bazel: Building with ccache fails with auto-configuration

Hi! I tried to recompile bazel, but I ran into “missing dependency declarations” errors:

ERROR: /home/alexander/source/bazel/src/BUILD:125:2 undeclared inclusion(s) in rule '//src/main/tools:process-wrapper':
this rule is missing dependency declarations for the following files included by 'src/main/tools/process-wrapper.c':
  '/usr/include/stdc-predef.h'
  '/usr/include/err.h'
  '/usr/include/features.h'
  '/usr/include/sys/cdefs.h'
....

The full output can be found here: https://gist.github.com/akors/16020dac060948e87c1d14a9794f12db

Note that this is very similar #715, HOWEVER, the directories listed are definitely present in my CROSSTOOL file.

$ grep cxx_builtin_include  tools/cpp/CROSSTOOL
  cxx_builtin_include_directory: "/usr/lib/gcc/"
  cxx_builtin_include_directory: "/usr/local/include"
  cxx_builtin_include_directory: "/usr/include"
  cxx_builtin_include_directory: "/"
  cxx_builtin_include_directory: "/usr/local/include"
  cxx_builtin_include_directory: "/usr/include"
...

I’m running on Fedora 23, and trying to get bazel to use a custom compiler - but I can’t even get it to use my system compiler.