
+      this.certificateBytes = Set.copyOf(certificateBytes);
       this.testPort = testPort;
     }
 
@@ -191,13 +190,13 @@ public final class ExecutorSpiImpl implements ExecutorSpi {
       }
       HttpClientKey that = (HttpClientKey) obj;
       return certificateFiles.equals(that.certificateFiles)
-          && certificateUris.equals(that.certificateUris)
+          && certificateBytes.equals(that.certificateBytes)
           && testPort == that.testPort;
     }
 
     @Override
     public int hashCode() {
-      return Objects.hash(certificateFiles, certificateUris, testPort);
+      return Objects.hash(certificateFiles, certificateBytes, testPort);
     }
   }
 }

pkl-core/src/test/kotlin/org/pkl/core/http/HttpClientTest.kt

@@ -12,9 +12,8 @@ import java.net.http.HttpRequest
 import java.net.http.HttpResponse
 import java.nio.file.Path
 import java.time.Duration
-import kotlin.io.path.copyTo
-import kotlin.io.path.createDirectories
 import kotlin.io.path.createFile
+import kotlin.io.path.readBytes
 
 class HttpClientTest {
   @Test
@@ -52,14 +51,21 @@ class HttpClientTest {
   }
 
   @Test
-  fun `can load certificates from file system`() {
+  fun `can load certificates from regular file`() {
     assertDoesNotThrow {
       HttpClient.builder().addCertificates(FileTestUtils.selfSignedCertificate).build()
     }
   }
 
   @Test
-  fun `certificate file located on file system cannot be empty`(@TempDir tempDir: Path) {
+  fun `can load certificates from a byte array`() {
+    assertDoesNotThrow {
+      HttpClient.builder().addCertificates(FileTestUtils.selfSignedCertificate.readBytes()).build()
+    }
+  }
+
+  @Test
+  fun `certificate file cannot be empty`(@TempDir tempDir: Path) {
     val file = tempDir.resolve("certs.pem").createFile()
 
     val e = assertThrows<HttpClientInitException> {
@@ -69,56 +75,10 @@ class HttpClientTest {
     assertThat(e).hasMessageContaining("empty")
   }
 
-  @Test
-  fun `can load certificates from class path`() {
-    assertDoesNotThrow {
-      HttpClient.builder().addCertificates(javaClass.getResource("/org/pkl/certs/PklCARoots.pem")!!.toURI()).build()
-    }
-  }
-
-  @Test
-  fun `only allows loading jar and file certificate URIs`() {
-    assertThrows<HttpClientInitException> {
-      HttpClient.builder().addCertificates(URI("https://example.com"))
-    }
-  }
-
-  @Test
-  fun `certificate file located on class path cannot be empty`() {
-    val uri = javaClass.getResource("emptyCerts.pem")!!.toURI()
-
-    val e = assertThrows<HttpClientInitException> {
-      HttpClient.builder().addCertificates(uri).build()
-    }
-
-    assertThat(e).hasMessageContaining("empty")
-  }
-
   @Test
   fun `can load built-in certificates`() {
     assertDoesNotThrow {
-      HttpClient.builder().addBuiltInCertificates().build()
-    }
-  }
-
-  @Test
-  fun `can load certificates from Pkl user home cacerts directory`(@TempDir tempDir: Path) {
-    val certsDir = tempDir.resolve(".pkl")
-      .resolve("cacerts")
-      .createDirectories()
-      .also { dir ->
-        FileTestUtils.selfSignedCertificate.copyTo(dir.resolve("certs.pem"))
-      }
-
-    assertDoesNotThrow {
-      HttpClientBuilder(certsDir).addDefaultCliCertificates().build()
-    }
-  }
-
-  @Test
-  fun `loading certificates from cacerts directory falls back to built-in certificates`(@TempDir certsDir: Path) {
-    assertDoesNotThrow {
-      HttpClientBuilder(certsDir).addDefaultCliCertificates().build()
+      HttpClient.builder().build()
     }
   }
 

pkl-core/src/test/kotlin/org/pkl/core/http/LazyHttpClientTest.kt

@@ -3,15 +3,20 @@ package org.pkl.core.http
 import org.junit.jupiter.api.Test
 import org.junit.jupiter.api.assertDoesNotThrow
 import org.junit.jupiter.api.assertThrows
+import org.junit.jupiter.api.io.TempDir
+import org.pkl.commons.createTempFile
+import org.pkl.commons.writeString
 import java.net.URI
 import java.net.http.HttpRequest
 import java.net.http.HttpResponse.BodyHandlers
+import java.nio.file.Path
 
