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

libpkl/libpkl.gradle.kts

@@ -511,7 +511,7 @@ spotless {
       rootProject.file("build-logic/src/main/resources/license-header.star-block.txt"),
       "// ",
     )
-    target("src/*/c/*.c", "src/*/c/*.h")
+    target("src/*/c/**/*.c", "src/*/c/**/*.h")
     eclipseCdt(libs.versions.eclipseCdtFormat.get())
   }
   shell {