Add '/usr/local/lib/cmtk/bin' to dirs to check for cmtk

* recent versions seem to install a cmtk script to /usr/local/bin
  and then put all the binaries under /usr/local/lib/
teach xyzmatrix to handle data.frames and matrices with >=3 cols

* 3 cols are assumed to be points regardless of names
* >=3 must have names
split off xyzmatrix methods for neurons and dotprops objects

* dispatch keeps functions simpler, but still keeping
  is.neuron check in xyzmatrix.default to handle older neurons without class
Remove Transpose argument to xyzmatrix

* somewhat complicates implementation for other methods
  and it is even quicker for users to do t()
Prepare for graph work by importing igraph package
initial implementation of ngraph class (ngraph, as.ngraph, xymatrix(<-).graph)

* general way to represent connectivity of neuron
* depends on igraph
* can also store points as graph attribute
fix and test for as.ngraph.dataframe method

* more tests can be ported from AnalysisSuite in due course
fix bug in xyzmatrix.default when dealing with matrix/dataframe input

* bug in fd9283cd5230f556d371c8ebbcbc4d7dbbfb1b0e
* example of over-elaborate if structure and danger of
  if/else structure without braces not be evaluated as expected
make sure that graph actually produces objects with ngraph class
add graph.nodes/rootpoints/branchpoints
fix rootpoints/startpoints/branchpoints - switch to as.ngraph for default method

* not as.igraph
exercise rootpoints functionality
STY: final newline
more tests for graph.nodes

* noticed an error in TKC8R
  (and likely a number of other neurons in Cell07PNs)
some namespace fixes
rename test-graph to test-graph-nodes for consistency
verbatim copy of graph->neuron code from AnalysisSuite
Add neuron() constructor function

* and tidy is.neuron, as.neuron
Add as.neuron generic and methods for igraph and dataframe
replace graph2seglist with as.seglist generic + method for igraph objects