Fix bug in precision_bscore (the fitness formula was trashed from version 3.6.4)

+ Increase moses to version 3.6.5 as the behavior has changed (to a
non buggy one).
Ubigraph now builds again after changes made to server/Request.h, hidden set to false for these calls.
Added a command 'listmodules' to the cog server shell. May need further filtering / expansion.
Changed it to only list module id's, rather than filenames.
Merge pull request #196 from Alex-van-der-Peet/ubigraphCMDissue

Ubigraph now builds again after changes made to server/Request.h
Merge pull request #197 from Alex-van-der-Peet/ListModules

Added a command 'listmodules' to the cog server shell.
Changed the output of listmodules.
remove a bogus .so dependency
Provide template for a trivial module

This is needed as a hack to automatically construct atom types
early enough in cogserver init.
Use the new atom-types-loading macro
Assert copyrights

Hmm .. I did large chunk of this file in 2008 ...
Use the new atom types module macro

We need to define this as a valid module, so that loading can
happen, error-free.
Declare a proper embodiment types module.

Required so that the atom types can load without errors.
Merge pull request #198 from Alex-van-der-Peet/ListModulesUpdate

Changed the output of listmodules.
Merge pull request #199 from linas/types-module

Atom types module
Moses: extend _perm_ratio in backwards-compat way.

It seems that the old code (a few months ago) build significantly
fewer pairs than the current code, and this strongly affects scores
and learning.  So extend the meaning of _perm_ratio in a backwards-
compatible way, so that this can be explicitly controlled and tested.
Merge pull request #200 from linas/moses

Moses: extend _perm_ratio in backwards-compat way.
Minor simplication of composite_score constructor
Add power diversity_parameters::dst2dp

When the diversity penalty is a probability (as the Tanimoto distance
sorta is) it makes sense to multiply it with the score (which should
rather be a probability too) rather than subtracting it. Then it also
makes more sense to have the diversity pressure be the pth-power of
the diveristy penalty.
Minor simplication of composite_score constructor