Move libgtextutils from core
trinity r20131110

The patch to fix building on a case insensitive file system is no
longer necessary.
Upgrade CoinMP to 1.7.3.

- add head ref
- add tests
- remove hack.

Fixes #460.
cufflinks: Fails with clang 500

./hits.h:829:10: error: unknown type name 'shared_ptr'
        MateHit(shared_ptr<ReadGroupProperties const> rg_props,

Closes #509
gmap-gsnap 2013-11-22
stacks: Fails with clang 500

error: 'tr1/unordered_map' file not found
stacks 1.07
stacks 1.08
stacks 1.09
Fix VTK issue on mavericks

Closes #410.
Corrected sha1 for hdf5-1.8.12.tar.bz2

Closes #513.
sga: Fails with clang 500
sga 0.9.42
Add caveat for GLPK-4.52 and Octave-3.6.4

https://bugs.archlinux.org/task/36835
> Octave cannot use the current version of GLPK, its API has apparently changed.

Closes #512.
Updated sha1 for netcdf-4.3.0.tar.gz

Closes #514.
gmap-gsnap 2013-11-23
armadillo: added C++11 option

Closes #507.
ViennaRNA 2.1.5

Closes #516.
hdf5: added C++11 option

Closes #508.
root: upgrade to 5.34.12 and introduce --with-cocoa flag

Closes #502.