[svn] Initial branch of version 4.1 development.

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branch : 4_1_development
[svn] Improvements:

    Added all the function bindings needed to include Maximum Likelihood
    characters. This prepares all the necessary bindings for Nick to add the ML
    functionality in the main program. Note that there is no user interface at
    the higher level available yet (in other words, no command to make a
    character a likelihood character). But adding that functionality is easy
    from this point.

Interface Changes:

    Added the Tags.Characters.likelihood keyword.
    Added the constructor Parser.SC.SCStaticLikelihood and associated types
    holding the model class.
    Added the module MlStaticCS with dummy function calls to leave the program
    compilable while with the bindings ready for Nick.
    Added the constructor Node.StaticMl to hold the static homology, Maximum
    Likelihood characters.

Makefile Changes:
    Updated the Makefile.in to include mlStaticCS.cmo.

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branch : 4_1_development
[svn] Bugfix:
    Small field definition after the Node.r addition of the time parameter.

--HG--
branch : 4_1_development
[svn] Improvements:

    Added some more bindings and in the MlStaticCS module, their corresponding
    calls in Node.

Interface Changes:
    Added the `StaticMl constructor to the has_single constant and the
    Node.distance_of_type function.

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branch : 4_1_development
[svn] New Commands:
transform -> likelihood:(constant[:FLOAT], none, [estimate | given:FLOAT])

    The likelihood transform creates a likelihood character with three
    arguments: the substitution parameters, the among site variation
    distribution, and the priors. Currently a limited (very limited) set of
    possible functions is accepted.

Interface Changes:
    Added Data.set_likelihood
    Added Methods.`UseLikelihood with its self descriptive contents.
    Minor changes to the specification of ML characters in Parser.SC.

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branch : 4_1_development
[svn] Merging from trunk to 4_1_development 2301:2310

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branch : 4_1_development
[svn] Merging from release5 to 4_1_development 2310:2312

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branch : 4_1_development
[svn] Merging from release5 to 4_1_development revision 2313:2314

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branch : 4_1_development
[svn] Improvements:
    Added the single assignment cost correction to the Kolmogorov character
    class.

    Refactored Node.to_single to maximize code reuse in this new feature.

Interface Changes:
    Added KolmoCS.to_single and it's function calls in Node.to_single
    Added `Kolmo to the list of character types in Node.has_to_single

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branch : 4_1_development
[svn] Merging from release5 to 4_1_development r2316:2317

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branch : 4_1_development
[svn] Partial merge from release5 2321:2323.

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[svn] Partial merge from release5 2318:2321.

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[svn] Merging changes from release5 2325:2328.

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[svn] Merging changes from release5 2329:2330.

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[svn] Merging changes from release5 2331:2332

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[svn] Merging changes from release5 revision 2335:2336

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branch : 4_1_development
[svn] Merging changes from release5 revision 2337:2338.

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branch : 4_1_development
[svn] Merging changes from release5 revision 2339:2340.

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branch : 4_1_development
[svn] Merging r2341:2342 (documentation update)

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branch : 4_1_development
[svn] Merging changes from release5 revision 2345:2346.

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branch : 4_1_development