fix a spurious warning in xyzmatriz<-
Fix WithAllPoints and WithLine in plot3d.neuron
skipRedraw argument for plot3d.neuronlist
git:ignore rstudio files
Make sure rootpoints/branchpoints come back as plain integers

* vertex sequences have funny subscripting rules
  vs[1] is not the first vertex in the sequence but actually
  vertex 1 iff it is present in vs and empty otherwise
Add branchpoints.default() & rootpoints.default()

* this means that you only need to define an as.igraph method
  for a new class and you will get branchpoints and rootpoints
  for free.
Docs for rootpoints
By default rootpoints now excludes isolated points
doc: correct definition of prune in as.igraph.neuron
fix (and test) for rootpoints.neuron

* barfed when the neuron _didn't_ have multiple trees
check rootpoints will return 2 roots
Docs for Read3DDensityFromNrrd

This includes changes from an outdated branch 'roxygen'
Fix bug in is.nrrd and add tests

* when trusting suffix
Fix (+test) for long standing bug in DirectPotentialSynapses

* apply was being used with the expectation that it would return
  a list. This was not the case when segswithin returned the same
  number of segments from b for each segment in matrix a
* the code assumed that matrix a had rownames

It is still not exactly beautiful code, but it should now work
for the corner cases that I can envisage.
Add round trip test for Amira hxzip data

* fails for existing java based implementation
New in memory, base R zlib compression/decompression
Make new implementation of hxzip decoding the default
Faster test for reading hxzip data

* tabulate is _much_ faster than table
Replace DecodeHxZip and EncodeHxZip with read.zlib and write.zlib

* these functions depend solely on base R 
  (i.e. not java code)
Allow runAllTests to be called as script