 class LazyHttpClientTest {
   @Test
-  fun `builds underlying client on first send`() {
+  fun `builds underlying client on first send`(@TempDir tempDir: Path) {
+    val certFile = tempDir.resolve("cert.pem").apply { writeString("broken") }
     val client = HttpClient.builder()
-      .addCertificates(javaClass.getResource("brokenCerts.pem")!!.toURI())
+      .addCertificates(certFile)
       .buildLazily()
     val request = HttpRequest.newBuilder(URI("https://example.com")).build()
     
@@ -21,9 +26,10 @@ class LazyHttpClientTest {
   }
   
   @Test
-  fun `does not build underlying client unnecessarily`() {
+  fun `does not build underlying client unnecessarily`(@TempDir tempDir: Path) {
+    val certFile = tempDir.createTempFile().apply { writeString("broken") }
     val client = HttpClient.builder()
-      .addCertificates(javaClass.getResource("brokenCerts.pem")!!.toURI())
+      .addCertificates(certFile)
       .buildLazily()
     
     assertDoesNotThrow {

pkl-core/src/test/kotlin/org/pkl/core/project/ProjectDependenciesResolverTest.kt

@@ -13,7 +13,6 @@ import org.pkl.core.SecurityManagers
 import org.pkl.core.packages.PackageResolver
 import java.io.ByteArrayOutputStream
 import java.nio.charset.StandardCharsets
-import java.nio.file.Path
 
 class ProjectDependenciesResolverTest {
   companion object {

pkl-core/src/test/resources/org/pkl/core/http/brokenCerts.pem

@@ -1 +0,0 @@
-broken

pkl-executor/src/main/java/org/pkl/executor/ExecutorOptions.java

@@ -15,7 +15,6 @@
  */
 package org.pkl.executor;
 
-import java.net.URI;
 import java.nio.file.Path;
 import java.time.Duration;
 import java.util.List;
@@ -52,7 +51,7 @@ public final class ExecutorOptions {
 
   private final List<Path> certificateFiles;
 
-  private final List<URI> certificateUris;
+  private final List<byte[]> certificateBytes;
 
   private final int testPort; // -1 means disabled
 
@@ -84,7 +83,7 @@ public final class ExecutorOptions {
     private /* @Nullable */ Path moduleCacheDir;
     private /* @Nullable */ Path projectDir;
     private List<Path> certificateFiles = List.of();
-    private List<URI> certificateUris = List.of();
+    private List<byte[]> certificateBytes = List.of();
     private int testPort = -1; // -1 means disabled
     private int spiOptionsVersion = -1; // -1 means use latest
 
@@ -188,15 +187,13 @@ public final class ExecutorOptions {
       return this;
     }
 
-    /** API equivalent of the {@code --ca-certificates} CLI option. */
-    public Builder certificateUris(List<URI> certificateUris) {
-      this.certificateUris = certificateUris;
+    public Builder certificateBytes(List<byte[]> certificateBytes) {
+      this.certificateBytes = certificateBytes;
       return this;
     }
 
-    /** API equivalent of the {@code --ca-certificates} CLI option. */
-    public Builder certificateUris(URI... certificateUris) {
-      this.certificateUris = List.of(certificateUris);
+    public Builder certificateBytes(byte[]... certificateBytes) {
+      this.certificateBytes = List.of(certificateBytes);
       return this;
     }
 
@@ -225,7 +222,7 @@ public final class ExecutorOptions {
           moduleCacheDir,
           projectDir,
           certificateFiles,
-          certificateUris,
+          certificateBytes,
           testPort,
           spiOptionsVersion);
     }
@@ -290,7 +287,7 @@ public final class ExecutorOptions {
       /* @Nullable */ Path moduleCacheDir,
       /* @Nullable */ Path projectDir,
       List<Path> certificateFiles,
-      List<URI> certificateUris,
+      List<byte[]> certificateBytes,
       int testPort,
       int spiOptionsVersion) {
 
