Omakeroot: organize contents better

No significant changes to any definitions. Partially addresses #121.
OMakeroot: automatically determine lists of modules

Partially addresses #121.
OMakeroot: rename many variables

Addresses #121.
OMakeroot: move around some definitions

Addresses #121.
OMakeroot: remove `dist` from PHONY list

The `dist` target no longer exists. Partially addresses #121.
OMakeroot: pure whitespace fix

Main changes are reducing indentation to 2 from 4. Helps #121.
OMakeroot: give explicit name to several targets

These rules were declared directly as .DEFAULT, but giving explicit
names makes intention more clear.
OMakeroot distclean: was accidentally removing source file
OMakeroot: rename local_configuration.om to configure.om

Helps #121.
OMakeroot: simplify local configuration

Helps #121.
OMakeroot: rename variables containing "BIOCAML"

It is redundant to say BIOCAML. Helps #121.
OMakeroot: rename tests app to `biocaml_tests`
rename `benchmark` dir to `benchmarks`

Consistently use the plural, and be consistent with plural `tests`.
Merge pull request #122 from smondet/master

Fix travis-ci build (Flow failure)
Merge branch 'master' into build
OMakeroot: improve doc build

* Clearly separate out compiling of ocamldoc custom generator and
creation of html files. Helps #121.
* Compilation of custom generator happens under _build.
* Use OCamlLibrary function to compile custom generator.
* .. and more.
travis: correct path to benchmarks app

Should have been done in 79574163b6c570db7b9f0bbeb72f1192a74a257a.
OMakeroot: undefine ensure_path

Function is too simple. More clear to write out body each time.
bench: add a BAM/SAM parsing benchmark

This benchmark is first step towards tackling #123.

To integrate with other benchmark I added a `main.ml` which creates the
`Command.group` which then allows to call the specific benchmarks.

The code is based on @pveber's code sent to the mailing-list.
travis: make benchmarks command return 0