tests,app: update to Core API changes (Command)
Transform.Line_oriented.feed_string: clarify possible cases

This doesn't affect the behavior.
Comments,Table: remove deprecated modules

These modules were already mostly commented and they are not Transform
or Core compliant.
Bmap: port to Internal_pervasives
Std: remove infix operators
Sgr: port to Internal_pervasives
Std: delete Biocaml_std (and propagate)
Merge remote-tracking branch 'origin/v0.2' into v0.2
Solexa_score: remove Batteries dependency
Interval_tree: use Internal_pervasives
Entrez: remove Batteries dependency
test_phred_score.ml: remove Batteries dependency
Internal_pervasives: include Core modules individually

Instead of a simple include Core.Std, now including each module
individually. This enables us to extend modules, e.g. supporting
Streamable for List.
Array, List: support Streamable
Array, List: support Streamable
Merge branch 'v0.2-jaspar-bat2core' into v0.2
type equation required on include Streamable
Jaspar: remove Batteries dependency
Jaspar: remove unnecessary function definition
Accu: port to core