@@ -305,7 +302,7 @@ public final class ExecutorOptions {
     this.moduleCacheDir = moduleCacheDir;
     this.projectDir = projectDir;
     this.certificateFiles = List.copyOf(certificateFiles);
-    this.certificateUris = List.copyOf(certificateUris);
+    this.certificateBytes = List.copyOf(certificateBytes);
     this.testPort = testPort;
     this.spiOptionsVersion = spiOptionsVersion;
   }
@@ -373,9 +370,8 @@ public final class ExecutorOptions {
     return certificateFiles;
   }
 
-  /** API equivalent of the {@code --ca-certificates} CLI option. */
-  public List<URI> getCertificateUris() {
-    return certificateUris;
+  public List<byte[]> getCertificateBytes() {
+    return certificateBytes;
   }
 
   @Override
@@ -395,7 +391,7 @@ public final class ExecutorOptions {
         && Objects.equals(moduleCacheDir, other.moduleCacheDir)
         && Objects.equals(projectDir, other.projectDir)
         && Objects.equals(certificateFiles, other.certificateFiles)
-        && Objects.equals(certificateUris, other.certificateUris)
+        && Objects.equals(certificateBytes, other.certificateBytes)
         && testPort == other.testPort
         && spiOptionsVersion == other.spiOptionsVersion;
   }
@@ -414,7 +410,7 @@ public final class ExecutorOptions {
         moduleCacheDir,
         projectDir,
         certificateFiles,
-        certificateUris,
+        certificateBytes,
         testPort,
         spiOptionsVersion);
   }
@@ -444,8 +440,8 @@ public final class ExecutorOptions {
         + projectDir
         + ", certificateFiles="
         + certificateFiles
-        + ", certificateUris="
-        + certificateUris
+        + ", certificateBytes="
+        + certificateBytes
         + ", testPort="
         + testPort
         + ", spiOptionsVersion="
@@ -468,7 +464,7 @@ public final class ExecutorOptions {
               moduleCacheDir,
               projectDir,
               certificateFiles,
-              certificateUris,
+              certificateBytes,
               testPort);
       case 1 -> // for testing only
           new ExecutorSpiOptions(

pkl-executor/src/main/java/org/pkl/executor/spi/v1/ExecutorSpiOptions2.java

@@ -15,7 +15,6 @@
  */
 package org.pkl.executor.spi.v1;
 
-import java.net.URI;
 import java.nio.file.Path;
 import java.time.Duration;
 import java.util.List;
@@ -24,7 +23,7 @@ import java.util.Map;
 public class ExecutorSpiOptions2 extends ExecutorSpiOptions {
   private final List<Path> certificateFiles;
 
-  private final List<URI> certificateUris;
+  private final List<byte[]> certificateBytes;
 
   private final int testPort;
 
@@ -40,7 +39,7 @@ public class ExecutorSpiOptions2 extends ExecutorSpiOptions {
       Path moduleCacheDir,
       Path projectDir,
       List<Path> certificateFiles,
-      List<URI> certificateUris,
+      List<byte[]> certificateBytes,
       int testPort) {
     super(
         allowedModules,
@@ -54,7 +53,7 @@ public class ExecutorSpiOptions2 extends ExecutorSpiOptions {
         moduleCacheDir,
         projectDir);
     this.certificateFiles = certificateFiles;
-    this.certificateUris = certificateUris;
+    this.certificateBytes = certificateBytes;
     this.testPort = testPort;
   }
 
@@ -62,8 +61,8 @@ public class ExecutorSpiOptions2 extends ExecutorSpiOptions {
     return certificateFiles;
   }
 
-  public List<URI> getCertificateUris() {
-    return certificateUris;
+  public List<byte[]> getCertificateBytes() {
+    return certificateBytes;
   }
 
   public int getTestPort() {

pkl-server/src/main/kotlin/org/pkl/server/Message.kt

@@ -20,7 +20,7 @@ import java.nio.file.Path
 import java.time.Duration
 import java.util.*
 import java.util.regex.Pattern
-import org.pkl.core.evaluatorSettings.PklEvaluatorSettings.*
+import org.pkl.core.evaluatorSettings.PklEvaluatorSettings.Proxy
 import org.pkl.core.module.PathElement
 import org.pkl.core.packages.Checksums
 
@@ -124,7 +124,7 @@ data class CreateEvaluatorRequest(
   val cacheDir: Path?,
   val outputFormat: String?,
   val project: Project?,
-  val http: Http?,
+  val http: Http?
 ) : ClientRequestMessage() {
   override val type = MessageType.CREATE_EVALUATOR_REQUEST
 
