Compilation Database ignores --sysroot option

I'm working on a project that builds for android. In this configuration, the command-line for compiled C++ files includes --sysroot=../../third_party/android_ndk/sysroot to ensure that the proper header files are being pulled in. However, the compilation database plugin doesn't seem to pick up this flag, and as a result I end up with lots of errors in the IDE due to the inability to locate the proper system headers and android-specific headers (e.g. jni.h).