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 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.