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

DEVELOPMENT.adoc

@@ -93,6 +93,14 @@ There is an IntelliJ plugin meant for development on the Pkl project itself loca
 
 See https://github.com/apple/pkl-project-commons?tab=readme-ov-file#internal-intellij-plugin[its readme] for instructions on how to set it up.
 
+== Working on libpkl
+
+libpkl is a native library written in C, and is best written in CLion, or VSCode.
+
+IntelliJ has limited support for editing C sources.
+
+There is a CMakeLists.txt file whose only job is to configure CLion with proper include paths.
+
 == Resources
 
 For automated build setup examples see our https://github.com/apple/pkl/blob/main/.github/[GitHub Actions] jobs like our https://github.com/apple/pkl/blob/main/.github/jobs/BuildNativeJob.pkl[BuildNativeJob.pkl], where we build Pkl automatically.