@@ -151,7 +151,8 @@ data class CreateEvaluatorRequest(
       rootDir.equalsNullable(other.rootDir) &&
       cacheDir.equalsNullable(other.cacheDir) &&
       outputFormat.equalsNullable(other.outputFormat) &&
-      project.equalsNullable(other.project)
+      project.equalsNullable(other.project) &&
+      http.equalsNullable(other.http)
   }
 
   @Suppress("DuplicatedCode") // false duplicate within method
@@ -170,6 +171,31 @@ data class CreateEvaluatorRequest(
     result = 31 * result + outputFormat.hashCode()
     result = 31 * result + project.hashCode()
     result = 31 * result + type.hashCode()
+    result = 31 * result + http.hashCode()
+    return result
+  }
+}
+
+data class Http(
+  /** PEM-format CA certificates as raw bytes. */
+  val caCertificates: ByteArray?,
+  /** Proxy settings */
+  val proxy: Proxy?
+) {
+  override fun equals(other: Any?): Boolean {
+    if (this === other) return true
+    if (other !is Http) return false
+
+    if (caCertificates != null) {
+      if (other.caCertificates == null) return false
+      if (!caCertificates.contentEquals(other.caCertificates)) return false
+    } else if (other.caCertificates != null) return false
+    return Objects.equals(proxy, other.proxy)
+  }
+
+  override fun hashCode(): Int {
+    var result = caCertificates?.contentHashCode() ?: 0
+    result = 31 * result + (proxy?.hashCode() ?: 0)
     return result
   }
 }

pkl-server/src/main/kotlin/org/pkl/server/MessagePackDecoder.kt

@@ -255,10 +255,11 @@ internal class MessagePackDecoder(private val unpacker: MessageUnpacker) : Messa
     return Project(projectFileUri, null, dependencies)
   }
 
-  private fun Map<Value, Value>.unpackHttp(): PklEvaluatorSettings.Http? {
+  private fun Map<Value, Value>.unpackHttp(): Http? {
     val httpMap = getNullable("http")?.asMapValue()?.map() ?: return null
     val proxy = httpMap.unpackProxy()
-    return PklEvaluatorSettings.Http(proxy)
+    val caCertificates = httpMap.getNullable("caCertificates")?.asBinaryValue()?.asByteArray()
+    return Http(caCertificates, proxy)
   }
 
   private fun Map<Value, Value>.unpackProxy(): PklEvaluatorSettings.Proxy? {

pkl-server/src/main/kotlin/org/pkl/server/MessagePackEncoder.kt

@@ -49,6 +49,21 @@ internal class MessagePackEncoder(private val packer: MessagePacker) : MessageEn
     packDependencies(project.dependencies)
   }
 
+  private fun MessagePacker.packHttp(http: Http) {
+    if ((http.caCertificates ?: http.proxy) == null) {
+      packMapHeader(0)
+      return
+    }
+    packMapHeader(0, http.caCertificates, http.proxy)
+    packKeyValue("caCertificates", http.caCertificates)
+    http.proxy?.let { proxy ->
+      packString("proxy")
+      packMapHeader(0, proxy.address, proxy.noProxy)
+      packKeyValue("address", proxy.address?.toString())
+      packKeyValue("noProxy", proxy.noProxy)
+    }
+  }
+
   private fun MessagePacker.packDependencies(dependencies: Map<String, Dependency>) {
     packMapHeader(dependencies.size)
     for ((name, dep) in dependencies) {
@@ -87,7 +102,15 @@ internal class MessagePackEncoder(private val packer: MessagePacker) : MessageEn
       when (msg.type.code) {
         MessageType.CREATE_EVALUATOR_REQUEST.code -> {
           msg as CreateEvaluatorRequest
-          packMapHeader(8, msg.timeout, msg.rootDir, msg.cacheDir, msg.outputFormat, msg.project)
+          packMapHeader(
+            8,
+            msg.timeout,
+            msg.rootDir,
+            msg.cacheDir,
+            msg.outputFormat,
+            msg.project,
+            msg.http
+          )
           packKeyValue("requestId", msg.requestId)
           packKeyValue("allowedModules", msg.allowedModules?.map { it.toString() })
           packKeyValue("allowedResources", msg.allowedResources?.map { it.toString() })
@@ -116,6 +139,10 @@ internal class MessagePackEncoder(private val packer: MessagePacker) : MessageEn
             packString("project")
             packProject(msg.project)
           }
+          if (msg.http != null) {
+            packString("http")
+            packHttp(msg.http)
+          }
         }
         MessageType.CREATE_EVALUATOR_RESPONSE.code -> {
           msg as CreateEvaluatorResponse
@@ -243,7 +270,8 @@ internal class MessagePackEncoder(private val packer: MessagePacker) : MessageEn
     value2: Any?,
     value3: Any?,
     value4: Any?,
-    value5: Any?
+    value5: Any?,
+    value6: Any?
   ) =
     packMapHeader(
       size +
@@ -251,7 +279,8 @@ internal class MessagePackEncoder(private val packer: MessagePacker) : MessageEn
         (if (value2 != null) 1 else 0) +
         (if (value3 != null) 1 else 0) +
         (if (value4 != null) 1 else 0) +
-        (if (value5 != null) 1 else 0)
+        (if (value5 != null) 1 else 0) +
+        (if (value6 != null) 1 else 0)
     )
 
