I use CLION to develop the C code for my Pebble apps.
To build/run I just have a terminal open within CLION, but I do like being able to refactor, have static analysis find errors, and to jump to the Pebble defs.
I created a new project based on the C source directory, and I've added all my source files to the CMakeLists.txt and the path to the Pebble include files and the generated resource file. Here is my CMakeLists.txt
cmake_minimum_required(VERSION 3.3)
project(src)
add_definitions(-DNOT_PEBBLE_BUILD)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
set(SOURCE_FILES
pblib/pblib.h ... main_menu_customizer.c main_menu_customizer.h string_values.c error_handler.c error_handler.h)
include_directories("~/Library/Application Support/Pebble SDK/SDKs/current/sdk-core/pebble/chalk/include" ../build/chalk/src)
add_executable(src ${SOURCE_FILES})
In a general header file I also have these definitions to ensure that the generated resource file gets picked up, and that I don't get spurious errors for APP_LOG (might be fixed in the latest CLION):
#if NOT_PEBBLE_BUILD
#include <resource_ids.auto.h>
#undef APP_LOG // Clion doesn't support
#endif
Although not directly related to your question, you can also now debug C code running in the emulator using GDB, although not within CLION. That would be cool.