The clean rebuild seems to have done it, although my local.conf now looks like this:

JAVA = ",java"
JAVA_arm = ",java"
FORTRAN = ",fortran"
FORTRAN_forcevariable = ",fortran"
RUNTIMETARGET_append_pn-gcc-runtime = " libquadmath"

After that I was able to build the libgfortran package; prior to the above I got the error about gcc needing to be built with fortran support.  There were also some warnings about collisions with gcc-runtime:

Poky ["raspberrypi"] >>> bitbake libgfortran
Loading cache: 100% |###############################################################################################################################################################################################| ETA:  00:00:00
Loaded 2086 entries from dependency cache.
Parsing recipes: 100% |#############################################################################################################################################################################################| Time: 00:00:00
Parsing of 1653 .bb files complete (1652 cached, 1 parsed). 2086 targets, 45 skipped, 0 masked, 0 errors.
NOTE: Resolving any missing task queue dependencies

Build Configuration:
BB_VERSION        = "1.21.0"
BUILD_SYS         = "x86_64-linux"
NATIVELSBSTRING   = "Ubuntu-12.04"
TARGET_SYS        = "arm-poky-linux-gnueabi"
MACHINE           = "raspberrypi"
DISTRO            = "poky"
DISTRO_VERSION    = "1.5+snapshot-20131217"
TUNE_FEATURES     = "armv6 vfp callconvention-hard arm1176jzfs no-thumb-interwork"
TARGET_FPU        = "vfp"
meta
meta-yocto
meta-yocto-bsp    = "master:dd1dbaaddc33a001d7f3b3c2151224a9f9cd7856"
meta-raspberrypi  = "master:6b0f84865634022fd5081162a5686bea16c2056f"
meta-erlang       = "master:ca7c12f3427280a3800f78fa511637de3925d056"
meta-oe
meta-gnome
meta-networking
meta-filesystems
meta-multimedia
meta-efl
meta-xfce         = "master:4d843338866dff4ed028b73278b22a5ad7dc35a2"

NOTE: Preparing runqueue
NOTE: Executing SetScene Tasks
NOTE: Executing RunQueue Tasks
WARNING: The recipe libgfortran is trying to install files into a shared area when those files already exist. Those files and their manifest location are:
   /home/sarnold/poky/build-rpihf/tmp/sysroots/raspberrypi/pkgdata/runtime/libgfortran-staticdev
   Matched in manifest-raspberrypi-gcc-runtime.packagedata
   /home/sarnold/poky/build-rpihf/tmp/sysroots/raspberrypi/pkgdata/runtime/libgfortran-dev
   Matched in manifest-raspberrypi-gcc-runtime.packagedata
   /home/sarnold/poky/build-rpihf/tmp/sysroots/raspberrypi/pkgdata/runtime/libgfortran
   Matched in manifest-raspberrypi-gcc-runtime.packagedata
   /home/sarnold/poky/build-rpihf/tmp/sysroots/raspberrypi/pkgdata/runtime-reverse/libgfortran-staticdev
   Matched in manifest-raspberrypi-gcc-runtime.packagedata
   /home/sarnold/poky/build-rpihf/tmp/sysroots/raspberrypi/pkgdata/runtime-reverse/libgfortran-dev
   Matched in manifest-raspberrypi-gcc-runtime.packagedata
Please verify which package should provide the above files.
NOTE: Tasks Summary: Attempted 684 tasks of which 672 didn't need to be rerun and all succeeded.

Summary: There was 1 WARNING message shown.

Added the rpi layer I'm building in to the URL field.

Firstly, with master you should just need:
"""
FORTRAN_forcevariable = ",fortran"
RUNTIMETARGET_append_pn-gcc-runtime = " libquadmath"
"""
as documented in local.conf.sample.extended.

As it mentioned there it is there as "best effort" and not an officially supported/tested code path. As such, bug reports like this aren't going to get much attention, we simply don't have the resources to cover fortran or java.

For java you probably need to do something like:

JAVA_forcevariable = ",java"

but again, its not a tested codepath so who knows what may happen from there.

Finally, the raspberrypi isn't an official Yocto Project BSP so as such a bug report for unsupported hardware and an unsupported toolchain components here in the bugzilla is really out of scope.

No feedback on the bug. Fortran should work as indicated, java simply isn't supported.