Command Line Tools installs the latest version of clang (and others) in /Library/Developer/CommandLineTools/... but not in /usr/bin/

I've upgraded Xcode to the latest 5.1 Installed Command Line Tools via xcode-select --install Homebrew tells me "A newer Command Line Tools release is available"
brew --config:
Xcode: 5.1 CLT: 5.1.0.0.1.1393561416 LLVM-GCC: build 2336 Clang: 3.1 build 318
Checking my clang executable:
$ /usr/bin/clang --version Apple clang version 3.1 (tags/Apple/clang-318.0.58) (based on LLVM 3.1svn)
$ /Library/Developer/CommandLineTools/usr/bin/clang --version Apple LLVM version 5.1 (clang-503.0.38) (based on LLVM 3.4svn)
So it appears Command Line Tools didn't install clang (and perhaps other executables) into /usr/bin? I checked my other laptop (w/ Mavericks), and /usr/bin/clang is version 5.1.
So I'm guessing this is the problem? I've tried to reinstall Command Line Tools as sudo, but now it won't let me install again (says software isn't currently available).
Can anyone help me with this? I've spent hours on it now, but can't find a solution.
Thanks

BTW, I installed Xcode 5.1 from the Store, but have never run xcode-select --install.  Here is the verbose output from a clang.
xew ~/$:clang -v -o hello main.c
Apple LLVM version 5.1 (clang-503.0.38) (based on LLVM 3.4svn)
Target: x86_64-apple-darwin13.1.0
Thread model: posix
"/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain /usr/bin/clang" -cc1 -triple x86_64-apple-macosx10.9.0 -emit-obj -mrelax-all -disable-free -disable-llvm-verifier -main-file-name main.c -mrelocation-model pic -pic-level 2 -mdisable-fp-elim -masm-verbose -munwind-tables -target-cpu core2 -target-linker-version 236.3 -v -resource-dir /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/ usr/bin/../lib/clang/5.1 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/ SDKs/MacOSX10.9.sdk -fdebug-compilation-dir /Users/xew -ferror-limit 19 -fmessage-length 100 -stack-protector 1 -mstackrealign -fblocks -fobjc-runtime=macosx-10.9.0 -fencode-extended-block-signature -fdiagnostics-show-option -fcolor-diagnostics -vectorize-slp -o /var/folders/zf/d5vqmmtn5mq7h6766jtlkrvr0000gn/T/main-353995.o -x c main.c
clang -cc1 version 5.1 based upon LLVM 3.4svn default target x86_64-apple-darwin13.1.0
ignoring nonexistent directory "/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer /SDKs/MacOSX10.9.sdk/usr/local/include"
ignoring nonexistent directory "/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer /SDKs/MacOSX10.9.sdk/Library/Frameworks"
#include "..." search starts here:
#include <...> search starts here:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/ usr/bin/../lib/clang/5.1/include
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/ usr/include
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/ SDKs/MacOSX10.9.sdk/usr/include
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/ SDKs/MacOSX10.9.sdk/System/Library/Frameworks (framework directory)
End of search list.
"/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain /usr/bin/ld" -demangle -dynamic -arch x86_64 -macosx_version_min 10.9.0 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/ SDKs/MacOSX10.9.sdk -o hello /var/folders/zf/d5vqmmtn5mq7h6766jtlkrvr0000gn/T/main-353995.o -lSystem /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/ usr/bin/../lib/clang/5.1/lib/darwin/libclang_rt.osx.a
xew ~/$:

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