Apparently upstream solved the underlying problem (of the library not using 
the same defaults as the command-line driver) by including required clang 
headers in the ycmd package directory. The completer forces addition of

    -isystem /usr/lib/ycmd/ycmd/../clang_includes

in the compiler flags. This directory, however, does not exist in the ycmd 
package.

Creating a symink /usr/lib/ycmd/clang_includes -> /usr/lib/clang-3.6/include
works around the issue.

-- 
 - Jan Hudec <[email protected]>

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