add new lphy doc for 1.3.0

lphy/doc/distributions/Cauchy.md

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+Cauchy distribution
+===================
+Cauchy(Number **median**, Number **scale**)
+-------------------------------------------
+
+The Cauchy distribution.
+
+### Parameters
+
+- Number **median** - the median of the Cauchy distribution.
+- Number **scale** - the scale of the Cauchy distribution.
+
+### Return type
+
+- Double
+
+
+

lphy/doc/distributions/Geometric.md

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+Geometric distribution
+======================
+Geometric(Double **p**)
+-----------------------
+
+The probability distribution of the number of failures before the first success given a fixed probability of success p, supported on the set { 0, 1, 2, 3, ... }.
+
+### Parameters
+
+- Double **p** - the probability of success.
+
+### Return type
+
+- Integer
+
+
+

lphy/doc/distributions/Weibull.md

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+Weibull distribution
+====================
+Weibull(Number **alpha**, Number **beta**)
+------------------------------------------
+
+The Weibull distribution.
+
+### Parameters
+
+- Number **alpha** - the first shape parameter of the Weibull distribution.
+- Number **beta** - the second shape parameter of the Weibull distribution.
+
+### Return type
+
+- Double
+
+
+

lphy/doc/functions/aminoAcids.md

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+aminoAcids function
+===================
+aminoAcids()
+------------
+
+The amino acid data type.
+
+
+
+### Return type
+
+- SequenceType
+
+
+

lphy/doc/functions/rangeInt.md

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+rangeInt function
+=================
+rangeInt(Integer **start**, Integer **end**)
+--------------------------------------------
+
+The range of integers from start to end. Boundaries are included.
+
+### Parameters
+
+- Integer **start** - start of the range (inclusive)
+- Integer **end** - end of the range (inclusive)
+
+### Return type
+
+- Integer[]
+
+
+

lphy/doc/types/MetaDataAlignment.md

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+MetaDataAlignment
+=================
+Methods
+-------
+
+- **ages**
+  - gets the ages of these taxa as an array of doubles.
+- **charset**
+  - return a partition alignment. If the string doesn't match charset's syntax, then check if the string matches a defined name in the nexus file. Otherwise it is an error. The string is referred to one partition at a call, but can be multiple blocks, such as d.charset("2-457\3 660-896\3").
+- **dataType**
+  - get the data type of this alignment.
+- **getTaxaNames**
+  - The names of the taxa.
+- **length**
+  - gets the number of taxa.
+- **nchar**
+  - The number of characters/sites.
+- **nodeCount**
+  - the total number of nodes (left + internal) in a binary tree with these taxa.
+- **stateCount**
+  - the number of possible states in the alignment.
+- **taxa**
+  - the taxa of the alignment.
+- **taxaNames**
+  - The names of the taxa.