Move some utils + update doc so that utilities are shown as examples

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/add_utils_in_gudhi_v2@2756 636b058d-ea47-450e-bf9e-a15bfbe3eedb

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+# Rips_complex #
+
+## `rips_persistence` ##
+This program computes the persistent homology with coefficient field *Z/pZ* of a Rips complex defined on a set of input points. The output diagram contains one bar per line, written with the convention:
+
+`p dim b d`
+
+where `dim` is the dimension of the homological feature, `b` and `d` are respectively the birth and death of the feature, and `p` is the characteristic of the field *Z/pZ* used for homology coefficients (`p = p1*...*pr` is the product of prime numbers *pi* such that the homology feature exists in homology with *Z/piZ* coefficients).
+
+**Usage**
+`rips_persistence [options] <OFF input file>`
+
+**Allowed options**
+
+* `-h [ --help ]` Produce help message
+* `-r [ --max-edge-length ]` (default = inf) Maximal length of an edge for the Rips complex construction.
+* `-d [ --cpx-dimension ]` (default = 1) Maximal dimension of the Rips complex we want to compute.
+* `-p [ --field-charac ]` (default = 11)     Characteristic p of the coefficient field Z/pZ for computing homology.
+* `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals.
+
+**Example 1 with Z/2Z coefficients**
+`rips_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 2`
+
+outputs:
+```
+2  0 0 inf
+2  1 0.0983494 inf 
+2  1 0.104347 inf 
+2  2 0.138335 inf 
+```
+
+**Example 2 with Z/3Z coefficients**
+
+rips_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 3
+
+outputs:
+```
+3  0 0 inf
+3  1 0.0983494 inf
+3  1 0.104347 inf
+3  2 0.138335 inf
+```
+
+
+
+
+## `rips_distance_matrix_persistence` ##
+Same as `rips_persistence` but taking an distance matrix as input.
+
+**Example**
+`rips_distance_matrix_persistence data/distance_matrix/full_square_distance_matrix.csv -r 15 -d 3 -p 3 -m 0`
+
+outputs:
+```
+The complex contains 46 simplices 
+   and has dimension 3 
+3  0 0 inf 
+3  0 0 8.94427 
+3  0 0 7.28011 
+3  0 0 6.08276 
+3  0 0 5.83095 
+3  0 0 5.38516 
+3  0 0 5 
+3  1 11 12.0416 
+3  1 6.32456 6.7082 
+```