   private fun MessagePacker.packKeyValue(name: String, value: Int?) {

pkl-server/src/main/kotlin/org/pkl/server/Server.kt

@@ -162,12 +162,13 @@ class Server(private val transport: MessageTransport) : AutoCloseable {
     val properties = message.properties ?: emptyMap()
     val timeout = message.timeout
     val cacheDir = message.cacheDir
-    val http =
+    val httpClient =
       with(HttpClient.builder()) {
         message.http?.proxy?.let { proxy ->
-          setProxy(proxy.address, message.http.proxy?.noProxy ?: listOf())
+          setProxy(proxy.address, proxy.noProxy ?: listOf())
           proxy.address?.let(IoUtils::setSystemProxy)
         }
+        message.http?.caCertificates?.let { caCertificates -> addCertificates(caCertificates) }
         buildLazily()
       }
     val dependencies =
@@ -183,7 +184,7 @@ class Server(private val transport: MessageTransport) : AutoCloseable {
         SecurityManagers.defaultTrustLevels,
         rootDir
       ),
-      http,
+      httpClient,
       ClientLogger(evaluatorId, transport),
       createModuleKeyFactories(message, evaluatorId, resolver),
       createResourceReaders(message, evaluatorId, resolver),

pkl-server/src/test/kotlin/org/pkl/server/AbstractServerTest.kt

@@ -1013,7 +1013,8 @@ abstract class AbstractServerTest {
     moduleReaders: List<ModuleReaderSpec> = listOf(),
     modulePaths: List<Path> = listOf(),
     project: Project? = null,
-    cacheDir: Path? = null
+    cacheDir: Path? = null,
+    http: Http? = null,
   ): Long {
     val message =
       CreateEvaluatorRequest(
@@ -1030,7 +1031,7 @@ abstract class AbstractServerTest {
         cacheDir = cacheDir,
         outputFormat = null,
         project = project,
-        http = null,
+        http = http
       )
 
     send(message)

pkl-server/src/test/kotlin/org/pkl/server/MessagePackCodecTest.kt

@@ -25,6 +25,7 @@ import org.assertj.core.api.Assertions.assertThat
 import org.junit.jupiter.api.Test
 import org.junit.jupiter.api.assertThrows
 import org.msgpack.core.MessagePack
+import org.pkl.core.evaluatorSettings.PklEvaluatorSettings
 import org.pkl.core.module.PathElement
 import org.pkl.core.packages.Checksums
 
@@ -73,6 +74,7 @@ class MessagePackCodecTest {
         isGlobbable = false,
         isLocal = false
       )
+    @Suppress("HttpUrlsUsage")
     roundtrip(
       CreateEvaluatorRequest(
         requestId = 123,
@@ -113,7 +115,11 @@ class MessagePackCodecTest {
                   RemoteDependency(URI("package://localhost:0/baz@1.1.0"), Checksums("abc123"))
               )
           ),
-        http = null,
+        http =
+          Http(
+            proxy = PklEvaluatorSettings.Proxy(URI("http://foo.com:1234"), listOf("bar", "baz")),
+            caCertificates = byteArrayOf(1, 2, 3, 4)
+          )
       )
     )
   }

settings.gradle.kts

@@ -4,7 +4,6 @@ include("bench")
 include("docs")
 include("stdlib")
 
-include("pkl-certs")
 include("pkl-cli")
 include("pkl-codegen-java")
 include("pkl-codegen-kotlin")