After I cloning a new openjdk repo, the configuration failed with the following output.

$ sh ./configure --with-freetype=/cygdrive/e/Dev/lib/freetype-amd64/ --with-boot-jdk=/cygdrive/e/Dev/jdk1.8.0/ --enable-debug
Configure source code has been updated, checking time stamps
Running generated-configure.sh
configure: Configuration created at Wed Jun 26 22:00:54 PDT 2013.
configure: configure script generated at timestamp 1372292257.
checking for basename... /usr/bin/basename
checking for bash... /usr/bin/bash
checking for cat... /usr/bin/cat
checking for chmod... /usr/bin/chmod
checking for cmp... /usr/bin/cmp
checking for comm... /usr/bin/comm
checking for cp... /usr/bin/cp
checking for cpio... /usr/bin/cpio
checking for cut... /usr/bin/cut
checking for date... /usr/bin/date
checking for gdiff... no
checking for diff... /usr/bin/diff
checking for dirname... /usr/bin/dirname
checking for echo... /usr/bin/echo
checking for expr... /usr/bin/expr
checking for file... /usr/bin/file
checking for find... /usr/bin/find
checking for head... /usr/bin/head
checking for ln... /usr/bin/ln
checking for ls... /usr/bin/ls
checking for mkdir... /usr/bin/mkdir
checking for mktemp... /usr/bin/mktemp
checking for mv... /usr/bin/mv
checking for printf... /usr/bin/printf
checking for rm... /usr/bin/rm
checking for sh... /usr/bin/sh
checking for sort... /usr/bin/sort
checking for tail... /usr/bin/tail
checking for tar... /usr/bin/tar
checking for tee... /usr/bin/tee
checking for touch... /usr/bin/touch
checking for tr... /usr/bin/tr
checking for uname... /usr/bin/uname
checking for uniq... /usr/bin/uniq
checking for wc... /usr/bin/wc
checking for which... /usr/bin/which
checking for xargs... /usr/bin/xargs
checking for gawk... gawk
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for a sed that does not truncate output... /usr/bin/sed
checking for nawk... no
checking for gawk... /usr/bin/gawk
checking for cygpath... /usr/bin/cygpath
checking for readlink... /usr/bin/readlink
checking for df... /usr/bin/df
checking for SetFile... no
checking build system type... x86_64-pc-cygwin
checking host system type... x86_64-pc-cygwin
checking target system type... x86_64-pc-cygwin
checking openjdk-build os-cpu... windows-x86_64
checking openjdk-target os-cpu... windows-x86_64
checking compilation type... native
checking cygwin release... 1.7.20(0.266/5/3)
checking cygwin root directory as unix-style path... /cygdrive/c/cygwin
checking what kind of 'find' is first on the PATH... unix style
checking for presence of closed sources... no
checking if closed source is suppressed (openjdk-only)... no
checking which variant of the JDK to build... normal
checking which variants of the JVM to build... server
checking which debug level to use... fastdebug
checking what configuration name to use... windows-x86_64-normal-server-fastdebug
checking for apt-get... no
checking for yum... no
checking for port... no
checking for pkgutil... no
checking for pkgadd... no
checking for gmake... no
checking for make... /usr/bin/make
configure: Testing potential make at /usr/bin/make, found using make in PATH
configure: Using GNU make 3.81 (or later) at /usr/bin/make (version: GNU Make 3.82.90)
checking if find supports -delete... yes
checking for unzip... /usr/bin/unzip
checking for zip... /usr/bin/zip
checking for ldd... /usr/bin/ldd
checking for otool... no
checking for readelf... /usr/bin/readelf
checking for hg... /cygdrive/c/Program Files/Mercurial/hg
checking for stat... /usr/bin/stat
checking for time... no
checking for comm... (cached) /usr/bin/comm
checking for pkg-config... no
checking for 7z... no
checking for unzip... unzip
checking for wget... no
checking for lftp... lftp
checking headful support... inlude support for both headful and headless
configure: Found potential Boot JDK using configure arguments
checking for Boot JDK... /cygdrive/e/Dev/jdk1.8.0/
checking Boot JDK version... java version "1.8.0-ea" Java(TM) SE Runtime Environment (build 1.8.0-ea-b71) Java HotSpot(TM) 64-Bit Server VM (build 25.0-b14, mixed mode)
checking for java in Boot JDK... ok
checking for javac in Boot JDK... ok
checking for javah in Boot JDK... ok
checking for javap in Boot JDK... ok
checking for jar in Boot JDK... ok
checking for rmic in Boot JDK... ok
checking for native2ascii in Boot JDK... ok
checking for jtreg... no
checking for link... /usr/bin/link
checking if the first found link.exe is actually the Cygwin link tool... yes
configure: Found Visual Studio installation at /cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/ using VS100COMNTOOLS variable
configure: Rewriting VS_ENV_CMD to "/cygdrive/c/progra~2/micros~2.0/vc/bin/amd64/vcvars64.bat"
configure: Trying to extract Visual Studio environment variables
Setting environment for using Microsoft Visual Studio 2010 x64 tools.
configure: Setting extracted environment variables
checking for Visual Studio variables... ok
checking for msvcr100.dll... configure: msvcr100.dll found in VCINSTALLDIR: c:\Program Files (x86)\Microsoft Visual Studio 10.0\VC\
c:\Program Files (x86)\Microsoft Visual Studio 10.0\VC\/redist/x64/Microsoft.VC100.CRT/msvcr100.dll
configure: Rewriting MSVCR_DLL to "/cygdrive/c/progra~2/micros~2.0/vc/redist/x64/micros~1.crt/msvcr100.dll"
checking for DirectX SDK... C:\Program Files (x86)\Microsoft DirectX 9.0 SDK (Summer 2004)\
configure: Rewriting dxsdk_path to "/cygdrive/c/progra~2/micros~1.0sd"
checking for DirectX SDK lib dir... /cygdrive/c/progra~2/micros~1.0sd/Lib/x64
configure: Rewriting DXSDK_LIB_PATH to "/cygdrive/c/progra~2/micros~1.0sd/lib/x64"
checking for DirectX SDK include dir... /cygdrive/c/progra~2/micros~1.0sd/Include
configure: Rewriting DXSDK_INCLUDE_PATH to "/cygdrive/c/progra~2/micros~1.0sd/include"
checking for cl... /cygdrive/c/Program Files (x86)/Microsoft Visual Studio 10.0/VC/BIN/amd64/cl
configure: Rewriting CC to "/cygdrive/c/progra~2/micros~2.0/vc/bin/amd64/cl"
checking resolved symbolic links for CC... /cygdrive/c/progra~2/micros~2.0/vc/bin/amd64/cl
checking if CC is disguised ccache... no, keeping CC
configure: error: Target CPU mismatch. We are building for x86_64 but CL is for "; expected "x64".
configure exiting with result code 1