First try (not compiling) keeping the number of cases in the pipeline type small

This doesn't seem compatible with a polymorphic parameterization of
the evaluation. It would require to define the core as a functor, but
then everything else would be a functor as well.
an equivalent implementation with GADT (not tested)

some changes in the API which forced to do a lot of mods
fixed incorred type for optional parameters of a pipeline

fixed bowtie index construction
Bed: pipeline to (re)name sequences in a Bed
bed: better typing for Bed.Named.make
restaured samtools
Major and untested rewrite of the eval function

the main new feature is an enriched contents for execution
[env]ironments. Now there is plenty of stuff to log and save
stdout/stderr, in a clean way.

This is a also a saner basis for developping a distributed evaluation
function.
fixed incorrect creating of symbolic links

now links in the to-be-linked path are first resolved using readlink
restaured repo building
bumped bowtie index revision
better API for choosing the location of the base directory
gzmCore: fixed incomplete creation of base directory
guizmin_table: extended signature to resemble tabular
ucsc.liftover: incorrect option
core: env now ships an sh and a bash plugged to the correct stdout/stderr and logs

dropped printf-like api for env.sh, was too difficult to parse the
command line to break it into meaningfull arguments. In particular,
splitting at spaces is incorrect (eg: grep 'foo bar')
ucsc.liftover: silenced the command
bowtie: silenced align
bowtie: fixed option for output
fixed log time stamp
minor fix