Recent changes to jdk9/dev configure have caused our build scripts to now fail:

checking where to store configuration... in current directory
configure: Current directory is /export/users/dh198349/jdk9-dev/build/b00/linux-i586-internal.
configure: Since this is not the source root, configure will output the configuration here
configure: (as opposed to creating a configuration in <src_root>/build/<conf-name>).
configure: However, this directory is not empty. This is not allowed, since it could
configure: seriously mess up just about everything.
configure: Try 'cd /export/users/dh198349/jdk9-dev' and restart configure
configure: (or create a new empty directory and cd to it).
configure: error: Will not continue creating configuration in /export/users/dh198349/jdk9-dev/build/b00/linux-i586-internal
Configure step failed - see previous output

Note that the script creates the "current directory" for the build output. The directory is not empty because configure is writing there:

 > dir b00/linux-i586-internal/
total 40
drwxr-xr-x 2 daholme uucp 4096 May 11 16:48 .
drwxr-xr-x 3 daholme uucp 4096 May 11 16:48 ..
-rw-r--r-- 1 daholme uucp 26938 May 11 16:48 config.log
-rw-r--r-- 1 daholme uucp 3730 May 11 16:48 configure.log

Also note that error message says:

configure: Try 'cd /export/users/dh198349/jdk9-dev' and restart configure
configure: (or create a new empty directory and cd to it).

but creating a new directory is what is failing:

/scratch/dh198349/jdk9-dev > mkdir mybuild
/scratch/dh198349/jdk9-dev > cd mybuild
/scratch/dh198349/jdk9-dev/mybuild > bash ../configure
Running custom generated-configure.sh
configure: Configuration created at Mon May 11 19:09:12 EDT 2015.
configure: configure script generated at timestamp 1431344623.
...
checking for extra path...
checking where to store configuration... in current directory
configure: Current directory is /scratch/dh198349/jdk9-dev/mybuild.
configure: Since this is not the source root, configure will output the configuration here
configure: (as opposed to creating a configuration in <src_root>/build/<conf-name>).
configure: However, this directory is not empty. This is not allowed, since it could
configure: seriously mess up just about everything.
configure: Try 'cd /scratch/dh198349/jdk9-dev' and restart configure
configure: (or create a new empty directory and cd to it).
configure: error: Will not continue creating configuration in /scratch/dh198349/jdk9-dev/mybuild