Fix various issues in libpkl (#1805)

* Fix possible SIGSEGV from host process.
   - Require that the same `pkl_exec_t` be used in the same OS thread; returning meaningful error if this fails
* Remove `System.exitProcess(1)` logic in NativeTransport; this would kill the host process too and isn't an appropriate action for a received ProtocolException
* Allow multiple calls to pkl_init without pkl_close; this limitation doesn't really make any sense
* Prefer calling methods defined in graal_isolate.h, instead of creating the same method via CEntryPoint
* Add a CMakeLists.txt so that CLion can follow the code and provide proper diagnostics
* Improve doc comments; describe params as either in or out

CMakeLists.txt

@@ -0,0 +1,24 @@
+# This file is only used to configure CLion with proper include paths.
+# Pkl builds everything through Gradle, not CMake.
+cmake_minimum_required(VERSION 4.2)
+project(pkl C)
+
+set(CMAKE_C_STANDARD 11)
+
+file(GLOB NATIVE_LIB_INCLUDE_DIRS CONFIGURE_DEPENDS
+  libpkl/build/native-libs/*/include)
+file(GLOB NATIVE_IMAGE_BUILD_DIRS CONFIGURE_DEPENDS
+  libpkl/build/tmp/native-image-build/*)
+
+include_directories(${NATIVE_LIB_INCLUDE_DIRS})
+include_directories(${NATIVE_IMAGE_BUILD_DIRS})
+include_directories(libpkl/src/main/c/include)
+
+file(GLOB_RECURSE GENERATED_HEADER_FILES CONFIGURE_DEPENDS
+  libpkl/build/tmp/native-libs/*/*.h)
+
+add_executable(pkl
+        ${GENERATED_HEADER_FILES}
+        libpkl/src/main/c/include/pkl.h
+        libpkl/src/main/c/pkl.c
+        libpkl/src/nativeTest/c/test_pkl.c)